From ab5491daf8d5a868825cbb92a5a90f6c9c3c35aa Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 19 May 2023 08:37:23 -0700 Subject: [PATCH 1/3] partially fixes Feedback #178 --- infores_catalog.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/infores_catalog.yaml b/infores_catalog.yaml index 19de24273b..663dbb94f3 100644 --- a/infores_catalog.yaml +++ b/infores_catalog.yaml @@ -164,11 +164,17 @@ information_resources: - https://github.com/NCATSTranslator/Translator-All/wiki/Automat#gwascatalog description: A graph based on the GWAS Catalog - id: infores:automat-hetio - status: released + status: deprecated name: Automat Hetio xref: - https://github.com/NCATSTranslator/Translator-All/wiki/Automat#hetio description: A graph based on [hetionet (het.io)](het.io). +- id: infores:automat-hetio-net + status: released + name: Automat Hetio Net + xref: + - https://github.com/NCATSTranslator/Translator-All/wiki/Automat#hetio + description: A graph based on [hetionet (het.io)](het.io). - id: infores:automat-hgnc status: released name: Automat HGNC @@ -2515,4 +2521,4 @@ information_resources: xref: - https://raresource.nih.gov/ synonym: - description: Integrated Bioinformatics Resource for Rare Diseases \ No newline at end of file + description: Integrated Bioinformatics Resource for Rare Diseases From 199fc71f54c5eda83f8b438639a87c4e4ac4572f Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 23 May 2023 15:44:42 -0700 Subject: [PATCH 2/3] fix pydantic generation --- biolink/pydanticmodel.py | 1969 ++++++++++++++++++++++---------------- poetry.lock | 1688 ++++++++++++++++---------------- 2 files changed, 1986 insertions(+), 1671 deletions(-) diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py index d5e1152388..4d55c59415 100644 --- a/biolink/pydanticmodel.py +++ b/biolink/pydanticmodel.py @@ -1,264 +1,415 @@ from __future__ import annotations from datetime import datetime, date from enum import Enum -from typing import List, Dict, Optional, Any, Union, Literal +from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field from linkml_runtime.linkml_model import Decimal +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + metamodel_version = "None" -version = "3.3.2" +version = "3.3.4" class WeakRefShimBaseModel(BaseModel): __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True): - pass +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass -class InformationResourceStatusEnum(str, Enum): - - released = "released" - deprecated = "deprecated" - draft = "draft" - - - -class AnatomicalContextQualifierEnum(str, Enum): - - - dummy = "dummy" - class DirectionQualifierEnum(str, Enum): + increased = "increased" + upregulated = "upregulated" + decreased = "decreased" + downregulated = "downregulated" class ChemicalEntityDerivativeEnum(str, Enum): + metabolite = "metabolite" class ChemicalOrGeneOrGeneProductFormOrVariantEnum(str, Enum): + genetic_variant_form = "genetic_variant_form" + modified_form = "modified_form" + loss_of_function_variant_form = "loss_of_function_variant_form" + gain_of_function_variant_form = "gain_of_function_variant_form" + polymorphic_form = "polymorphic_form" + snp_form = "snp_form" + analog_form = "analog_form" class GeneOrGeneProductOrChemicalPartQualifierEnum(str, Enum): + number_3_prime_utr = "3_prime_utr" + number_5_prime_utr = "5_prime_utr" + polya_tail = "polya_tail" + promoter = "promoter" + enhancer = "enhancer" + exon = "exon" + intron = "intron" class GeneOrGeneProductOrChemicalEntityAspectEnum(str, Enum): + # Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used. activity_or_abundance = "activity_or_abundance" + abundance = "abundance" + activity = "activity" + expression = "expression" + synthesis = "synthesis" + degradation = "degradation" + cleavage = "cleavage" + hydrolysis = "hydrolysis" + metabolic_processing = "metabolic_processing" + mutation_rate = "mutation_rate" + stability = "stability" + folding = "folding" + localization = "localization" + transport = "transport" + secretion = "secretion" + uptake = "uptake" + molecular_modification = "molecular_modification" + acetylation = "acetylation" + acylation = "acylation" + alkylation = "alkylation" + amination = "amination" + carbamoylation = "carbamoylation" + ethylation = "ethylation" + glutathionylation = "glutathionylation" + glycation = "glycation" + glycosylation = "glycosylation" + glucuronidation = "glucuronidation" + n_linked_glycosylation = "n_linked_glycosylation" + o_linked_glycosylation = "o_linked_glycosylation" + hydroxylation = "hydroxylation" + lipidation = "lipidation" + farnesylation = "farnesylation" + geranoylation = "geranoylation" + myristoylation = "myristoylation" + palmitoylation = "palmitoylation" + prenylation = "prenylation" + methylation = "methylation" + nitrosation = "nitrosation" + nucleotidylation = "nucleotidylation" + phosphorylation = "phosphorylation" + ribosylation = "ribosylation" + ADP_ribosylation = "ADP-ribosylation" + sulfation = "sulfation" + sumoylation = "sumoylation" + ubiquitination = "ubiquitination" + oxidation = "oxidation" + reduction = "reduction" + carboxylation = "carboxylation" class CausalMechanismQualifierEnum(str, Enum): + # A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction. binding = "binding" + # A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway. inhibition = "inhibition" + # A causal mechanism in which an antibody specifically binds to and interferes with the target. antibody_inhibition = "antibody_inhibition" + # A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site. antagonism = "antagonism" + # A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it. molecular_channel_blockage = "molecular_channel_blockage" + # A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling. inverse_agonism = "inverse_agonism" + # A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) negative_allosteric_modulation = "negative_allosteric_modulation" + # A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand. agonism = "agonism" + # A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it. molecular_channel_opening = "molecular_channel_opening" + # A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) positive_allosteric_modulation = "positive_allosteric_modulation" + # A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target. potentiation = "potentiation" + # A causal mechanism in which the effector binds to and positively affects the normal functioning of its target. activation = "activation" + # A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body. inducer = "inducer" + # A causal mechanism mediated by through the control of target gene transcription transcriptional_regulation = "transcriptional_regulation" + # A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc) signaling_mediated_control = "signaling_mediated_control" + stabilization = "stabilization" + stimulation = "stimulation" + releasing_activity = "releasing_activity" class LogicalInterpretationEnum(str, Enum): + # A modifier on a triple that causes the triple to be interpreted as a some-some statement some_some = "some_some" + # A modifier on a triple that causes the triple to be interpreted as an all-some statement. all_some = "all_some" + inverse_all_some = "inverse_all_some" class ReactionDirectionEnum(str, Enum): + left_to_right = "left_to_right" + right_to_left = "right_to_left" + bidirectional = "bidirectional" + neutral = "neutral" class ReactionSideEnum(str, Enum): + left = "left" + right = "right" class PhaseEnum(str, Enum): + """ + phase + """ number_0 = "0" + number_1 = "1" + number_2 = "2" class StrandEnum(str, Enum): - + """ + strand + """ + # Positive PLUS_SIGN = "+" + # Negative _ = "-" + # Unstranded FULL_STOP = "." + # Unknown QUESTION_MARK = "?" class SequenceEnum(str, Enum): - + """ + type of sequence + """ + # nucleic acid na = "na" + # amino acid aa = "aa" class DruggableGeneCategoryEnum(str, Enum): + # These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action. tclin = "tclin" + # These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below. tbio = "tbio" + # These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code tchem = "tchem" + # These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com. tdark = "tdark" class DrugAvailabilityEnum(str, Enum): + # chemical entity is available over the counter without a prescription. over_the_counter = "over_the_counter" + # chemical entity is available by prescription. prescription = "prescription" class DrugDeliveryEnum(str, Enum): + inhalation = "inhalation" + oral = "oral" + absorption_through_the_skin = "absorption_through_the_skin" + intravenous_injection = "intravenous_injection" class ResourceRoleEnum(str, Enum): + """ + The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience. + """ primary_knowledge_source = "primary_knowledge_source" + aggregator_knowledge_source = "aggregator_knowledge_source" + supporting_data_source = "supporting_data_source" class FDAApprovalStatusEnum(str, Enum): + # Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments. discovery_and_development_phase = "discovery_and_development_phase" + # Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo. preclinical_research_phase = "preclinical_research_phase" + # Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer. fda_clinical_research_phase = "fda_clinical_research_phase" + # FDA Review fda_review_phase_4 = "fda_review_phase_4" + # FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. fda_post_market_safety_review = "fda_post_market_safety_review" + # In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase. fda_clinical_research_phase_1 = "fda_clinical_research_phase_1" + # In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur. fda_clinical_research_phase_2 = "fda_clinical_research_phase_2" + # In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions. fda_clinical_research_phase_3 = "fda_clinical_research_phase_3" + # In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review. fda_clinical_research_phase_4 = "fda_clinical_research_phase_4" + # Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track fda_fast_track = "fda_fast_track" + # Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy fda_breakthrough_therapy = "fda_breakthrough_therapy" + # When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval fda_accelerated_approval = "fda_accelerated_approval" + # Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review fda_priority_review = "fda_priority_review" + # Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. regular_fda_approval = "regular_fda_approval" + post_approval_withdrawal = "post_approval_withdrawal" class FDAIDAAdverseEventEnum(str, Enum): - + """ + please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32 + """ + # An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death. life_threatening_adverse_event = "life_threatening_adverse_event" + # An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse. serious_adverse_event = "serious_adverse_event" + # means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug. suspected_adverse_reaction = "suspected_adverse_reaction" + # An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation. unexpected_adverse_event = "unexpected_adverse_event" +class InformationResourceStatusEnum(str, Enum): + + + released = "released" + + deprecated = "deprecated" + + draft = "draft" + + modified = "modified" + + + class MappingCollection(ConfiguredBaseModel): """ A collection of deprecated mappings. @@ -278,7 +429,7 @@ class PredicateMapping(ConfiguredBaseModel): subject_part_qualifier: Optional[str] = Field(None) subject_derivative_qualifier: Optional[str] = Field(None) subject_context_qualifier: Optional[str] = Field(None) - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") qualified_predicate: Optional[str] = Field(None, description="""Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.""") object_aspect_qualifier: Optional[str] = Field(None) object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) @@ -287,7 +438,7 @@ class PredicateMapping(ConfiguredBaseModel): object_derivative_qualifier: Optional[str] = Field(None) object_context_qualifier: Optional[str] = Field(None) causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, description="""A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')""") - anatomical_context_qualifier: Optional[AnatomicalContextQualifierEnum] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") species_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.""") exact_match: Optional[List[str]] = Field(None, description="""holds between two entities that have strictly equivalent meanings, with a high degree of confidence""") narrow_match: Optional[List[str]] = Field(None, description="""a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.""") @@ -299,7 +450,7 @@ class OntologyClass(ConfiguredBaseModel): """ a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type. """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -365,7 +516,7 @@ class Entity(ConfiguredBaseModel): """ Root Biolink Model class for all things and informational relationships, real or imagined. """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Entity","biolink:Entity"]] = Field(["biolink:Entity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -374,7 +525,7 @@ class Entity(ConfiguredBaseModel): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -385,7 +536,7 @@ class NamedThing(Entity): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThing","biolink:NamedThing"]] = Field(["biolink:NamedThing"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -394,7 +545,7 @@ class NamedThing(Entity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -404,11 +555,11 @@ class Attribute(NamedThing, OntologyClass): A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/Attribute","biolink:Attribute"]] = Field(["biolink:Attribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -417,7 +568,7 @@ class Attribute(NamedThing, OntologyClass): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -427,11 +578,11 @@ class ChemicalRole(Attribute): A role played by the molecular entity or part thereof within a chemical context. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalRole","biolink:ChemicalRole"]] = Field(["biolink:ChemicalRole"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -440,7 +591,7 @@ class ChemicalRole(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -448,11 +599,11 @@ class ChemicalRole(Attribute): class BiologicalSex(Attribute): name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalSex","biolink:BiologicalSex"]] = Field(["biolink:BiologicalSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -461,7 +612,7 @@ class BiologicalSex(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -471,11 +622,11 @@ class PhenotypicSex(BiologicalSex): An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicSex","biolink:PhenotypicSex"]] = Field(["biolink:PhenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -484,7 +635,7 @@ class PhenotypicSex(BiologicalSex): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -494,11 +645,11 @@ class GenotypicSex(BiologicalSex): An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypicSex","biolink:GenotypicSex"]] = Field(["biolink:GenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -507,7 +658,7 @@ class GenotypicSex(BiologicalSex): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -517,11 +668,11 @@ class SeverityValue(Attribute): describes the severity of a phenotypic feature or disease """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/SeverityValue","biolink:SeverityValue"]] = Field(["biolink:SeverityValue"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -530,7 +681,7 @@ class SeverityValue(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -539,7 +690,7 @@ class RelationshipType(OntologyClass): """ An OWL property used as an edge label """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -547,7 +698,7 @@ class TaxonomicRank(OntologyClass): """ A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -557,7 +708,7 @@ class OrganismTaxon(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxon","biolink:OrganismTaxon"]] = Field(["biolink:OrganismTaxon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -566,7 +717,7 @@ class OrganismTaxon(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -577,7 +728,7 @@ class Event(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Event","biolink:Event"]] = Field(["biolink:Event"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -586,7 +737,7 @@ class Event(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -595,7 +746,7 @@ class AdministrativeEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AdministrativeEntity","biolink:AdministrativeEntity"]] = Field(["biolink:AdministrativeEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -604,7 +755,7 @@ class AdministrativeEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -617,7 +768,7 @@ class Agent(AdministrativeEntity): address: Optional[str] = Field(None, description="""the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") + id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Agent","biolink:Agent"]] = Field(["biolink:Agent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -626,7 +777,7 @@ class Agent(AdministrativeEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -641,7 +792,7 @@ class InformationContentEntity(NamedThing): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntity","biolink:InformationContentEntity"]] = Field(["biolink:InformationContentEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -650,7 +801,7 @@ class InformationContentEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -665,7 +816,7 @@ class StudyResult(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyResult","biolink:StudyResult"]] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -674,7 +825,7 @@ class StudyResult(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -689,7 +840,7 @@ class StudyVariable(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyVariable","biolink:StudyVariable"]] = Field(["biolink:StudyVariable"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -698,7 +849,7 @@ class StudyVariable(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -713,7 +864,7 @@ class CommonDataElement(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CommonDataElement","biolink:CommonDataElement"]] = Field(["biolink:CommonDataElement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -722,7 +873,7 @@ class CommonDataElement(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -737,7 +888,7 @@ class ConceptCountAnalysisResult(StudyResult): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConceptCountAnalysisResult","biolink:ConceptCountAnalysisResult"]] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -746,7 +897,7 @@ class ConceptCountAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -761,7 +912,7 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult","biolink:ObservedExpectedFrequencyAnalysisResult"]] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -770,7 +921,7 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -785,7 +936,7 @@ class RelativeFrequencyAnalysisResult(StudyResult): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult","biolink:RelativeFrequencyAnalysisResult"]] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -794,7 +945,7 @@ class RelativeFrequencyAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -809,7 +960,7 @@ class TextMiningResult(StudyResult): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TextMiningResult","biolink:TextMiningResult"]] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -818,7 +969,7 @@ class TextMiningResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -833,7 +984,7 @@ class ChiSquaredAnalysisResult(StudyResult): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult","biolink:ChiSquaredAnalysisResult"]] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -842,7 +993,31 @@ class ChiSquaredAnalysisResult(StudyResult): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class LogOddsAnalysisResult(StudyResult): + """ + A result of a log odds ratio analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/LogOddsAnalysisResult","biolink:LogOddsAnalysisResult"]] = Field(["biolink:LogOddsAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -857,7 +1032,7 @@ class Dataset(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Dataset","biolink:Dataset"]] = Field(["biolink:Dataset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -866,7 +1041,7 @@ class Dataset(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -882,7 +1057,7 @@ class DatasetDistribution(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetDistribution","biolink:DatasetDistribution"]] = Field(["biolink:DatasetDistribution"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -891,7 +1066,7 @@ class DatasetDistribution(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -909,7 +1084,7 @@ class DatasetVersion(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetVersion","biolink:DatasetVersion"]] = Field(["biolink:DatasetVersion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -918,7 +1093,7 @@ class DatasetVersion(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -935,7 +1110,7 @@ class DatasetSummary(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetSummary","biolink:DatasetSummary"]] = Field(["biolink:DatasetSummary"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -944,7 +1119,7 @@ class DatasetSummary(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -959,7 +1134,7 @@ class ConfidenceLevel(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConfidenceLevel","biolink:ConfidenceLevel"]] = Field(["biolink:ConfidenceLevel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -968,7 +1143,7 @@ class ConfidenceLevel(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -983,7 +1158,7 @@ class EvidenceType(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EvidenceType","biolink:EvidenceType"]] = Field(["biolink:EvidenceType"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -992,45 +1167,11 @@ class EvidenceType(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") -class InformationResource(InformationContentEntity): - """ - A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. - """ - information_resource_status: Optional[InformationResourceStatusEnum] = Field(None, description="""the status of the infores identifier, default is released""") - name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") - license: Optional[str] = Field(None) - rights: Optional[str] = Field(None) - format: Optional[str] = Field(None) - creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") - provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - category: List[Literal["https://w3id.org/biolink/vocab/InformationResource","biolink:InformationResource"]] = Field(["biolink:InformationResource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) - has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - - - -class InformationResourceCollection(ConfiguredBaseModel): - """ - A collection of information resources - """ - information_resources: Optional[List[InformationResource]] = Field(None, description="""a collection of information resources""") - - - class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). @@ -1046,7 +1187,7 @@ class Publication(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Publication","biolink:Publication"]] = Field(["biolink:Publication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1055,7 +1196,7 @@ class Publication(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1075,7 +1216,7 @@ class Book(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Books should have industry-standard identifier such as from ISBN.""") + id: str = Field(..., description="""Books should have industry-standard identifier such as from ISBN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Book","biolink:Book"]] = Field(["biolink:Book"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1084,14 +1225,14 @@ class Book(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'book'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class BookChapter(Publication): - published_in: str = Field(None, description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") + published_in: str = Field(..., description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") chapter: Optional[str] = Field(None, description="""chapter of a book""") authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") @@ -1105,7 +1246,7 @@ class BookChapter(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BookChapter","biolink:BookChapter"]] = Field(["biolink:BookChapter"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1114,7 +1255,7 @@ class BookChapter(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1137,7 +1278,7 @@ class Serial(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") + id: str = Field(..., description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Serial","biolink:Serial"]] = Field(["biolink:Serial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1146,7 +1287,7 @@ class Serial(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1155,7 +1296,7 @@ class Article(Publication): """ a piece of writing on a particular topic presented as a stand-alone section of a larger publication """ - published_in: str = Field(None, description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") + published_in: str = Field(..., description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") @@ -1170,7 +1311,7 @@ class Article(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Article","biolink:Article"]] = Field(["biolink:Article"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1179,7 +1320,7 @@ class Article(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1188,7 +1329,7 @@ class JournalArticle(Article): """ an article, typically presenting results of research, that is published in an issue of a scientific journal. """ - published_in: str = Field(None, description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") + published_in: str = Field(..., description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") @@ -1203,7 +1344,7 @@ class JournalArticle(Article): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/JournalArticle","biolink:JournalArticle"]] = Field(["biolink:JournalArticle"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1212,7 +1353,7 @@ class JournalArticle(Article): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1232,7 +1373,7 @@ class Patent(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Patent","biolink:Patent"]] = Field(["biolink:Patent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1241,7 +1382,7 @@ class Patent(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1261,7 +1402,7 @@ class WebPage(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/WebPage","biolink:WebPage"]] = Field(["biolink:WebPage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1270,7 +1411,7 @@ class WebPage(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1290,7 +1431,7 @@ class PreprintPublication(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PreprintPublication","biolink:PreprintPublication"]] = Field(["biolink:PreprintPublication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1299,7 +1440,7 @@ class PreprintPublication(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1319,7 +1460,7 @@ class DrugLabel(Publication): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugLabel","biolink:DrugLabel"]] = Field(["biolink:DrugLabel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1328,7 +1469,7 @@ class DrugLabel(Publication): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1337,8 +1478,8 @@ class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. """ - resource_id: str = Field(None, description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") - resource_role: ResourceRoleEnum = Field(None, description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") + resource_id: str = Field(..., description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") + resource_role: ResourceRoleEnum = Field(..., description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") upstream_resource_ids: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") license: Optional[str] = Field(None) @@ -1346,7 +1487,7 @@ class RetrievalSource(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RetrievalSource","biolink:RetrievalSource"]] = Field(["biolink:RetrievalSource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1355,7 +1496,7 @@ class RetrievalSource(InformationContentEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1382,7 +1523,7 @@ class PhysicalEntity(PhysicalEssence, NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysicalEntity","biolink:PhysicalEntity"]] = Field(["biolink:PhysicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1391,7 +1532,7 @@ class PhysicalEntity(PhysicalEssence, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1418,7 +1559,7 @@ class Activity(ActivityAndBehavior, NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Activity","biolink:Activity"]] = Field(["biolink:Activity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1427,7 +1568,7 @@ class Activity(ActivityAndBehavior, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1438,7 +1579,7 @@ class Study(Activity): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Study","biolink:Study"]] = Field(["biolink:Study"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1447,7 +1588,7 @@ class Study(Activity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1458,7 +1599,7 @@ class Procedure(ActivityAndBehavior, NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Procedure","biolink:Procedure"]] = Field(["biolink:Procedure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1467,7 +1608,7 @@ class Procedure(ActivityAndBehavior, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1478,7 +1619,7 @@ class Phenomenon(Occurrent, NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Phenomenon","biolink:Phenomenon"]] = Field(["biolink:Phenomenon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1487,7 +1628,7 @@ class Phenomenon(Occurrent, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1498,7 +1639,7 @@ class Device(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Device","biolink:Device"]] = Field(["biolink:Device"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1507,7 +1648,7 @@ class Device(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1518,7 +1659,7 @@ class DiagnosticAid(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiagnosticAid","biolink:DiagnosticAid"]] = Field(["biolink:DiagnosticAid"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1527,7 +1668,7 @@ class DiagnosticAid(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1546,7 +1687,7 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSample","biolink:MaterialSample"]] = Field(["biolink:MaterialSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1555,7 +1696,7 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1566,7 +1707,7 @@ class PlanetaryEntity(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PlanetaryEntity","biolink:PlanetaryEntity"]] = Field(["biolink:PlanetaryEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1575,7 +1716,7 @@ class PlanetaryEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1584,7 +1725,7 