From 157540b57d27f6957c4abd73898a009508c66b68 Mon Sep 17 00:00:00 2001 From: puja-trivedi Date: Fri, 20 Dec 2024 00:04:18 +0000 Subject: [PATCH 1/2] Generate new version of the linkml model for assertion_evidence --- linkml-schema/assertion_evidence.yaml | 307 ++++++++++-------- .../gsheet_output/Classes.tsv | 29 +- .../gsheet_output/Prefixes.tsv | 18 +- .../gsheet_output/Relations.tsv | 20 +- .../gsheet_output/Slots.tsv | 23 +- .../gsheet_output/ValueSets.tsv | 78 +++-- 6 files changed, 254 insertions(+), 221 deletions(-) diff --git a/linkml-schema/assertion_evidence.yaml b/linkml-schema/assertion_evidence.yaml index 07f69b531..f25763fa5 100644 --- a/linkml-schema/assertion_evidence.yaml +++ b/linkml-schema/assertion_evidence.yaml @@ -4,23 +4,26 @@ id: https://identifiers.org/brain-bican/assertion-evidence-schema imports: - linkml:types prefixes: - linkml: https://w3id.org/linkml/ bican: https://identifiers.org/brain-bican/vocab/ - spdx: http://spdx.org/rdf/terms# - schema: http://schema.org/ brainkb: https://brainkb.org/ - prov: http://www.w3.org/ns/prov# + datacite: http://purl.org/spar/datacite/ + dcterms: http://purl.org/dc/terms/ eco: http://purl.obolibrary.org/obo/ECO_ + edam: http://edamontology.org/ + foaf: http://xmlns.com/foaf/0.1/ + iao: http://purl.obolibrary.org/obo/IAO_ + linkml: https://w3id.org/linkml/ + oa: http://www.w3.org/ns/oa# + prov: http://www.w3.org/ns/prov# + ro: http://purl.obolibrary.org/obo/RO_ + schema: http://schema.org/ sepio: http://purl.obolibrary.org/obo/SEPIO_ + sio: http://semanticscience.org/resource/SIO_ + spdx: http://spdx.org/rdf/terms# + braiankb: http://example.org/braiankb/ default_prefix: brainkb default_range: string enums: - AssertionType: - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - permissible_values: - Positive: {} - Negative: {} - Inconclusive: {} Categories: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema permissible_values: @@ -52,7 +55,7 @@ enums: Translational: {} Therapeutic: {} CognitiveNeuroscience: {} - SignificanceLevel: + EvidenceStrength: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema permissible_values: HighlySignificant: @@ -66,94 +69,41 @@ enums: Unknown: description: Specifies that the significance level is unknown as the information is not present in the study. - Significance: + EvidenceDirection: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema permissible_values: - Clinical: {} - NonClinical: {} + supporting: {} + disputing: {} + inconclusive: {} slots: - uses: - description: The eco:uses property is the inverse of the eco:used_in property - and defines the relationship between eco:Assertion and eco:Evidence, indicating - that an assertion relies on the evidence. + was_associate_with: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - range: Evidence - used_in: - description: The eco:used_in property establishes a relationship between eco:Evidence - and eco:Assertion, indicating that the evidence is utilized to support the corresponding - assertion. + has_identifier: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - range: Assertion - has_assertion_method: - description: The brainkb:hasAssertionMethod property relates an eco:Assertion - to an brainkb:AssertionMethod that differentiates different types of assertions - techniques used while making an assertion. + has_annotation: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - range: AssertionMethod - is_associated_with: + was_generated_by: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - has_data_annotation: + has_evidence_line: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema -classes: - Assertion: - description: A statement made by a particular agent on a particular occasion that - a particular proposition is true, based on the evaluation of one or more lines - of evidence. + reference: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slots: - - has_assertion_method - - is_associated_with - - has_data_annotation - slot_usage: - has_assertion_method: - description: The brainkb:hasAssertionMethod property relates an eco:Assertion - to an brainkb:AssertionMethod that differentiates different types of assertions - techniques used while making an assertion. - is_associated_with: - description: The brainkb:isAssociatedWith property establishes relationships - between different entities:it links sepio:Assertion to brainkb:AssertionSummary, - indicating the association between an assertion and its corresponding summary. - range: AssertionSummary - has_data_annotation: - range: DataAnnotation - - attributes: - has_assertion_category: - description: The brainkb:hasAssertionCategory property relates brainkb:Evidence - and brainkb:Categories, specifying the classification or category that the - assertion belongs to. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasAssertionCategory - alias: hasAssertionCategory - range: Categories - has_assertion_text: - description: The brainkb:hasAssertionText property relates an eco:Assertion - to an xsd:string, providing a textual excerpt of the assertion being made. