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Regenerate artifacts from biolink-model.yaml
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actions-user committed Jul 8, 2022
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2 changes: 1 addition & 1 deletion biolink-model.graphql
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# metamodel_version: 1.7.0
# version: 2.4.4
# version: 2.4.5
type Activity implements ActivityAndBehavior
{
id: String!
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752 changes: 376 additions & 376 deletions biolink-model.owl.ttl

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2 changes: 1 addition & 1 deletion biolink-model.proto
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// metamodel_version: 1.7.0
// version: 2.4.4
// version: 2.4.5
// An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
message Activity
{
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2 changes: 1 addition & 1 deletion biolink-model.shex
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# metamodel_version: 1.7.0
# version: 2.4.4
# version: 2.4.5
BASE <https://w3id.org/biolink/vocab/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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2 changes: 1 addition & 1 deletion biolink-model.shexj
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# metamodel_version: 1.7.0
# version: 2.4.4
# version: 2.4.5
{
"type": "Schema",
"@context": [
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740 changes: 370 additions & 370 deletions biolink-model.ttl

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2 changes: 1 addition & 1 deletion biolink-modeln.shex
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# metamodel_version: 1.7.0
# version: 2.4.4
# version: 2.4.5
BASE <https://w3id.org/biolink/vocab/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
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2 changes: 1 addition & 1 deletion biolink-modeln.shexj
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# metamodel_version: 1.7.0
# version: 2.4.4
# version: 2.4.5
{
"type": "Schema",
"@context": [
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4 changes: 2 additions & 2 deletions biolink/model.py
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# Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0
# Generation date: 2022-07-08T22:39:50
# Generation date: 2022-07-08T23:18:02
# Schema: Biolink-Model
#
# id: https://w3id.org/biolink/biolink-model
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from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDate, XSDTime

metamodel_version = "1.7.0"
version = "2.4.4"
version = "2.4.5"

# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
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2 changes: 1 addition & 1 deletion context.jsonld
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{
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-07-08T22:39:16\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.4\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-07-08T23:17:31\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
"@context": {
"APO": {
"@id": "http://purl.obolibrary.org/obo/APO_",
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2 changes: 1 addition & 1 deletion contextn.jsonld
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{
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-07-08T22:39:20\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.4\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-07-08T23:17:35\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 2.4.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
"@context": {
"APO": {
"@id": "http://purl.obolibrary.org/obo/APO_",
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2 changes: 1 addition & 1 deletion golr-views/RNA_product_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: RNA_product
# metamodel_version: 1.7.0# version: 2.4.5id: RNA_product
schema_generating: true
display_name: RNA product
document_category: RNA product
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2 changes: 1 addition & 1 deletion golr-views/RNA_product_isoform_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: RNA_product_isoform
# metamodel_version: 1.7.0# version: 2.4.5id: RNA_product_isoform
schema_generating: true
description: Represents a protein that is a specific isoform of the canonical or reference
RNA
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2 changes: 1 addition & 1 deletion golr-views/activity_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: activity
# metamodel_version: 1.7.0# version: 2.4.5id: activity
schema_generating: true
description: An activity is something that occurs over a period of time and acts upon
or with entities; it may include consuming, processing, transforming, modifying,
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2 changes: 1 addition & 1 deletion golr-views/agent_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: agent
# metamodel_version: 1.7.0# version: 2.4.5id: agent
schema_generating: true
description: person, group, organization or project that provides a piece of information
(i.e. a knowledge association)
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2 changes: 1 addition & 1 deletion golr-views/anatomical_entity_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: anatomical_entity
# metamodel_version: 1.7.0# version: 2.4.5id: anatomical_entity
schema_generating: true
description: A subcellular location, cell type or gross anatomical part
display_name: anatomical entity
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# metamodel_version: 1.7.0# version: 2.4.4id: anatomical_entity_to_anatomical_entity_ontogenic_association
# metamodel_version: 1.7.0# version: 2.4.5id: anatomical_entity_to_anatomical_entity_ontogenic_association
schema_generating: true