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalProcess","biolink:EnvironmentalProcess"]] = Field(["biolink:EnvironmentalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1593,7 +1734,7 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1602,7 +1743,7 @@ class EnvironmentalFeature(PlanetaryEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFeature","biolink:EnvironmentalFeature"]] = Field(["biolink:EnvironmentalFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1611,7 +1752,7 @@ class EnvironmentalFeature(PlanetaryEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1624,7 +1765,7 @@ class GeographicLocation(PlanetaryEntity): longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocation","biolink:GeographicLocation"]] = Field(["biolink:GeographicLocation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1633,7 +1774,7 @@ class GeographicLocation(PlanetaryEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1647,7 +1788,7 @@ class GeographicLocationAtTime(GeographicLocation): longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocationAtTime","biolink:GeographicLocationAtTime"]] = Field(["biolink:GeographicLocationAtTime"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1656,7 +1797,7 @@ class GeographicLocationAtTime(GeographicLocation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1674,7 +1815,7 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalEntity","biolink:BiologicalEntity"]] = Field(["biolink:BiologicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1683,7 +1824,7 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1707,7 +1848,7 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -1719,7 +1860,7 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1728,7 +1869,7 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): """ An execution of a molecular function carried out by a gene product or macromolecular complex. """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""A chemical entity that is the input for the reaction""") has_output: Optional[List[str]] = Field(None, description="""A chemical entity that is the output for the reaction""") enabled_by: Optional[List[str]] = Field(None, description="""The gene product, gene, or complex that catalyzes the reaction""") @@ -1743,7 +1884,7 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1752,7 +1893,7 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): """ One or more causally connected executions of molecular functions """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") @@ -1767,14 +1908,14 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class Pathway(BiologicalProcess, OntologyClass): - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") @@ -1789,14 +1930,14 @@ class Pathway(BiologicalProcess, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class PhysiologicalProcess(BiologicalProcess, OntologyClass): - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") @@ -1811,14 +1952,14 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") @@ -1833,7 +1974,7 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1843,11 +1984,11 @@ class OrganismAttribute(Attribute): describes a characteristic of an organismal entity. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismAttribute","biolink:OrganismAttribute"]] = Field(["biolink:OrganismAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1856,7 +1997,7 @@ class OrganismAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1866,11 +2007,11 @@ class PhenotypicQuality(OrganismAttribute): A property of a phenotype """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicQuality","biolink:PhenotypicQuality"]] = Field(["biolink:PhenotypicQuality"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1879,7 +2020,7 @@ class PhenotypicQuality(OrganismAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1891,7 +2032,7 @@ class GeneticInheritance(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneticInheritance","biolink:GeneticInheritance"]] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1900,7 +2041,7 @@ class GeneticInheritance(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1912,7 +2053,7 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntity","biolink:OrganismalEntity"]] = Field(["biolink:OrganismalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1921,7 +2062,7 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1933,7 +2074,7 @@ class Bacterium(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Bacterium","biolink:Bacterium"]] = Field(["biolink:Bacterium"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1942,7 +2083,7 @@ class Bacterium(OrganismalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1954,7 +2095,7 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Virus","biolink:Virus"]] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1963,7 +2104,7 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1973,7 +2114,7 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularOrganism","biolink:CellularOrganism"]] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1982,7 +2123,7 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1994,7 +2135,7 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Mammal","biolink:Mammal"]] = Field(["biolink:Mammal"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2003,7 +2144,7 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2015,7 +2156,7 @@ class Human(Mammal, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Human","biolink:Human"]] = Field(["biolink:Human"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2024,7 +2165,7 @@ class Human(Mammal, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2034,7 +2175,7 @@ class Plant(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Plant","biolink:Plant"]] = Field(["biolink:Plant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2043,7 +2184,7 @@ class Plant(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2055,7 +2196,7 @@ class Invertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Invertebrate","biolink:Invertebrate"]] = Field(["biolink:Invertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2064,7 +2205,7 @@ class Invertebrate(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2076,7 +2217,7 @@ class Vertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Vertebrate","biolink:Vertebrate"]] = Field(["biolink:Vertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2085,7 +2226,7 @@ class Vertebrate(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2097,7 +2238,7 @@ class Fungus(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Fungus","biolink:Fungus"]] = Field(["biolink:Fungus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2106,7 +2247,7 @@ class Fungus(CellularOrganism): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2118,7 +2259,7 @@ class LifeStage(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LifeStage","biolink:LifeStage"]] = Field(["biolink:LifeStage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2127,7 +2268,7 @@ class LifeStage(OrganismalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2139,7 +2280,7 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/IndividualOrganism","biolink:IndividualOrganism"]] = Field(["biolink:IndividualOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2148,7 +2289,7 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2160,7 +2301,7 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms","biolink:PopulationOfIndividualOrganisms"]] = Field(["biolink:PopulationOfIndividualOrganisms"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2169,7 +2310,7 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2181,7 +2322,7 @@ class StudyPopulation(PopulationOfIndividualOrganisms): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyPopulation","biolink:StudyPopulation"]] = Field(["biolink:StudyPopulation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2190,7 +2331,7 @@ class StudyPopulation(PopulationOfIndividualOrganisms): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2202,7 +2343,7 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature","biolink:DiseaseOrPhenotypicFeature"]] = Field(["biolink:DiseaseOrPhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2211,7 +2352,7 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2223,7 +2364,7 @@ class Disease(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Disease","biolink:Disease"]] = Field(["biolink:Disease"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2232,7 +2373,7 @@ class Disease(DiseaseOrPhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2244,7 +2385,7 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeature","biolink:PhenotypicFeature"]] = Field(["biolink:PhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2253,7 +2394,7 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2265,7 +2406,7 @@ class BehavioralFeature(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralFeature","biolink:BehavioralFeature"]] = Field(["biolink:BehavioralFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2274,7 +2415,7 @@ class BehavioralFeature(PhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2286,7 +2427,7 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntity","biolink:AnatomicalEntity"]] = Field(["biolink:AnatomicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2295,7 +2436,7 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2307,7 +2448,7 @@ class CellularComponent(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularComponent","biolink:CellularComponent"]] = Field(["biolink:CellularComponent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2316,7 +2457,7 @@ class CellularComponent(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2326,7 +2467,7 @@ class Cell(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cell","biolink:Cell"]] = Field(["biolink:Cell"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2335,7 +2476,7 @@ class Cell(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2345,7 +2486,7 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLine","biolink:CellLine"]] = Field(["biolink:CellLine"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2354,7 +2495,7 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2364,7 +2505,7 @@ class GrossAnatomicalStructure(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GrossAnatomicalStructure","biolink:GrossAnatomicalStructure"]] = Field(["biolink:GrossAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2373,7 +2514,7 @@ class GrossAnatomicalStructure(AnatomicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2391,7 +2532,7 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -2403,7 +2544,7 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2413,7 +2554,7 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -2425,7 +2566,7 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2435,7 +2576,7 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -2447,7 +2588,7 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2471,7 +2612,7 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntity","biolink:ChemicalEntity"]] = Field(["biolink:ChemicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2480,7 +2621,7 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2497,7 +2638,7 @@ class MolecularEntity(ChemicalEntity): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularEntity","biolink:MolecularEntity"]] = Field(["biolink:MolecularEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2506,7 +2647,7 @@ class MolecularEntity(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2523,7 +2664,7 @@ class SmallMolecule(MolecularEntity): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SmallMolecule","biolink:SmallMolecule"]] = Field(["biolink:SmallMolecule"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2532,7 +2673,7 @@ class SmallMolecule(MolecularEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2552,7 +2693,7 @@ class ChemicalMixture(ChemicalEntity): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalMixture","biolink:ChemicalMixture"]] = Field(["biolink:ChemicalMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2561,7 +2702,7 @@ class ChemicalMixture(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2572,7 +2713,7 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -2589,7 +2730,7 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2609,7 +2750,7 @@ class MolecularMixture(ChemicalMixture): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularMixture","biolink:MolecularMixture"]] = Field(["biolink:MolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2618,7 +2759,7 @@ class MolecularMixture(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2638,7 +2779,7 @@ class ComplexMolecularMixture(ChemicalMixture): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexMolecularMixture","biolink:ComplexMolecularMixture"]] = Field(["biolink:ComplexMolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2647,7 +2788,7 @@ class ComplexMolecularMixture(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2667,7 +2808,7 @@ class ProcessedMaterial(ChemicalMixture): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessedMaterial","biolink:ProcessedMaterial"]] = Field(["biolink:ProcessedMaterial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2676,7 +2817,7 @@ class ProcessedMaterial(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2685,7 +2826,7 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): """ A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_supplement: Optional[str] = Field(None) highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") @@ -2705,7 +2846,7 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2719,7 +2860,7 @@ class EnvironmentalFoodContaminant(ChemicalEntity): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant","biolink:EnvironmentalFoodContaminant"]] = Field(["biolink:EnvironmentalFoodContaminant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2728,7 +2869,7 @@ class EnvironmentalFoodContaminant(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2742,7 +2883,7 @@ class FoodAdditive(ChemicalEntity): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FoodAdditive","biolink:FoodAdditive"]] = Field(["biolink:FoodAdditive"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2751,7 +2892,7 @@ class FoodAdditive(ChemicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2771,7 +2912,7 @@ class Food(ChemicalMixture): has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Food","biolink:Food"]] = Field(["biolink:Food"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2780,7 +2921,7 @@ class Food(ChemicalMixture): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2809,7 +2950,7 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -2820,7 +2961,7 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2853,7 +2994,7 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularComplex","biolink:MacromolecularComplex"]] = Field(["biolink:MacromolecularComplex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2861,7 +3002,7 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2874,7 +3015,7 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleosomeModification","biolink:NucleosomeModification"]] = Field(["biolink:NucleosomeModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2883,7 +3024,7 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -2894,7 +3035,7 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): A genome is the sum of genetic material within a cell or virion. """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -2906,7 +3047,7 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2917,7 +3058,7 @@ class Exon(NucleicAcidEntity): """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -2934,7 +3075,7 @@ class Exon(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2945,7 +3086,7 @@ class Transcript(NucleicAcidEntity): """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -2962,7 +3103,7 @@ class Transcript(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2971,7 +3112,7 @@ class CodingSequence(NucleicAcidEntity): has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -2988,7 +3129,7 @@ class CodingSequence(NucleicAcidEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3000,7 +3141,7 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Polypeptide","biolink:Polypeptide"]] = Field(["biolink:Polypeptide"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3009,7 +3150,7 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3022,7 +3163,7 @@ class Protein(Polypeptide, GeneProductMixin): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Protein","biolink:Protein"]] = Field(["biolink:Protein"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3031,7 +3172,7 @@ class Protein(Polypeptide, GeneProductMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3044,7 +3185,7 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinIsoform","biolink:ProteinIsoform"]] = Field(["biolink:ProteinIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3053,7 +3194,7 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3065,7 +3206,7 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PosttranslationalModification","biolink:PosttranslationalModification"]] = Field(["biolink:PosttranslationalModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3074,7 +3215,7 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3087,7 +3228,7 @@ class NucleicAcidSequenceMotif(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif","biolink:NucleicAcidSequenceMotif"]] = Field(["biolink:NucleicAcidSequenceMotif"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3096,7 +3237,7 @@ class NucleicAcidSequenceMotif(BiologicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3107,7 +3248,7 @@ class RNAProduct(Transcript, GeneProductMixin): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -3123,7 +3264,7 @@ class RNAProduct(Transcript, GeneProductMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3136,7 +3277,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -3152,7 +3293,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3163,7 +3304,7 @@ class NoncodingRNAProduct(RNAProduct): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -3179,7 +3320,7 @@ class NoncodingRNAProduct(RNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3190,7 +3331,7 @@ class MicroRNA(NoncodingRNAProduct): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -3206,7 +3347,7 @@ class MicroRNA(NoncodingRNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3219,7 +3360,7 @@ class SiRNA(NoncodingRNAProduct): xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") trade_name: Optional[str] = Field(None) available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) @@ -3235,7 +3376,7 @@ class SiRNA(NoncodingRNAProduct): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3256,7 +3397,7 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinDomain","biolink:ProteinDomain"]] = Field(["biolink:ProteinDomain"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3265,7 +3406,7 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3276,7 +3417,7 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinFamily","biolink:ProteinFamily"]] = Field(["biolink:ProteinFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3285,7 +3426,7 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3298,7 +3439,7 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneFamily","biolink:GeneFamily"]] = Field(["biolink:GeneFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3307,7 +3448,7 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3315,11 +3456,11 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica class Zygosity(Attribute): name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/Zygosity","biolink:Zygosity"]] = Field(["biolink:Zygosity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3328,7 +3469,7 @@ class Zygosity(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3339,7 +3480,7 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ has_zygosity: Optional[str] = Field(None) has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -3351,7 +3492,7 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3361,7 +3502,7 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) A set of zero or more Alleles on a single instance of a Sequence[VMC] """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -3373,7 +3514,7 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3384,7 +3525,7 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology """ has_gene: Optional[List[str]] = Field(None, description="""Each allele can be associated with any number of genes""") has_biological_sequence: Optional[str] = Field(None, description="""The state of the sequence w.r.t a reference sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -3396,7 +3537,7 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3407,7 +3548,7 @@ class Snv(SequenceVariant): """ has_gene: Optional[List[str]] = Field(None, description="""Each allele can be associated with any number of genes""") has_biological_sequence: Optional[str] = Field(None, description="""The state of the sequence w.r.t a reference sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -3419,7 +3560,7 @@ class Snv(SequenceVariant): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3429,7 +3570,7 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. """ has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") @@ -3441,7 +3582,7 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3451,11 +3592,11 @@ class ClinicalAttribute(Attribute): Attributes relating to a clinical manifestation """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalAttribute","biolink:ClinicalAttribute"]] = Field(["biolink:ClinicalAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3464,7 +3605,7 @@ class ClinicalAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3474,11 +3615,11 @@ class ClinicalMeasurement(ClinicalAttribute): A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalMeasurement","biolink:ClinicalMeasurement"]] = Field(["biolink:ClinicalMeasurement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3487,7 +3628,7 @@ class ClinicalMeasurement(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3497,11 +3638,11 @@ class ClinicalModifier(ClinicalAttribute): Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalModifier","biolink:ClinicalModifier"]] = Field(["biolink:ClinicalModifier"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3510,7 +3651,7 @@ class ClinicalModifier(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3520,11 +3661,11 @@ class ClinicalCourse(ClinicalAttribute): The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalCourse","biolink:ClinicalCourse"]] = Field(["biolink:ClinicalCourse"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3533,7 +3674,7 @@ class ClinicalCourse(ClinicalAttribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3543,11 +3684,11 @@ class Onset(ClinicalCourse): The age group in which (disease) symptom manifestations appear """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/Onset","biolink:Onset"]] = Field(["biolink:Onset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3556,7 +3697,7 @@ class Onset(ClinicalCourse): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3567,7 +3708,7 @@ class ClinicalEntity(NamedThing): """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalEntity","biolink:ClinicalEntity"]] = Field(["biolink:ClinicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3576,7 +3717,7 @@ class ClinicalEntity(NamedThing): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3585,7 +3726,7 @@ class ClinicalTrial(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalTrial","biolink:ClinicalTrial"]] = Field(["biolink:ClinicalTrial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3594,7 +3735,7 @@ class ClinicalTrial(ClinicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3603,7 +3744,7 @@ class ClinicalIntervention(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalIntervention","biolink:ClinicalIntervention"]] = Field(["biolink:ClinicalIntervention"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3612,7 +3753,7 @@ class ClinicalIntervention(ClinicalEntity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3624,7 +3765,7 @@ class ClinicalFinding(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalFinding","biolink:ClinicalFinding"]] = Field(["biolink:ClinicalFinding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3633,7 +3774,7 @@ class ClinicalFinding(PhenotypicFeature): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3642,7 +3783,7 @@ class Hospitalization(ClinicalIntervention): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Hospitalization","biolink:Hospitalization"]] = Field(["biolink:Hospitalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3651,7 +3792,7 @@ class Hospitalization(ClinicalIntervention): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3661,11 +3802,11 @@ class SocioeconomicAttribute(Attribute): Attributes relating to a socioeconomic manifestation """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicAttribute","biolink:SocioeconomicAttribute"]] = Field(["biolink:SocioeconomicAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3674,7 +3815,7 @@ class SocioeconomicAttribute(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3686,7 +3827,7 @@ class Case(IndividualOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Case","biolink:Case"]] = Field(["biolink:Case"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3695,7 +3836,7 @@ class Case(IndividualOrganism, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3707,7 +3848,7 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cohort","biolink:Cohort"]] = Field(["biolink:Cohort"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3716,7 +3857,7 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3726,7 +3867,7 @@ class ExposureEvent(OntologyClass): A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes """ timepoint: Optional[str] = Field(None, description="""a point in time""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -3738,9 +3879,9 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -3752,7 +3893,7 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3769,7 +3910,7 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): """ A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. """ - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") @@ -3784,7 +3925,7 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3795,11 +3936,11 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcessExposure","biolink:PathologicalProcessExposure"]] = Field(["biolink:PathologicalProcessExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3808,7 +3949,7 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3820,7 +3961,7 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure","biolink:PathologicalAnatomicalStructure"]] = Field(["biolink:PathologicalAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3829,7 +3970,7 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3840,11 +3981,11 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure","biolink:PathologicalAnatomicalExposure"]] = Field(["biolink:PathologicalAnatomicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3853,7 +3994,7 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3864,11 +4005,11 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure","biolink:DiseaseOrPhenotypicFeatureExposure"]] = Field(["biolink:DiseaseOrPhenotypicFeatureExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3877,7 +4018,7 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3889,10 +4030,10 @@ class ChemicalExposure(ExposureEvent, Attribute): has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalExposure","biolink:ChemicalExposure"]] = Field(["biolink:ChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3901,7 +4042,7 @@ class ChemicalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3911,11 +4052,11 @@ class ComplexChemicalExposure(Attribute): A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. """ name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexChemicalExposure","biolink:ComplexChemicalExposure"]] = Field(["biolink:ComplexChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3924,7 +4065,7 @@ class ComplexChemicalExposure(Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3936,10 +4077,10 @@ class DrugExposure(ChemicalExposure, ExposureEvent): timepoint: Optional[str] = Field(None, description="""a point in time""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugExposure","biolink:DrugExposure"]] = Field(["biolink:DrugExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3948,7 +4089,7 @@ class DrugExposure(ChemicalExposure, ExposureEvent): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3961,10 +4102,10 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): timepoint: Optional[str] = Field(None, description="""a point in time""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure","biolink:DrugToGeneInteractionExposure"]] = Field(["biolink:DrugToGeneInteractionExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3973,7 +4114,7 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3988,7 +4129,7 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): timepoint: Optional[str] = Field(None, description="""a point in time""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Treatment","biolink:Treatment"]] = Field(["biolink:Treatment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3997,7 +4138,7 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4008,11 +4149,11 @@ class BioticExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/BioticExposure","biolink:BioticExposure"]] = Field(["biolink:BioticExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4021,7 +4162,7 @@ class BioticExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4032,11 +4173,11 @@ class EnvironmentalExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalExposure","biolink:EnvironmentalExposure"]] = Field(["biolink:EnvironmentalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4045,7 +4186,7 @@ class EnvironmentalExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4056,11 +4197,11 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicExposure","biolink:GeographicExposure"]] = Field(["biolink:GeographicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4069,7 +4210,7 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4080,11 +4221,11 @@ class BehavioralExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralExposure","biolink:BehavioralExposure"]] = Field(["biolink:BehavioralExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4093,7 +4234,7 @@ class BehavioralExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4104,11 +4245,11 @@ class SocioeconomicExposure(ExposureEvent, Attribute): """ timepoint: Optional[str] = Field(None, description="""a point in time""") name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") - has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicExposure","biolink:SocioeconomicExposure"]] = Field(["biolink:SocioeconomicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4117,8 +4258,8 @@ class SocioeconomicExposure(ExposureEvent, Attribute): This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list) - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") - has_attribute: List[str] = Field(None, description="""connects any entity to an attribute""") + description: Optional[str] = Field(None) + has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") @@ -4198,9 +4339,9 @@ class