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasAssertionText - alias: hasAssertionText - range: string - has_assertion_method: - description: The brainkb:hasAssertionMethod property relates an eco:Assertion - to an eco:assertion method that differentiates different types of assertions - techniques used while making an assertion. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasAssertionMethod - alias: hasAssertionMethod - range: AssertionMethod - class_uri: sepio:Assertion - Document: - description: A collection of information content entities intended to be understood - together as a whole + has_evidence_item: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: sepio:Document + member: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema +classes: Activity: 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, relocating, using, or generating entities. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - + slots: + - was_associate_with + slot_usage: + was_associate_with: + slot_uri: prov:wasAssociatedWith + range: Agent attributes: ended_at_time: description: The prov:endedAtTime establishes the relationship between prov:Activity @@ -174,83 +124,152 @@ classes: activity. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema slots: - - is_associated_with + - has_identifier slot_usage: - is_associated_with: - description: 'The brainkb:isAssociatedWith property establishes relationships - between different entities: it connects prov:Agent to prov:Activity, reflecting - the involvement or connection between an agent and an activity.' - range: Activity - + has_identifier: + slot_uri: edam:has_identifier + range: Identifier class_uri: prov:Agent - AssertionSummary: - description: A summary is a brief statement or description of the main points, - especially as a conclusion to a work about the assertion. + Annotation: + description: An annotation is a written explanatory or critical description, or + other in-context information (e.g., pattern, motif, link), that has been associated + with data or other types of information. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + class_uri: oa:Annotation + Assertion: + description: A statement made by a particular agent on a particular occasion that + a particular proposition is true, based on the evaluation of one or more lines + of evidence. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - + slots: + - has_annotation + - was_generated_by + - has_evidence_line + slot_usage: + has_annotation: + slot_uri: sio:000255 + range: Annotation + was_generated_by: + slot_uri: prov:wasGeneratedBy + range: Activity + has_evidence_line: + description: A relationship between an assertion or proposition and an evidence + line used in evaluating its validity. + slot_uri: sepio:0000006 + range: EvidenceLine attributes: + has_assertion_category: + description: The brainkb:hasAssertionCategory property relates brainkb:Evidence + and brainkb:Categories, specifying the classification or category that the + assertion belongs to. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:has_assertion_category + range: Categories + has_assertion_description: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:has_assertion_description + range: string has_assertion_summary: - description: The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary - to an xsd:string, providing a concise overview that differentiates various - assertions. This summary encapsulates the core content of the assertion, - allowing for easy identification and understanding of its essence. + description: The brainkb:has_assertion_text property relates an eco:Assertion + to an xsd:string, providing a textual excerpt of the assertion being made. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasAssertionSummary - alias: hasAssertionSummary + slot_uri: brainkb:has_assertion_summary range: string - class_uri: brainkb:AssertionSummary - EvidenceSummary: - description: A summary is a brief statement or description of the main points, - especially as a conclusion to a work about the evidence. + class_uri: sepio:0000001 + CellAnnotation: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - + is_a: Annotation + class_uri: brainkb:CellAnnotation + Document: + description: A collection of information content entities intended to be understood + together as a whole + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: EvidenceItem attributes: - has_evidence_summary: - description: The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary - to an xsd:string, providing a concise overview that differentiates various - evidence. This summary encapsulates the core content of the evidence, allowing - for easy identification and understanding of its essence. + identifier: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasEvidenceSummary - alias: hasEvidenceSummary - range: string - class_uri: brainkb:EvidenceSummary - AssertionMethod: - description: A means by which a statement is made about the entity - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: eco:0000217 - DataAnnotation: + slot_uri: datacite:identifier + range: uri + class_uri: iao:0000310 + EvidenceItem: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: brainkb:DataAnnotation - Evidence: + slots: + - reference + slot_usage: + reference: + slot_uri: sepio:0000442 + range: Document + class_uri: sepio:0000149 + EvidenceLine: + description: An evidence line represents an independent and meaningful argument + for or against a particular proposition, that is based on the interpretation + of one or more pieces of information as evidence. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema slots: - - used_in - - is_associated_with + - has_evidence_item + - was_generated_by slot_usage: - used_in: {} - is_associated_with: - description: 'The brainkb:isAssociatedWith property establishes relationships - between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, - signifying the connection between evidence and its summarized representation.' - range: EvidenceSummary - + has_evidence_item: + description: A relation holding between an evidence line and an individual + information entity that contributes to the argument it represents. + slot_uri: sepio:0000084 + range: EvidenceItem + was_generated_by: + slot_uri: prov:wasGeneratedBy + range: Activity attributes: + evidence_direction: + description: A relation indicating whether an evidence line supports or disputes + a target proposition (or represents inconclusive evidence that is not sufficient + for either). + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: sepio:0000183 + range: EvidenceDirection + evidence_line_strength: + description: A relation describing the degree of support provided by an evidence + line for a target assertion or proposition. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: sepio:0000132 + range: EvidenceStrength has_evidence_category: - description: The brainkb:hasEvidenceCategory property relates brainkb:Evidence - and brainkb:Categories, specifying the classification or category that the - evidence belongs to. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasEvidenceCategory - alias: hasEvidenceCategory + slot_uri: brainkb:has_evidence_category range: Categories - has_evidence_text: - description: The brainkb:hasEvidenceText property relates an eco:Evidence - to an xsd:string, providing a textual excerpt of the evidence supporting - the assertion. + has_evidenceline_description: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasEvidenceText - alias: hasEvidenceText + slot_uri: braiankb:has_evidenceline_description range: string + class_uri: sepio:0000002 + Group: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Agent + class_uri: foaf:Group + Identifier: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + class_uri: edam:data_0842 + OrcidIdentifier: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: PersonIdentifier + class_uri: edam:data_4022 + Organization: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Group + class_uri: prov:Organization + Person: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Agent + slots: + - member + slot_usage: + member: + slot_uri: foaf:member + range: Organization + class_uri: prov:Person + PersonIdentifier: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Identifier + class_uri: edam:data_2118 + SoftwareAgent: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Agent + class_uri: prov:SoftwareAgent diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv index 4e2bb737c..9ac066501 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv @@ -1,11 +1,18 @@ -รง Inheritance: is_a Inheritance: mixin Inheritance: slot usage Subsets Definition -> class is_a mixins ignore in_subset description class_uri mixin -> internal_separator: "|" internal_separator: "|" -Assertion A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. sepio:Assertion -Document A collection of information content entities intended to be understood together as a whole sepio:Document -Activity 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. prov:Activity -Agent An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. prov:Agent -AssertionSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion. brainkb:AssertionSummary -EvidenceSummary A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. brainkb:EvidenceSummary -AssertionMethod A means by which a statement is made about the entity eco:0000217 -DataAnnotation brainkb:DataAnnotation \ No newline at end of file +class Inheritance: is_a Inheritance: mixin Subsets Definition +> class is_a mixins in_subset description class_uri mixin +> internal_separator: "|" internal_separator: "|" +Activity 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. prov:Activity +Agent An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. prov:Agent +Annotation An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. oa:Annotation +Assertion A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. sepio:0000001 +CellAnnotation Annotation