description: A relationship between two anatomical entities where the relationship
is ontogenic, i.e. the two entities are related by development. A number of different
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# metamodel_version: 1.7.0# version: 2.4.4id: anatomical_entity_to_anatomical_entity_part_of_association
# metamodel_version: 1.7.0# version: 2.4.5id: anatomical_entity_to_anatomical_entity_part_of_association
schema_generating: true
description: A relationship between two anatomical entities where the relationship
is mereological, i.e the two entities are related by parthood. This includes relationships
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2 changes: 1 addition & 1 deletion golr-views/article_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: article
# metamodel_version: 1.7.0# version: 2.4.5id: article
schema_generating: true
display_name: article
document_category: article
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2 changes: 1 addition & 1 deletion golr-views/association_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: association
# metamodel_version: 1.7.0# version: 2.4.5id: association
schema_generating: true
description: A typed association between two entities, supported by evidence
display_name: association
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2 changes: 1 addition & 1 deletion golr-views/attribute_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: attribute
# metamodel_version: 1.7.0# version: 2.4.5id: attribute
schema_generating: true
description: A property or characteristic of an entity. For example, an apple may
have properties such as color, shape, age, crispiness. An environmental sample may
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2 changes: 1 addition & 1 deletion golr-views/behavior_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: behavior
# metamodel_version: 1.7.0# version: 2.4.5id: behavior
schema_generating: true
display_name: behavior
document_category: behavior
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# metamodel_version: 1.7.0# version: 2.4.4id: behavior_to_behavioral_feature_association
# metamodel_version: 1.7.0# version: 2.4.5id: behavior_to_behavioral_feature_association
schema_generating: true
description: An association between an mixture behavior and a behavioral feature manifested
by the individual exhibited or has exhibited the behavior.
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2 changes: 1 addition & 1 deletion golr-views/behavioral_exposure_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: behavioral_exposure
# metamodel_version: 1.7.0# version: 2.4.5id: behavioral_exposure
schema_generating: true
description: A behavioral exposure is a factor relating to behavior impacting an individual.
display_name: behavioral exposure
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2 changes: 1 addition & 1 deletion golr-views/behavioral_feature_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: behavioral_feature
# metamodel_version: 1.7.0# version: 2.4.5id: behavioral_feature
schema_generating: true
description: A phenotypic feature which is behavioral in nature.
display_name: behavioral feature
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2 changes: 1 addition & 1 deletion golr-views/biological_process_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: biological_process
# metamodel_version: 1.7.0# version: 2.4.5id: biological_process
schema_generating: true
description: One or more causally connected executions of molecular functions
display_name: biological process
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2 changes: 1 addition & 1 deletion golr-views/biological_process_or_activity_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: biological_process_or_activity
# metamodel_version: 1.7.0# version: 2.4.5id: biological_process_or_activity
schema_generating: true
description: Either an individual molecular activity, or a collection of causally
connected molecular activities in a biological system.
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2 changes: 1 addition & 1 deletion golr-views/biological_sex_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: biological_sex
# metamodel_version: 1.7.0# version: 2.4.5id: biological_sex
schema_generating: true
display_name: biological sex
document_category: biological sex
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2 changes: 1 addition & 1 deletion golr-views/biotic_exposure_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: biotic_exposure
# metamodel_version: 1.7.0# version: 2.4.5id: biotic_exposure
schema_generating: true
description: An external biotic exposure is an intake of (sometimes pathological)
biological organisms (including viruses).
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2 changes: 1 addition & 1 deletion golr-views/book_chapter_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: book_chapter
# metamodel_version: 1.7.0# version: 2.4.5id: book_chapter
schema_generating: true
display_name: book chapter
document_category: book chapter
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2 changes: 1 addition & 1 deletion golr-views/book_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: book
# metamodel_version: 1.7.0# version: 2.4.5id: book
schema_generating: true
description: This class may rarely be instantiated except if use cases of a given
knowledge graph support its utility.
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2 changes: 1 addition & 1 deletion golr-views/case_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: case
# metamodel_version: 1.7.0# version: 2.4.5id: case
schema_generating: true
description: An individual (human) organism that has a patient role in some clinical
context.