Association(Entity): """ A typed association between two entities, supported by evidence """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4223,7 +4364,7 @@ class Association(Entity): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Association","biolink:Association"]] = Field(["biolink:Association"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4232,16 +4373,16 @@ class Association(Entity): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class ChemicalEntityAssessesNamedThingAssociation(Association): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4264,7 +4405,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityAssessesNamedThingAssociation","biolink:ChemicalEntityAssessesNamedThingAssociation"]] = Field(["biolink:ChemicalEntityAssessesNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4273,7 +4414,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4282,9 +4423,9 @@ class ContributorAssociation(Association): """ Any association between an entity (such as a publication) and various agents that contribute to its realisation """ - subject: str = Field(None, description="""information content entity which an agent has helped realise""") - predicate: str = Field(None, description="""generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'""") - object: str = Field(None, description="""agent helping to realise the given entity (e.g. such as a publication)""") + subject: str = Field(..., description="""information content entity which an agent has helped realise""") + predicate: str = Field(..., description="""generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'""") + object: str = Field(..., description="""agent helping to realise the given entity (e.g. such as a publication)""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4307,7 +4448,7 @@ class ContributorAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ContributorAssociation","biolink:ContributorAssociation"]] = Field(["biolink:ContributorAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4316,7 +4457,7 @@ class ContributorAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4325,9 +4466,9 @@ class GenotypeToGenotypePartAssociation(Association): """ Any association between one genotype and a genotypic entity that is a sub-component of it """ - subject: str = Field(None, description="""parent genotype""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""child genotype""") + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""child genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4350,7 +4491,7 @@ class GenotypeToGenotypePartAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation","biolink:GenotypeToGenotypePartAssociation"]] = Field(["biolink:GenotypeToGenotypePartAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4359,7 +4500,7 @@ class GenotypeToGenotypePartAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4368,9 +4509,9 @@ class GenotypeToGeneAssociation(Association): """ Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality """ - subject: str = Field(None, description="""parent genotype""") - predicate: str = Field(None, description="""the relationship type used to connect genotype to gene""") - object: str = Field(None, description="""gene implicated in genotype""") + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""the relationship type used to connect genotype to gene""") + object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4393,7 +4534,7 @@ class GenotypeToGeneAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGeneAssociation","biolink:GenotypeToGeneAssociation"]] = Field(["biolink:GenotypeToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4402,7 +4543,7 @@ class GenotypeToGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4411,9 +4552,9 @@ class GenotypeToVariantAssociation(Association): """ Any association between a genotype and a sequence variant. """ - subject: str = Field(None, description="""parent genotype""") - predicate: str = Field(None, description="""the relationship type used to connect genotype to gene""") - object: str = Field(None, description="""gene implicated in genotype""") + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""the relationship type used to connect genotype to gene""") + object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4436,7 +4577,7 @@ class GenotypeToVariantAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToVariantAssociation","biolink:GenotypeToVariantAssociation"]] = Field(["biolink:GenotypeToVariantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4445,7 +4586,7 @@ class GenotypeToVariantAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4454,9 +4595,9 @@ class GeneToGeneAssociation(Association): """ abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction. """ - subject: str = Field(None, description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4479,7 +4620,7 @@ class GeneToGeneAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneAssociation","biolink:GeneToGeneAssociation"]] = Field(["biolink:GeneToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4488,7 +4629,7 @@ class GeneToGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4497,9 +4638,9 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): """ A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same) """ - subject: str = Field(None, description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") - predicate: str = Field(None, description="""homology relationship type""") - object: str = Field(None, description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""homology relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4522,7 +4663,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneHomologyAssociation","biolink:GeneToGeneHomologyAssociation"]] = Field(["biolink:GeneToGeneHomologyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4531,7 +4672,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4540,9 +4681,9 @@ class GeneToGeneFamilyAssociation(Association): """ Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships. """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""membership of the gene in the given gene family.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""membership of the gene in the given gene family.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4565,7 +4706,7 @@ class GeneToGeneFamilyAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation","biolink:GeneToGeneFamilyAssociation"]] = Field(["biolink:GeneToGeneFamilyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4574,7 +4715,7 @@ class GeneToGeneFamilyAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4598,9 +4739,9 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati expression_site: Optional[str] = Field(None, description="""location in which gene or protein expression takes place. May be cell, tissue, or organ.""") stage_qualifier: Optional[str] = Field(None, description="""stage during which gene or protein expression of takes place.""") phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") - subject: str = Field(None, description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4623,7 +4764,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneCoexpressionAssociation","biolink:GeneToGeneCoexpressionAssociation"]] = Field(["biolink:GeneToGeneCoexpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4632,7 +4773,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4641,9 +4782,9 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): """ An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation) """ - subject: str = Field(None, description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") - predicate: str = Field(None, description="""interaction relationship type""") - object: str = Field(None, description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""interaction relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4666,7 +4807,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseGeneToGeneInteraction","biolink:PairwiseGeneToGeneInteraction"]] = Field(["biolink:PairwiseGeneToGeneInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4675,7 +4816,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4685,9 +4826,9 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): An interaction at the molecular level between two physical entities """ interacting_molecules_category: Optional[str] = Field(None) - subject: str = Field(None, description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") - predicate: str = Field(None, description="""interaction relationship type""") - object: str = Field(None, description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""interaction relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4710,7 +4851,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") + id: str = Field(..., description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseMolecularInteraction","biolink:PairwiseMolecularInteraction"]] = Field(["biolink:PairwiseMolecularInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4719,7 +4860,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4768,9 +4909,9 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio """ A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. """ - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the chemical element that is the target of the statement""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4793,7 +4934,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalAssociation","biolink:ChemicalToChemicalAssociation"]] = Field(["biolink:ChemicalToChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4802,7 +4943,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4812,9 +4953,9 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") reaction_direction: Optional[ReactionDirectionEnum] = Field(None, description="""the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)""") reaction_side: Optional[ReactionSideEnum] = Field(None, description="""the side of a reaction being modeled (ie: left or right)""") - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the chemical element that is the target of the statement""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4837,7 +4978,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToParticipantAssociation","biolink:ReactionToParticipantAssociation"]] = Field(["biolink:ReactionToParticipantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4846,7 +4987,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4856,9 +4997,9 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") reaction_direction: Optional[ReactionDirectionEnum] = Field(None, description="""the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)""") reaction_side: Optional[ReactionSideEnum] = Field(None, description="""the side of a reaction being modeled (ie: left or right)""") - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the chemical element that is the target of the statement""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4881,7 +5022,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToCatalystAssociation","biolink:ReactionToCatalystAssociation"]] = Field(["biolink:ReactionToCatalystAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4890,7 +5031,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4907,9 +5048,9 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): C1 derives-into C2 <> """ catalyst_qualifier: Optional[List[str]] = Field(None, description="""this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.""") - subject: str = Field(None, description="""the upstream chemical entity""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the downstream chemical entity""") + subject: str = Field(..., description="""the upstream chemical entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the downstream chemical entity""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4932,7 +5073,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalDerivationAssociation","biolink:ChemicalToChemicalDerivationAssociation"]] = Field(["biolink:ChemicalToChemicalDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4941,7 +5082,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4950,9 +5091,9 @@ class MolecularActivityToPathwayAssociation(Association): """ Association that holds the relationship between a reaction and the pathway it participates in. """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -4975,7 +5116,7 @@ class MolecularActivityToPathwayAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToPathwayAssociation","biolink:MolecularActivityToPathwayAssociation"]] = Field(["biolink:MolecularActivityToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4984,7 +5125,7 @@ class MolecularActivityToPathwayAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4993,9 +5134,9 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association """ An interaction between a chemical entity and a biological process or pathway. """ - subject: str = Field(None, description="""the chemical entity that is affecting the pathway""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the pathway that is affected by the chemical""") + subject: str = Field(..., description="""the chemical entity that is affecting the pathway""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the pathway that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5018,7 +5159,7 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToPathwayAssociation","biolink:ChemicalToPathwayAssociation"]] = Field(["biolink:ChemicalToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5027,16 +5168,16 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5059,7 +5200,7 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation","biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5068,7 +5209,7 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5085,9 +5226,9 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) object_context_qualifier: Optional[str] = Field(None) anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5110,7 +5251,7 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation","biolink:ChemicalGeneInteractionAssociation"]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5119,7 +5260,7 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5141,9 +5282,9 @@ class ChemicalAffectsGeneAssociation(Association): causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, description="""A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')""") anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") qualified_predicate: Optional[str] = Field(None, description="""Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.""") - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5166,7 +5307,7 @@ class ChemicalAffectsGeneAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation","biolink:ChemicalAffectsGeneAssociation"]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5175,7 +5316,7 @@ class ChemicalAffectsGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5184,9 +5325,9 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): """ An interaction between a drug and a gene or gene product. """ - subject: str = Field(None, description="""the drug that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the gene or gene product that is affected by the drug""") + subject: str = Field(..., description="""the drug that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the gene or gene product that is affected by the drug""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5209,7 +5350,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneAssociation","biolink:DrugToGeneAssociation"]] = Field(["biolink:DrugToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5218,7 +5359,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5235,9 +5376,9 @@ class MaterialSampleDerivationAssociation(Association): """ An association between a material sample and the material entity from which it is derived. """ - subject: str = Field(None, description="""the material sample being described""") - predicate: str = Field(None, description="""derivation relationship""") - object: str = Field(None, description="""the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.""") + subject: str = Field(..., description="""the material sample being described""") + predicate: str = Field(..., description="""derivation relationship""") + object: str = Field(..., description="""the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5260,7 +5401,7 @@ class MaterialSampleDerivationAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleDerivationAssociation","biolink:MaterialSampleDerivationAssociation"]] = Field(["biolink:MaterialSampleDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5269,7 +5410,7 @@ class MaterialSampleDerivationAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5292,9 +5433,9 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D """ An association between an exposure event and a disease. """ - subject: str = Field(None, description="""disease class""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""disease class""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5317,7 +5458,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToExposureEventAssociation","biolink:DiseaseToExposureEventAssociation"]] = Field(["biolink:DiseaseToExposureEventAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5326,7 +5467,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5345,9 +5486,9 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa """ population_context_qualifier: Optional[str] = Field(None, description="""a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.""") temporal_context_qualifier: Optional[str] = Field(None, description="""a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.""") - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5370,7 +5511,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation","biolink:ExposureEventToOutcomeAssociation"]] = Field(["biolink:ExposureEventToOutcomeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5379,7 +5520,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5419,9 +5560,9 @@ class InformationContentEntityToNamedThingAssociation(Association): """ association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property). """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5444,7 +5585,7 @@ class InformationContentEntityToNamedThingAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation","biolink:InformationContentEntityToNamedThingAssociation"]] = Field(["biolink:InformationContentEntityToNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5453,7 +5594,7 @@ class InformationContentEntityToNamedThingAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5478,9 +5619,9 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature """ An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. """ - subject: str = Field(None, description="""disease or phenotype""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""anatomical entity in which the disease or feature is found.""") + subject: str = Field(..., description="""disease or phenotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""anatomical entity in which the disease or feature is found.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5503,7 +5644,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToLocationAssociation","biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5512,7 +5653,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5521,9 +5662,9 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty """ An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. """ - subject: str = Field(None, description="""disease or phenotype""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""genetic inheritance associated with the specified disease or phenotypic feature.""") + subject: str = Field(..., description="""disease or phenotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""genetic inheritance associated with the specified disease or phenotypic feature.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5546,7 +5687,7 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation","biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5555,7 +5696,7 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5570,9 +5711,9 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi """ An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""disease or phenotype""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5595,7 +5736,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineToDiseaseOrPhenotypicFeatureAssociation","biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5604,7 +5745,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5613,9 +5754,9 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi """ An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. """ - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the disease or phenotype that is affected by the chemical""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the disease or phenotype that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5638,7 +5779,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5647,7 +5788,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5657,9 +5798,9 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. """ FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""disease or phenotype""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5682,7 +5823,7 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5691,7 +5832,7 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5701,9 +5842,9 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect. """ FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) - subject: str = Field(None, description="""the chemical entity or entity that is an interactor""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""disease or phenotype""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5726,7 +5867,7 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5735,7 +5876,7 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5744,9 +5885,9 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe """ An association between a material sample and a disease or phenotype. """ - subject: str = Field(None, description="""the material sample being described""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""disease or phenotype""") + subject: str = Field(..., description="""the material sample being described""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5769,7 +5910,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleToDiseaseOrPhenotypicFeatureAssociation","biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5778,7 +5919,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5794,9 +5935,9 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment """ sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""genotype that is associated with the phenotypic feature""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""genotype that is associated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5819,7 +5960,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToPhenotypicFeatureAssociation","biolink:GenotypeToPhenotypicFeatureAssociation"]] = Field(["biolink:GenotypeToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5828,7 +5969,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -5845,9 +5986,9 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. """ sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5870,7 +6011,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation","biolink:ExposureEventToPhenotypicFeatureAssociation"]] = Field(["biolink:ExposureEventToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5879,7 +6020,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -5896,9 +6037,9 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. """ sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""disease class""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""disease class""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5921,7 +6062,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation","biolink:DiseaseToPhenotypicFeatureAssociation"]] = Field(["biolink:DiseaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5930,7 +6071,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -5947,9 +6088,9 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. """ sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""the case (e.g. patient) that has the property""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""the case (e.g. patient) that has the property""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -5972,7 +6113,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CaseToPhenotypicFeatureAssociation","biolink:CaseToPhenotypicFeatureAssociation"]] = Field(["biolink:CaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -5981,7 +6122,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -5998,9 +6139,9 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. """ sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""behavior that is the subject of the association""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""behavioral feature that is the object of the association""") + subject: str = Field(..., description="""behavior that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""behavioral feature that is the object of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6023,7 +6164,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehaviorToBehavioralFeatureAssociation","biolink:BehaviorToBehavioralFeatureAssociation"]] = Field(["biolink:BehaviorToBehavioralFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6032,7 +6173,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6054,9 +6195,9 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): """ An interaction between a gene or gene product and a biological process or pathway. """ - subject: str = Field(None, description="""the gene or gene product entity that participates or influences the pathway""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the pathway that includes or is affected by the gene or gene product""") + subject: str = Field(..., description="""the gene or gene product entity that participates or influences the pathway""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the pathway that includes or is affected by the gene or gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6079,7 +6220,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToPathwayAssociation","biolink:GeneToPathwayAssociation"]] = Field(["biolink:GeneToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6088,7 +6229,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6104,9 +6245,9 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""gene in which variation is correlated with the phenotypic feature""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""gene in which variation is correlated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6129,7 +6270,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation","biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6138,7 +6279,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6150,11 +6291,14 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, -class GeneToDiseaseAssociation(Association): +class GeneToPhenotypeAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + subject: str = Field(..., description="""gene in which variation is correlated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6177,7 +6321,58 @@ class GeneToDiseaseAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation","biolink:GeneToPhenotypeAssociation"]] = Field(["biolink:GeneToPhenotypeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseAssociation","biolink:GeneToDiseaseAssociation"]] = Field(["biolink:GeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6186,16 +6381,26 @@ class GeneToDiseaseAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") -class GeneToPhenotypeAssociation(Association): +class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is shown to cause the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6218,25 +6423,86 @@ class GeneToPhenotypeAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") - category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation","biolink:GeneToPhenotypeAssociation"]] = Field(["biolink:GeneToPhenotypeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + category: List[Literal["https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation","biolink:CausalGeneToDiseaseAssociation"]] = Field(["biolink:CausalGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is shown to correlate with the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation","biolink:CorrelatedGeneToDiseaseAssociation"]] = Field(["biolink:CorrelatedGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""disease""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6259,7 +6525,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation","biolink:DruggableGeneToDiseaseAssociation"]] = Field(["biolink:DruggableGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6268,8 +6534,12 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") @@ -6280,9 +6550,9 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): """ An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) """ - subject: str = Field(None, description="""a sequence variant in which the allele state is associated with some other entity""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated with some other entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6305,7 +6575,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneAssociation","biolink:VariantToGeneAssociation"]] = Field(["biolink:VariantToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6314,7 +6584,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6327,9 +6597,9 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio expression_site: Optional[str] = Field(None, description="""location in which gene or protein expression takes place. May be cell, tissue, or organ.""") stage_qualifier: Optional[str] = Field(None, description="""stage during which gene or protein expression of takes place.""") phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") - subject: str = Field(None, description="""a sequence variant in which the allele state is associated with some other entity""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated with some other entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6352,7 +6622,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneExpressionAssociation","biolink:VariantToGeneExpressionAssociation"]] = Field(["biolink:VariantToGeneExpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6361,7 +6631,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6375,9 +6645,9 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ has_quotient: Optional[float] = Field(None, description="""frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency""") has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - subject: str = Field(None, description="""an allele that has a certain frequency in a given population""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the population that is observed to have the frequency""") + subject: str = Field(..., description="""an allele that has a certain frequency in a given population""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the population that is observed to have the frequency""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6400,7 +6670,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPopulationAssociation","biolink:VariantToPopulationAssociation"]] = Field(["biolink:VariantToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6409,7 +6679,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6418,9 +6688,9 @@ class PopulationToPopulationAssociation(Association): """ An association between a two populations """ - subject: str = Field(None, description="""the population that form the subject of the association""") - predicate: str = Field(None, description="""A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used""") - object: str = Field(None, description="""the population that form the object of the association""") + subject: str = Field(..., description="""the population that form the subject of the association""") + predicate: str = Field(..., description="""A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used""") + object: str = Field(..., description="""the population that form the object of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6443,7 +6713,7 @@ class PopulationToPopulationAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationToPopulationAssociation","biolink:PopulationToPopulationAssociation"]] = Field(["biolink:PopulationToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6452,7 +6722,7 @@ class PopulationToPopulationAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6460,9 +6730,9 @@ class PopulationToPopulationAssociation(Association): class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") - subject: str = Field(None, description="""a sequence variant in which the allele state is associated in some way with the phenotype state""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated in some way with the phenotype state""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6485,7 +6755,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation","biolink:VariantToPhenotypicFeatureAssociation"]] = Field(["biolink:VariantToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6494,7 +6764,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") @@ -6508,9 +6778,9 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): - subject: str = Field(None, description="""a sequence variant in which the allele state is associated in some way with the disease state""") - predicate: str = Field(None, description="""E.g. is pathogenic for""") - object: str = Field(None, description="""a disease that is associated with that variant""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated in some way with the disease state""") + predicate: str = Field(..., description="""E.g. is pathogenic for""") + object: str = Field(..., description="""a disease that is associated with that variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6533,7 +6803,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToDiseaseAssociation","biolink:VariantToDiseaseAssociation"]] = Field(["biolink:VariantToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6542,7 +6812,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6552,9 +6822,9 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): - subject: str = Field(None, description="""a genotype that is associated in some way with a disease state""") - predicate: str = Field(None, description="""E.g. is pathogenic for""") - object: str = Field(None, description="""a disease that is associated with that genotype""") + subject: str = Field(..., description="""a genotype that is associated in some way with a disease state""") + predicate: str = Field(..., description="""E.g. is pathogenic for""") + object: str = Field(..., description="""a disease that is associated with that genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6577,7 +6847,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation","biolink:GenotypeToDiseaseAssociation"]] = Field(["biolink:GenotypeToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6586,7 +6856,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6604,9 +6874,12 @@ class ModelToDiseaseAssociationMixin(ConfiguredBaseModel): class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDiseaseAssociation, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") - predicate: str = Field(None, description="""The relationship to the disease""") - object: str = Field(None, description="""disease""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6629,7 +6902,7 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation","biolink:GeneAsAModelOfDiseaseAssociation"]] = Field(["biolink:GeneAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6638,8 +6911,12 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") @@ -6648,9 +6925,9 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, VariantToDiseaseAssociation, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""A variant that has a role in modeling the disease.""") - predicate: str = Field(None, description="""The relationship to the disease""") - object: str = Field(None, description="""disease""") + subject: str = Field(..., description="""A variant that has a role in modeling the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6673,7 +6950,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation","biolink:VariantAsAModelOfDiseaseAssociation"]] = Field(["biolink:VariantAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6682,7 +6959,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6692,9 +6969,9 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GenotypeToDiseaseAssociation, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""A genotype that has a role in modeling the disease.""") - predicate: str = Field(None, description="""The relationship to the disease""") - object: str = Field(None, description="""disease""") + subject: str = Field(..., description="""A genotype that has a role in modeling the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6717,7 +6994,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation","biolink:GenotypeAsAModelOfDiseaseAssociation"]] = Field(["biolink:GenotypeAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6726,7 +7003,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6736,9 +7013,9 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellLineToDiseaseOrPhenotypicFeatureAssociation, EntityToDiseaseAssociationMixin): - subject: str = Field(None, description="""A cell line derived from an organismal entity with a disease state that is used as a model of that disease.""") - predicate: str = Field(None, description="""The relationship to the disease""") - object: str = Field(None, description="""disease""") + subject: str = Field(..., description="""A cell line derived from an organismal entity with a disease state that is used as a model of that disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6761,7 +7038,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation","biolink:CellLineAsAModelOfDiseaseAssociation"]] = Field(["biolink:CellLineAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6770,7 +7047,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6780,9 +7057,9 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, EntityToDiseaseAssociationMixin, Association): - subject: str = Field(None, description="""A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.""") - predicate: str = Field(None, description="""The relationship to the disease""") - object: str = Field(None, description="""disease""") + subject: str = Field(..., description="""A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6805,7 +7082,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation","biolink:OrganismalEntityAsAModelOfDiseaseAssociation"]] = Field(["biolink:OrganismalEntityAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6814,7 +7091,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") @@ -6824,9 +7101,9 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi class OrganismToOrganismAssociation(Association): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""An association between two individual organisms.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""An association between two individual organisms.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6849,7 +7126,7 @@ class OrganismToOrganismAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismToOrganismAssociation","biolink:OrganismToOrganismAssociation"]] = Field(["biolink:OrganismToOrganismAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6858,16 +7135,16 @@ class OrganismToOrganismAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class TaxonToTaxonAssociation(Association): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""An association between individuals of different taxa.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""An association between individuals of different taxa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6890,7 +7167,7 @@ class TaxonToTaxonAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TaxonToTaxonAssociation","biolink:TaxonToTaxonAssociation"]] = Field(["biolink:TaxonToTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6899,7 +7176,7 @@ class TaxonToTaxonAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6907,9 +7184,12 @@ class TaxonToTaxonAssociation(Association): class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): subject_form_or_variant_qualifier: Optional[str] = Field(None) - subject: str = Field(None, description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6932,7 +7212,7 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation","biolink:GeneHasVariantThatContributesToDiseaseAssociation"]] = Field(["biolink:GeneHasVariantThatContributesToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6941,8 +7221,15 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") @@ -6952,9 +7239,9 @@ class GeneToExpressionSiteAssociation(Association): """ stage_qualifier: Optional[str] = Field(None, description="""stage at which the gene is expressed in the site""") quantifier_qualifier: Optional[str] = Field(None, description="""can be used to indicate magnitude, or also ranking""") - subject: str = Field(None, description="""Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location.""") - predicate: str = Field(None, description="""expression relationship""") - object: str = Field(None, description="""location in which the gene is expressed""") + subject: str = Field(..., description="""Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location.""") + predicate: str = Field(..., description="""expression relationship""") + object: str = Field(..., description="""location in which the gene is expressed""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -6977,7 +7264,7 @@ class GeneToExpressionSiteAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation","biolink:GeneToExpressionSiteAssociation"]] = Field(["biolink:GeneToExpressionSiteAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -6986,7 +7273,7 @@ class GeneToExpressionSiteAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6995,9 +7282,9 @@ class SequenceVariantModulatesTreatmentAssociation(Association): """ An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used. """ - subject: str = Field(None, description="""variant that modulates the treatment of some disease""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""treatment whose efficacy is modulated by the subject variant""") + subject: str = Field(..., description="""variant that modulates the treatment of some disease""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""treatment whose efficacy is modulated by the subject variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7020,7 +7307,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariantModulatesTreatmentAssociation","biolink:SequenceVariantModulatesTreatmentAssociation"]] = Field(["biolink:SequenceVariantModulatesTreatmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7029,7 +7316,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7038,9 +7325,9 @@ class FunctionalAssociation(Association): """ An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed. """ - subject: str = Field(None, description="""gene, product or macromolecular complex that has the function associated with the GO term""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""class describing the activity, process or localization of the gene product""") + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7063,7 +7350,7 @@ class FunctionalAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FunctionalAssociation","biolink:FunctionalAssociation"]] = Field(["biolink:FunctionalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7072,7 +7359,7 @@ class FunctionalAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7089,9 +7376,9 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT """ A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution. """ - subject: str = Field(None, description="""gene, product or macromolecular complex that has the function associated with the GO term""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""class describing the activity, process or localization of the gene product""") + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7114,7 +7401,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToMolecularActivityAssociation","biolink:MacromolecularMachineToMolecularActivityAssociation"]] = Field(["biolink:MacromolecularMachineToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7123,7 +7410,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7132,9 +7419,9 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT """ A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it. """ - subject: str = Field(None, description="""gene, product or macromolecular complex that has the function associated with the GO term""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""class describing the activity, process or localization of the gene product""") + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7157,7 +7444,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToBiologicalProcessAssociation","biolink:MacromolecularMachineToBiologicalProcessAssociation"]] = Field(["biolink:MacromolecularMachineToBiologicalProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7166,7 +7453,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7175,9 +7462,9 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT """ A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component. """ - subject: str = Field(None, description="""gene, product or macromolecular complex that has the function associated with the GO term""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""class describing the activity, process or localization of the gene product""") + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7200,7 +7487,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToCellularComponentAssociation","biolink:MacromolecularMachineToCellularComponentAssociation"]] = Field(["biolink:MacromolecularMachineToCellularComponentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7209,7 +7496,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7218,9 +7505,9 @@ class MolecularActivityToChemicalEntityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7243,7 +7530,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToChemicalEntityAssociation","biolink:MolecularActivityToChemicalEntityAssociation"]] = Field(["biolink:MolecularActivityToChemicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7252,7 +7539,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7261,9 +7548,9 @@ class MolecularActivityToMolecularActivityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7286,7 +7573,7 @@ class MolecularActivityToMolecularActivityAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToMolecularActivityAssociation","biolink:MolecularActivityToMolecularActivityAssociation"]] = Field(["biolink:MolecularActivityToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7295,16 +7582,16 @@ class MolecularActivityToMolecularActivityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class GeneToGoTermAssociation(FunctionalAssociation): - subject: str = Field(None, description="""gene, product or macromolecular complex that has the function associated with the GO term""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""class describing the activity, process or localization of the gene product""") + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7327,7 +7614,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGoTermAssociation","biolink:GeneToGoTermAssociation"]] = Field(["biolink:GeneToGoTermAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7336,7 +7623,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7344,9 +7631,9 @@ class GeneToGoTermAssociation(FunctionalAssociation): class EntityToDiseaseAssociation(Association): FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7369,7 +7656,7 @@ class EntityToDiseaseAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToDiseaseAssociation","biolink:EntityToDiseaseAssociation"]] = Field(["biolink:EntityToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7378,7 +7665,7 @@ class EntityToDiseaseAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7386,9 +7673,9 @@ class EntityToDiseaseAssociation(Association): class EntityToPhenotypicFeatureAssociation(Association): FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7411,7 +7698,7 @@ class EntityToPhenotypicFeatureAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation","biolink:EntityToPhenotypicFeatureAssociation"]] = Field(["biolink:EntityToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7420,7 +7707,7 @@ class EntityToPhenotypicFeatureAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7429,9 +7716,9 @@ class SequenceAssociation(Association): """ An association between a sequence feature and a nucleic acid entity it is localized to. """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7454,7 +7741,7 @@ class SequenceAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceAssociation","biolink:SequenceAssociation"]] = Field(["biolink:SequenceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7463,7 +7750,7 @@ class SequenceAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7477,9 +7764,9 @@ class GenomicSequenceLocalization(SequenceAssociation): genome_build: Optional[StrandEnum] = Field(None, description="""The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.""") strand: Optional[StrandEnum] = Field(None, description="""The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).""") phase: Optional[PhaseEnum] = Field(None, description="""The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.""") - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7502,7 +7789,7 @@ class GenomicSequenceLocalization(SequenceAssociation): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicSequenceLocalization","biolink:GenomicSequenceLocalization"]] = Field(["biolink:GenomicSequenceLocalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7511,7 +7798,7 @@ class GenomicSequenceLocalization(SequenceAssociation): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7520,9 +7807,9 @@ class SequenceFeatureRelationship(Association): """ For example, a particular exon is part of a particular transcript or gene """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7545,7 +7832,7 @@ class SequenceFeatureRelationship(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceFeatureRelationship","biolink:SequenceFeatureRelationship"]] = Field(["biolink:SequenceFeatureRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7554,7 +7841,7 @@ class SequenceFeatureRelationship(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7563,9 +7850,9 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): """ A gene is a collection of transcripts """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7588,7 +7875,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptToGeneRelationship","biolink:TranscriptToGeneRelationship"]] = Field(["biolink:TranscriptToGeneRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7597,7 +7884,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7606,9 +7893,9 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): """ A gene is transcribed and potentially translated to a gene product """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7631,7 +7918,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneProductRelationship","biolink:GeneToGeneProductRelationship"]] = Field(["biolink:GeneToGeneProductRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7640,7 +7927,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7649,9 +7936,9 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): """ A transcript is formed from multiple exons """ - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7674,7 +7961,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExonToTranscriptRelationship","biolink:ExonToTranscriptRelationship"]] = Field(["biolink:ExonToTranscriptRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7683,7 +7970,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7693,9 +7980,9 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): A regulatory relationship between two genes """ object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""the direction is always from regulator to regulated""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""the direction is always from regulator to regulated""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7718,7 +8005,7 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation","biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7727,16 +8014,16 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class AnatomicalEntityToAnatomicalEntityAssociation(Association): - subject: str = Field(None, description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7759,7 +8046,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation","biolink:AnatomicalEntityToAnatomicalEntityAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7768,7 +8055,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7777,9 +8064,9 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat """ A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms """ - subject: str = Field(None, description="""the part""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the whole""") + subject: str = Field(..., description="""the part""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the whole""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7802,7 +8089,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityPartOfAssociation","biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7811,7 +8098,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7820,9 +8107,9 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA """ A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship. """ - subject: str = Field(None, description="""the structure at a later time""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the structure at an earlier time""") + subject: str = Field(..., description="""the structure at a later time""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the structure at an earlier time""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7845,7 +8132,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityOntogenicAssociation","biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7854,7 +8141,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7871,9 +8158,9 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, """ A relationship between two organism taxon nodes """ - subject: str = Field(None, description="""organism taxon that is the subject of the association""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + subject: str = Field(..., description="""organism taxon that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7896,7 +8183,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation","biolink:OrganismTaxonToOrganismTaxonAssociation"]] = Field(["biolink:OrganismTaxonToOrganismTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7905,7 +8192,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7914,9 +8201,9 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss """ A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo """ - subject: str = Field(None, description="""the more specific taxon""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the more general taxon""") + subject: str = Field(..., description="""the more specific taxon""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the more general taxon""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7939,7 +8226,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonSpecialization","biolink:OrganismTaxonToOrganismTaxonSpecialization"]] = Field(["biolink:OrganismTaxonToOrganismTaxonSpecialization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7948,7 +8235,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7958,9 +8245,9 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens """ associated_environmental_context: Optional[str] = Field(None, description="""the environment in which the two taxa interact""") - subject: str = Field(None, description="""the taxon that is the subject of the association""") - predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") - object: str = Field(None, description="""the taxon that is the subject of the association""") + subject: str = Field(..., description="""the taxon that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the taxon that is the subject of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -7983,7 +8270,7 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonInteraction","biolink:OrganismTaxonToOrganismTaxonInteraction"]] = Field(["biolink:OrganismTaxonToOrganismTaxonInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -7992,16 +8279,16 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, Association): - subject: str = Field(None, description="""the taxon that is the subject of the association""") - predicate: str = Field(None, description="""predicate describing the relationship between the taxon and the environment""") - object: str = Field(None, description="""the environment in which the organism occurs""") + subject: str = Field(..., description="""the taxon that is the subject of the association""") + predicate: str = Field(..., description="""predicate describing the relationship between the taxon and the environment""") + object: str = Field(..., description="""the environment in which the organism occurs""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") @@ -8024,7 +8311,7 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") - id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation","biolink:OrganismTaxonToEnvironmentAssociation"]] = Field(["biolink:OrganismTaxonToEnvironmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -8033,11 +8320,32 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + description: Optional[str] = Field(None) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") +class InformationResourceContainer(ConfiguredBaseModel): + """ + A collection of information resources + """ + information_resources: Optional[List[InformationResource]] = Field(default_factory=list, description="""a collection of information resources""") + + + +class InformationResource(ConfiguredBaseModel): + """ + A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. + """ + status: Optional[InformationResourceStatusEnum] = Field(None, description="""the status of the infores identifier, the default is \"released\"""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + description: Optional[str] = Field(None) + + + # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ @@ -8075,14 +8383,13 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As RelativeFrequencyAnalysisResult.update_forward_refs() TextMiningResult.update_forward_refs() ChiSquaredAnalysisResult.update_forward_refs() +LogOddsAnalysisResult.update_forward_refs() Dataset.update_forward_refs() DatasetDistribution.update_forward_refs() DatasetVersion.update_forward_refs() DatasetSummary.update_forward_refs() ConfidenceLevel.update_forward_refs() EvidenceType.update_forward_refs() -InformationResource.update_forward_refs() -InformationResourceCollection.update_forward_refs() Publication.update_forward_refs() Book.update_forward_refs() BookChapter.update_forward_refs() @@ -8295,8 +8602,10 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As GeneToPathwayAssociation.update_forward_refs() VariantToEntityAssociationMixin.update_forward_refs() GeneToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GeneToDiseaseAssociation.update_forward_refs() GeneToPhenotypeAssociation.update_forward_refs() +GeneToDiseaseAssociation.update_forward_refs() +CausalGeneToDiseaseAssociation.update_forward_refs() +CorrelatedGeneToDiseaseAssociation.update_forward_refs() DruggableGeneToDiseaseAssociation.update_forward_refs() VariantToGeneAssociation.update_forward_refs() VariantToGeneExpressionAssociation.update_forward_refs() @@ -8341,4 +8650,6 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As OrganismTaxonToOrganismTaxonSpecialization.update_forward_refs() OrganismTaxonToOrganismTaxonInteraction.update_forward_refs() OrganismTaxonToEnvironmentAssociation.update_forward_refs() +InformationResourceContainer.update_forward_refs() +InformationResource.update_forward_refs() diff --git a/poetry.lock b/poetry.lock index 2e35a2c9d4..5c617d44a2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.13" @@ -5,6 +7,10 @@ description = "A configurable sidebar-enabled Sphinx theme" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] [[package]] name = "antlr4-python3-runtime" @@ -13,6 +19,9 @@ description = "ANTLR 4.9.3 runtime for Python 3.7" category = "main" optional = false python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] [[package]] name = "arrow" @@ -21,6 +30,10 @@ description = "Better dates & times for Python" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, +] [package.dependencies] python-dateutil = ">=2.7.0" @@ -32,6 +45,10 @@ description = "Classes Without Boilerplate" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"}, + {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"}, +] [package.extras] cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] @@ -47,6 +64,10 @@ description = "Internationalization utilities" category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, + {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, +] [[package]] name = "beautifulsoup4" @@ -55,6 +76,10 @@ description = "Screen-scraping library" category = "main" optional = false python-versions = ">=3.6.0" +files = [ + {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, + {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, +] [package.dependencies] soupsieve = ">1.2" @@ -70,6 +95,9 @@ description = "Dummy package for Beautiful Soup" category = "main" optional = false python-versions = "*" +files = [ + {file = "bs4-0.0.1.tar.gz", hash = "sha256:36ecea1fd7cc5c0c6e4a1ff075df26d50da647b75376626cc186e2212886dd3a"}, +] [package.dependencies] beautifulsoup4 = "*" @@ -81,6 +109,10 @@ description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, + {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, +] [[package]] name = "cfgraph" @@ -89,6 +121,9 @@ description = "rdflib collections flattening graph" category = "main" optional = false python-versions = "*" +files = [ + {file = "CFGraph-0.2.1.tar.gz", hash = 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