brainkb:CellAnnotation +Document EvidenceItem A collection of information content entities intended to be understood together as a whole iao:0000310 +EvidenceItem sepio:0000149 +EvidenceLine An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence. sepio:0000002 +Group Agent foaf:Group +Identifier edam:data_0842 +OrcidIdentifier PersonIdentifier edam:data_4022 +Organization Group prov:Organization +Person Agent prov:Person +PersonIdentifier Identifier edam:data_2118 +SoftwareAgent Agent prov:SoftwareAgent \ No newline at end of file diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv index db66ef2b6..5483de9d2 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv @@ -1,11 +1,19 @@ prefix uri default schema imports title description id brainkb assertion-evidence-schema Assertion Evidence Schema https://identifiers.org/brain-bican/assertion-evidence-schema > prefix prefix_reference default_prefix schema imports title description id -linkml https://w3id.org/linkml/ bican https://identifiers.org/brain-bican/vocab/ -spdx http://spdx.org/rdf/terms# -schema http://schema.org/ brainkb https://brainkb.org/ -prov http://www.w3.org/ns/prov# +datacite http://purl.org/spar/datacite/ +dcterms http://purl.org/dc/terms/ eco http://purl.obolibrary.org/obo/ECO_ -sepio http://purl.obolibrary.org/obo/SEPIO_ \ No newline at end of file +edam http://edamontology.org/ +foaf http://xmlns.com/foaf/0.1/ +iao http://purl.obolibrary.org/obo/IAO_ +linkml https://w3id.org/linkml/ +oa http://www.w3.org/ns/oa# +prov http://www.w3.org/ns/prov# +ro http://purl.obolibrary.org/obo/RO_ +schema http://schema.org/ +sepio http://purl.obolibrary.org/obo/SEPIO_ +sio http://semanticscience.org/resource/SIO_ +spdx http://spdx.org/rdf/terms# \ No newline at end of file diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv index 0e799b2cb..226bc15b8 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv @@ -1,12 +1,12 @@ Object Predicate (more general) Subject Multivalued ExactlyOneOf (True/False, default=False) Required (True/False) Slot Definition Property Type Characteristics Addition information Suggestions/Comments Suggested/Commented by > class slot range slot_uri multivalued ignore required description ignore ignore ignore ignore ignore -> - uses Evidence The eco:uses property is the inverse of the eco:used_in property and defines the relationship between eco:Assertion and eco:Evidence, indicating that an assertion relies on the evidence. Object Property Functional inverse of eco:used_in - used_in Assertion The eco:used_in property establishes a relationship between eco:Evidence and eco:Assertion, indicating that the evidence is utilized to support the corresponding assertion. Object Property Functional inverse of eco:uses - has_assertion_method AssertionMethod The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional -Evidence used_in Object Property Functional inverse of eco:uses -Assertion has_assertion_method The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion. Object Property Functional -Agent is_associated_with Activity The brainkb:isAssociatedWith property establishes relationships between different entities: it connects prov:Agent to prov:Activity, reflecting the involvement or connection between an agent and an activity. Object Property -Assertion is_associated_with AssertionSummary The brainkb:isAssociatedWith property establishes relationships between different entities:it links sepio:Assertion to brainkb:AssertionSummary, indicating the association between an assertion and its corresponding summary. Object Property -Assertion has_data_annotation DataAnnotation -Evidence is_associated_with EvidenceSummary The brainkb:isAssociatedWith property establishes relationships between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, signifying the connection between evidence and its summarized representation. Object Property \ No newline at end of file +> internal_separator: "|" +Activity was_associate_with Agent prov:wasAssociatedWith +Agent has_identifier Identifier edam:has_identifier +Assertion has_annotation Annotation sio:000255 +Assertion was_generated_by Activity prov:wasGeneratedBy +Assertion has_evidence_line EvidenceLine sepio:0000006 A relationship between an assertion or proposition and an evidence line used in evaluating its validity. Object Property Functional +EvidenceItem reference Document sepio:0000442 +EvidenceLine has_evidence_item EvidenceItem sepio:0000084 A relation holding between an evidence line and an individual information entity that contributes to the argument it represents. +EvidenceLine was_generated_by Activity prov:wasGeneratedBy +Person member Organization foaf:member \ No newline at end of file diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv index 8448840c8..b99ac43c1 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv @@ -1,12 +1,13 @@ - LinkML Slot or Attribute Name BICAN UUID SubGroup/LinkML Class Name Aliases Definition Nullable Multivalued Permissible Values Data Type Data Examples Min Value Max Value