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# metamodel_version: 1.7.0# version: 2.4.4id: case_to_phenotypic_feature_association
# metamodel_version: 1.7.0# version: 2.4.5id: case_to_phenotypic_feature_association
schema_generating: true
description: An association between a case (e.g. individual patient) and a phenotypic
feature in which the individual has or has had the phenotype.
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2 changes: 1 addition & 1 deletion golr-views/cell_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: cell
# metamodel_version: 1.7.0# version: 2.4.5id: cell
schema_generating: true
display_name: cell
document_category: cell
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# metamodel_version: 1.7.0# version: 2.4.4id: cell_line_as_a_model_of_disease_association
# metamodel_version: 1.7.0# version: 2.4.5id: cell_line_as_a_model_of_disease_association
schema_generating: true
display_name: cell line as a model of disease association
document_category: cell line as a model of disease association
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2 changes: 1 addition & 1 deletion golr-views/cell_line_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: cell_line
# metamodel_version: 1.7.0# version: 2.4.5id: cell_line
schema_generating: true
display_name: cell line
document_category: cell line
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# metamodel_version: 1.7.0# version: 2.4.4id: cell_line_to_disease_or_phenotypic_feature_association
# metamodel_version: 1.7.0# version: 2.4.5id: cell_line_to_disease_or_phenotypic_feature_association
schema_generating: true
description: 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.
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2 changes: 1 addition & 1 deletion golr-views/cellular_component_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: cellular_component
# metamodel_version: 1.7.0# version: 2.4.5id: cellular_component
schema_generating: true
description: A location in or around a cell
display_name: cellular component
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_entity_assesses_named_thing_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_entity_assesses_named_thing_association
schema_generating: true
display_name: chemical entity assesses named thing association
document_category: chemical entity assesses named thing association
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2 changes: 1 addition & 1 deletion golr-views/chemical_entity_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_entity
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_entity
schema_generating: true
description: A chemical entity is a physical entity that pertains to chemistry or
biochemistry.
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2 changes: 1 addition & 1 deletion golr-views/chemical_exposure_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_exposure
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_exposure
schema_generating: true
description: A chemical exposure is an intake of a particular chemical entity.
display_name: chemical exposure
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2 changes: 1 addition & 1 deletion golr-views/chemical_mixture_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_mixture
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_mixture
schema_generating: true
description: A chemical mixture is a chemical entity composed of two or more molecular
entities.
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2 changes: 1 addition & 1 deletion golr-views/chemical_role_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_role
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_role
schema_generating: true
display_name: chemical role
document_category: chemical role
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2 changes: 1 addition & 1 deletion golr-views/chemical_to_chemical_association_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_to_chemical_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_to_chemical_association
schema_generating: true
description: A relationship between two chemical entities. This can encompass actual
interactions as well as temporal causal edges, e.g. one chemical converted to another.
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_to_chemical_derivation_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_to_chemical_derivation_association
schema_generating: true
description: "A causal relationship between two chemical entities, where the subject\
\ represents the upstream entity and the object represents the downstream. For any\
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_to_disease_or_phenotypic_feature_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_to_disease_or_phenotypic_feature_association
schema_generating: true
description: An interaction between a chemical entity and a phenotype or disease,
where the presence of the chemical gives rise to or exacerbates the phenotype.
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2 changes: 1 addition & 1 deletion golr-views/chemical_to_gene_association_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_to_gene_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_to_gene_association
schema_generating: true
description: An interaction between a chemical entity and a gene or gene product.
display_name: chemical to gene association
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2 changes: 1 addition & 1 deletion golr-views/chemical_to_pathway_association_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: chemical_to_pathway_association
# metamodel_version: 1.7.0# version: 2.4.5id: chemical_to_pathway_association
schema_generating: true
description: An interaction between a chemical entity and a biological process or
pathway.