Unit Statistical Type Subsets Notes -> alias attribute slot_uri class ignore description ignore multivalued ignore range ignore ignore ignore ignore ignore in_subset ignore +SubGroup/LinkML Class Name LinkML Slot or Attribute Name BICAN UUID Alias Aliases Definition Nullable Multivalued Permissible Values Data Type Data Examples Min Value Max Value Unit Statistical Type Subsets Notes +> class attribute slot_uri alias ignore description ignore multivalued ignore range ignore ignore ignore ignore ignore in_subset ignore > internal_separator: "|" -hasAssertionCategory has_assertion_category brainkb:hasAssertionCategory Assertion The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to. FALSE Categories Object Property -hasEvidenceCategory has_evidence_category brainkb:hasEvidenceCategory Evidence The brainkb:hasEvidenceCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the evidence belongs to. FALSE Categories Object Property -hasEvidenceText has_evidence_text brainkb:hasEvidenceText Evidence The brainkb:hasEvidenceText property relates an eco:Evidence to an xsd:string, providing a textual excerpt of the evidence supporting the assertion. FALSE string Data Property -hasAssertionText has_assertion_text brainkb:hasAssertionText Assertion The brainkb:hasAssertionText property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made. FALSE string Data Property -hasAssertionMethod has_assertion_method brainkb:hasAssertionMethod Assertion The brainkb:hasAssertionMethod property relates an eco:Assertion to an eco:assertion method that differentiates different types of assertions techniques used while making an assertion. FALSE AssertionMethod Object Property -hasAssertionSummary has_assertion_summary brainkb:hasAssertionSummary AssertionSummary The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary to an xsd:string, providing a concise overview that differentiates various assertions. This summary encapsulates the core content of the assertion, allowing for easy identification and understanding of its essence. FALSE string Data Property -hasEvidenceSummary has_evidence_summary brainkb:hasEvidenceSummary EvidenceSummary The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary to an xsd:string, providing a concise overview that differentiates various evidence. This summary encapsulates the core content of the evidence, allowing for easy identification and understanding of its essence. FALSE string Data Property -endedAtTime ended_at_time Activity The prov:endedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity ended. FALSE datetime Data Property -startedAtTime started_at_time Activity The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started. FALSE datetime Data Property \ No newline at end of file +Activity ended_at_time endedAtTime The prov:endedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity ended. FALSE datetime Data Property +Activity started_at_time startedAtTime The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started. FALSE datetime Data Property +Assertion has_assertion_category brainkb:has_assertion_category The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to. FALSE Categories Object Property +Assertion has_assertion_description brainkb:has_assertion_description string +Assertion has_assertion_summary brainkb:has_assertion_summary The brainkb:has_assertion_text property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made. FALSE string Data Property +Document identifier datacite:identifier FALSE uri +EvidenceLine evidence_direction sepio:0000183 A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either). EvidenceDirection +EvidenceLine evidence_line_strength sepio:0000132 A relation describing the degree of support provided by an evidence line for a target assertion or proposition. EvidenceStrength +EvidenceLine has_evidence_category brainkb:has_evidence_category Categories +EvidenceLine has_evidenceline_description braiankb:has_evidenceline_description string \ No newline at end of file diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv index 010b554ac..2a3abf02e 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv @@ -1,40 +1,38 @@ -variable_name value description category terminology_nhash -> enum permissible_value description ignore ignore -AssertionType Positive -AssertionType Negative -AssertionType Inconclusive -Categories Behavioral -Categories Biomarker -Categories DrugTarget -Categories Genetic -Categories ClinicalTrial -Categories Etiologic -Categories Neuroimaging -Categories Electrophysiological -Categories Molecular -Categories Pharmacological -Categories Neuropsychological -Categories Neurogenetic -Categories Neurochemical -Categories Neuroanatomical -Categories Neurodevelopmental -Categories Neuroinflammatory -Categories Neuroplasticity -Categories Neuropathological -Categories Neurocomputational -Categories Neuroendocrine -Categories Neuropharmacogenomic -Categories Neuroproteomic -Categories Neurogenomic -Categories Epigenetic -Categories Environmental -Categories Translational -Categories Therapeutic -Categories CognitiveNeuroscience -SignificanceLevel HighlySignificant P value less than 0.01 -SignificanceLevel Significant P value less than 0.05 -SignificanceLevel MarginallySignificant P value less than 0.10 -SignificanceLevel NotSignificant P value greater than or equal to 0.10 -SignificanceLevel Unknown Specifies that the significance level is unknown as the information is not present in the study. -Significance Clinical -Significance NonClinical \ No newline at end of file +variable_name value title description category terminology_nhash meaning +> enum permissible_value title description ignore ignore ignore +Categories Behavioral +Categories Biomarker +Categories DrugTarget +Categories Genetic +Categories ClinicalTrial +Categories Etiologic +Categories Neuroimaging +Categories Electrophysiological +Categories Molecular +Categories Pharmacological +Categories Neuropsychological +Categories Neurogenetic +Categories Neurochemical +Categories Neuroanatomical +Categories Neurodevelopmental +Categories Neuroinflammatory +Categories Neuroplasticity +Categories Neuropathological +Categories Neurocomputational +Categories Neuroendocrine +Categories Neuropharmacogenomic +Categories Neuroproteomic +Categories Neurogenomic +Categories Epigenetic +Categories Environmental +Categories Translational +Categories Therapeutic +Categories CognitiveNeuroscience +EvidenceStrength HighlySignificant P value less than 0.01 +EvidenceStrength Significant P value less than 0.05 +EvidenceStrength MarginallySignificant P value less than 0.10 +EvidenceStrength NotSignificant P value greater than or equal to 0.10 +EvidenceStrength Unknown Specifies that the significance level is unknown as the information is not present in the study. +EvidenceDirection supporting sepio:0000403 +EvidenceDirection disputing sepio:0000404 +EvidenceDirection inconclusive sepio:0000405 \ No newline at end of file From 8073cc6d259e64f773d09fa4826789b7bcacf774 Mon Sep 17 00:00:00 2001 From: "action@github.com" Date: Fri, 20 Dec 2024 00:05:12 +0000 Subject: [PATCH 2/2] generate another formats for assertion_evidence model --- erdiagram-autogen/assertion_evidence.md | 69 +++- json-schema-autogen/assertion_evidence.json | 214 +++++++---- .../assertion_evidence.context.jsonld | 137 +++++-- models_py-autogen/assertion_evidence.py | 346 +++++++++++------- 4 files changed, 495 insertions(+), 271 deletions(-) diff --git a/erdiagram-autogen/assertion_evidence.md b/erdiagram-autogen/assertion_evidence.md index c534ffef6..e1c379ecc 100644 --- a/erdiagram-autogen/assertion_evidence.md +++ b/erdiagram-autogen/assertion_evidence.md @@ -1,42 +1,71 @@ ```mermaid erDiagram +Activity { + datetime ended_at_time + datetime started_at_time +} +Agent { + +} +Annotation { + +} Assertion { Categories has_assertion_category - string has_assertion_text + string has_assertion_description + string has_assertion_summary +} +CellAnnotation { + } Document { + uri identifier +} +EvidenceItem { } -Activity { - datetime ended_at_time - datetime started_at_time +EvidenceLine { + EvidenceDirection evidence_direction + EvidenceStrength evidence_line_strength + Categories has_evidence_category + string has_evidenceline_description } -Agent { +Group { } -AssertionSummary { - string has_assertion_summary +Identifier { + } -EvidenceSummary { - string has_evidence_summary +OrcidIdentifier { + } -AssertionMethod { +Organization { } -DataAnnotation { +Person { } -Evidence { - Categories has_evidence_category - string has_evidence_text +PersonIdentifier { + +} +SoftwareAgent { + } -Assertion ||--|o AssertionMethod : "has_assertion_method" -Assertion ||--|o AssertionSummary : "is_associated_with" -Assertion ||--|o DataAnnotation : "has_data_annotation" -Agent ||--|o Activity : "is_associated_with" -Evidence ||--|o Assertion : "used_in" -Evidence ||--|o EvidenceSummary : "is_associated_with" +Activity ||--|o Agent : "was_associate_with" +Agent ||--|o Identifier : "has_identifier" +Assertion ||--|o Annotation : "has_annotation" +Assertion ||--|o Activity : "was_generated_by" +Assertion ||--|o EvidenceLine : "has_evidence_line" +Document ||--|o Document : "reference" +EvidenceItem ||--|o Document : "reference" +EvidenceLine ||--|o EvidenceItem : "has_evidence_item" +EvidenceLine ||--|o Activity : "was_generated_by" +Group ||--|o Identifier : "has_identifier" +Organization ||--|o Identifier : "has_identifier" +Person ||--|o Organization : "member" +Person ||--|o Identifier : "has_identifier" +SoftwareAgent ||--|o Identifier : "has_identifier" ``` diff --git a/json-schema-autogen/assertion_evidence.json b/json-schema-autogen/assertion_evidence.json index 6d8fd4db1..b0950580f 100644 --- a/json-schema-autogen/assertion_evidence.json +++ b/json-schema-autogen/assertion_evidence.json @@ -13,6 +13,9 @@ "description": "The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started.", "format": "date-time", "type": "string" + }, + "was_associate_with": { + "$ref": "#/$defs/Agent" } }, "title": "Activity", @@ -22,69 +25,48 @@ "additionalProperties": false, "description": "An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.", "properties": { - "is_associated_with": { - "$ref": "#/$defs/Activity", - "description": "The brainkb:isAssociatedWith property establishes relationships between different entities: it connects prov:Agent to prov:Activity, reflecting the involvement or connection between an agent and an activity." + "has_identifier": { + "$ref": "#/$defs/Identifier" } }, "title": "Agent", "type": "object" }, + "Annotation": { + "additionalProperties": false, + "description": "An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information.", + "title": "Annotation", + "type": "object" + }, "Assertion": { "additionalProperties": false, "description": "A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence.", "properties": { - "hasAssertionCategory": { + "has_annotation": { + "$ref": "#/$defs/Annotation" + }, + "has_assertion_category": { "$ref": "#/$defs/Categories", "description": "The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to." }, - "hasAssertionMethod": { - "$ref": "#/$defs/AssertionMethod", - "description": "The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion." + "has_assertion_description": { + "type": "string" }, - "hasAssertionText": { - "description": "The brainkb:hasAssertionText property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.", + "has_assertion_summary": { + "description": "The brainkb:has_assertion_text property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.", "type": "string" }, - "has_data_annotation": { - "$ref": "#/$defs/DataAnnotation" + "has_evidence_line": { + "$ref": "#/$defs/EvidenceLine", + "description": "A relationship between an assertion or proposition and an evidence line used in evaluating its validity." }, - "is_associated_with": { - "$ref": "#/$defs/AssertionSummary", - "description": "The brainkb:isAssociatedWith property establishes relationships between different entities:it links sepio:Assertion to brainkb:AssertionSummary, indicating the association between an assertion and its corresponding summary." + "was_generated_by": { + "$ref": "#/$defs/Activity" } }, "title": "Assertion", "type": "object" }, - "AssertionMethod": { - "additionalProperties": false, - "description": "A means by which a statement is made about the entity", - "title": "AssertionMethod", - "type": "object" - }, - "AssertionSummary": { - "additionalProperties": false, - "description": "A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion.", - "properties": { - "hasAssertionSummary": { - "description": "The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary to an xsd:string, providing a concise overview that differentiates various assertions. This summary encapsulates the core content of the assertion, allowing for easy identification and understanding of its essence.", - "type": "string" - } - }, - "title": "AssertionSummary", - "type": "object" - }, - "AssertionType": { - "description": "", - "enum": [ - "Positive", - "Negative", - "Inconclusive" - ], - "title": "AssertionType", - "type": "string" - }, "Categories": { "description": "", "enum": [ @@ -120,64 +102,77 @@ "title": "Categories", "type": "string" }, - "DataAnnotation": { + "CellAnnotation": { "additionalProperties": false, "description": "", - "title": "DataAnnotation", + "title": "CellAnnotation", "type": "object" }, "Document": { "additionalProperties": false, "description": "A collection of information content entities intended to be understood together as a whole", + "properties": { + "identifier": { + "type": "string" + }, + "reference": { + "$ref": "#/$defs/Document" + } + }, "title": "Document", "type": "object" }, - "Evidence": { + "EvidenceDirection": { + "description": "", + "enum": [ + "supporting", + "disputing", + "inconclusive" + ], + "title": "EvidenceDirection", + "type": "string" + }, + "EvidenceItem": { "additionalProperties": false, "description": "", "properties": { - "hasEvidenceCategory": { - "$ref": "#/$defs/Categories", - "description": "The brainkb:hasEvidenceCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the evidence belongs to." - }, - "hasEvidenceText": { - "description": "The brainkb:hasEvidenceText property relates an eco:Evidence to an xsd:string, providing a textual excerpt of the evidence supporting the assertion.", - "type": "string" - }, - "is_associated_with": { - "$ref": "#/$defs/EvidenceSummary", - "description": "The brainkb:isAssociatedWith property establishes relationships between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, signifying the connection between evidence and its summarized representation." - }, - "used_in": { - "$ref": "#/$defs/Assertion", - "description": "The eco:used_in property establishes a relationship between eco:Evidence and eco:Assertion, indicating that the evidence is utilized to support the corresponding