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2 changes: 1 addition & 1 deletion golr-views/clinical_attribute_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_attribute
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_attribute
schema_generating: true
description: Attributes relating to a clinical manifestation
display_name: clinical attribute
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2 changes: 1 addition & 1 deletion golr-views/clinical_course_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_course
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_course
schema_generating: true
description: The course a disease typically takes from its onset, progression in time,
and eventual resolution or death of the affected individual
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2 changes: 1 addition & 1 deletion golr-views/clinical_entity_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_entity
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_entity
schema_generating: true
description: Any entity or process that exists in the clinical domain and outside
the biological realm. Diseases are placed under biological entities
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2 changes: 1 addition & 1 deletion golr-views/clinical_finding_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_finding
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_finding
schema_generating: true
description: this category is currently considered broad enough to tag clinical lab
measurements and other biological attributes taken as 'clinical traits' with some
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2 changes: 1 addition & 1 deletion golr-views/clinical_intervention_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_intervention
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_intervention
schema_generating: true
display_name: clinical intervention
document_category: clinical intervention
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2 changes: 1 addition & 1 deletion golr-views/clinical_measurement_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_measurement
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_measurement
schema_generating: true
description: A clinical measurement is a special kind of attribute which results from
a laboratory observation from a subject individual or sample. Measurements can be
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2 changes: 1 addition & 1 deletion golr-views/clinical_modifier_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_modifier
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_modifier
schema_generating: true
description: Used to characterize and specify the phenotypic abnormalities defined
in the phenotypic abnormality sub-ontology, with respect to severity, laterality,
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2 changes: 1 addition & 1 deletion golr-views/clinical_trial_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: clinical_trial
# metamodel_version: 1.7.0# version: 2.4.5id: clinical_trial
schema_generating: true
display_name: clinical trial
document_category: clinical trial
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2 changes: 1 addition & 1 deletion golr-views/coding_sequence_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: coding_sequence
# metamodel_version: 1.7.0# version: 2.4.5id: coding_sequence
schema_generating: true
display_name: coding sequence
document_category: coding sequence
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2 changes: 1 addition & 1 deletion golr-views/cohort_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: cohort
# metamodel_version: 1.7.0# version: 2.4.5id: cohort
schema_generating: true
description: A group of people banded together or treated as a group who share common
characteristics. A cohort 'study' is a particular form of longitudinal study that
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2 changes: 1 addition & 1 deletion golr-views/complex_chemical_exposure_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: complex_chemical_exposure
# metamodel_version: 1.7.0# version: 2.4.5id: complex_chemical_exposure
schema_generating: true
description: A complex chemical exposure is an intake of a chemical mixture (e.g.
gasoline), other than a drug.
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2 changes: 1 addition & 1 deletion golr-views/complex_molecular_mixture_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: complex_molecular_mixture
# metamodel_version: 1.7.0# version: 2.4.5id: complex_molecular_mixture
schema_generating: true
description: A complex molecular mixture is a chemical mixture composed of two or
more molecular entities with unknown concentration and stoichiometry.
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2 changes: 1 addition & 1 deletion golr-views/confidence_level_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: confidence_level
# metamodel_version: 1.7.0# version: 2.4.5id: confidence_level
schema_generating: true
description: Level of confidence in a statement
display_name: confidence level
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2 changes: 1 addition & 1 deletion golr-views/contributor_association_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: contributor_association
# metamodel_version: 1.7.0# version: 2.4.5id: contributor_association
schema_generating: true
description: Any association between an entity (such as a publication) and various
agents that contribute to its realisation
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2 changes: 1 addition & 1 deletion golr-views/dataset_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: dataset
# metamodel_version: 1.7.0# version: 2.4.5id: dataset
schema_generating: true
description: an item that refers to a collection of data from a data source.
display_name: dataset
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2 changes: 1 addition & 1 deletion golr-views/dataset_distribution_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: dataset_distribution
# metamodel_version: 1.7.0# version: 2.4.5id: dataset_distribution
schema_generating: true
description: an item that holds distribution level information about a dataset.
display_name: dataset distribution
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2 changes: 1 addition & 1 deletion golr-views/dataset_summary_config.yaml
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# metamodel_version: 1.7.0# version: 2.4.4id: dataset_summary
# metamodel_version: 1.7.0# version: 2.4.5id: dataset_summary
schema_generating: true
description: an item that holds summary level information about a dataset.
display_name: dataset summary
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