assertion." + "reference": { + "$ref": "#/$defs/Document" } }, - "title": "Evidence", + "title": "EvidenceItem", "type": "object" }, - "EvidenceSummary": { + "EvidenceLine": { "additionalProperties": false, - "description": "A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence.", + "description": "An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence.", "properties": { - "hasEvidenceSummary": { - "description": "The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary to an xsd:string, providing a concise overview that differentiates various evidence. This summary encapsulates the core content of the evidence, allowing for easy identification and understanding of its essence.", + "evidence_direction": { + "$ref": "#/$defs/EvidenceDirection", + "description": "A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either)." + }, + "evidence_line_strength": { + "$ref": "#/$defs/EvidenceStrength", + "description": "A relation describing the degree of support provided by an evidence line for a target assertion or proposition." + }, + "has_evidence_category": { + "$ref": "#/$defs/Categories" + }, + "has_evidence_item": { + "$ref": "#/$defs/EvidenceItem", + "description": "A relation holding between an evidence line and an individual information entity that contributes to the argument it represents." + }, + "has_evidenceline_description": { "type": "string" + }, + "was_generated_by": { + "$ref": "#/$defs/Activity" } }, - "title": "EvidenceSummary", + "title": "EvidenceLine", "type": "object" }, - "Significance": { - "description": "", - "enum": [ - "Clinical", - "NonClinical" - ], - "title": "Significance", - "type": "string" - }, - "SignificanceLevel": { + "EvidenceStrength": { "description": "", "enum": [ "HighlySignificant", @@ -186,8 +181,73 @@ "NotSignificant", "Unknown" ], - "title": "SignificanceLevel", + "title": "EvidenceStrength", "type": "string" + }, + "Group": { + "additionalProperties": false, + "description": "", + "properties": { + "has_identifier": { + "$ref": "#/$defs/Identifier" + } + }, + "title": "Group", + "type": "object" + }, + "Identifier": { + "additionalProperties": false, + "description": "", + "title": "Identifier", + "type": "object" + }, + "OrcidIdentifier": { + "additionalProperties": false, + "description": "", + "title": "OrcidIdentifier", + "type": "object" + }, + "Organization": { + "additionalProperties": false, + "description": "", + "properties": { + "has_identifier": { + "$ref": "#/$defs/Identifier" + } + }, + "title": "Organization", + "type": "object" + }, + "Person": { + "additionalProperties": false, + "description": "", + "properties": { + "has_identifier": { + "$ref": "#/$defs/Identifier" + }, + "member": { + "$ref": "#/$defs/Organization" + } + }, + "title": "Person", + "type": "object" + }, + "PersonIdentifier": { + "additionalProperties": false, + "description": "", + "title": "PersonIdentifier", + "type": "object" + }, + "SoftwareAgent": { + "additionalProperties": false, + "description": "", + "properties": { + "has_identifier": { + "$ref": "#/$defs/Identifier" + } + }, + "title": "SoftwareAgent", + "type": "object" } }, "$id": "https://identifiers.org/brain-bican/assertion-evidence-schema", diff --git a/jsonld-context-autogen/assertion_evidence.context.jsonld b/jsonld-context-autogen/assertion_evidence.context.jsonld index 2175fccb2..552ad74ff 100644 --- a/jsonld-context-autogen/assertion_evidence.context.jsonld +++ b/jsonld-context-autogen/assertion_evidence.context.jsonld @@ -5,18 +5,36 @@ }, "@context": { "bican": "https://identifiers.org/brain-bican/vocab/", + "braiankb": "http://example.org/braiankb/", "brainkb": "https://brainkb.org/", + "datacite": "http://purl.org/spar/datacite/", + "dcterms": "http://purl.org/dc/terms/", "eco": { "@id": "http://purl.obolibrary.org/obo/ECO_", "@prefix": true }, + "edam": "http://edamontology.org/", + "foaf": "http://xmlns.com/foaf/0.1/", + "iao": { + "@id": "http://purl.obolibrary.org/obo/IAO_", + "@prefix": true + }, "linkml": "https://w3id.org/linkml/", + "oa": "http://www.w3.org/ns/oa#", "prov": "http://www.w3.org/ns/prov#", + "ro": { + "@id": "http://purl.obolibrary.org/obo/RO_", + "@prefix": true + }, "schema": "http://schema.org/", "sepio": { "@id": "http://purl.obolibrary.org/obo/SEPIO_", "@prefix": true }, + "sio": { + "@id": "http://semanticscience.org/resource/SIO_", + "@prefix": true + }, "skos": "http://www.w3.org/2004/02/skos/core#", "spdx": "http://spdx.org/rdf/terms#", "@vocab": "https://brainkb.org/", @@ -28,57 +46,78 @@ "@type": "xsd:dateTime", "@id": "startedAtTime" }, - "hasAssertionCategory": { + "has_assertion_category": { "@context": { "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" }, - "@id": "hasAssertionCategory" + "@id": "has_assertion_category" + }, + "has_assertion_description": { + "@id": "has_assertion_description" }, - "hasAssertionMethod": { + "has_assertion_summary": { + "@id": "has_assertion_summary" + }, + "identifier": { "@type": "@id", - "@id": "hasAssertionMethod" + "@id": "datacite:identifier" }, - "hasAssertionText": { - "@id": "hasAssertionText" + "evidence_direction": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + }, + "@id": "sepio:0000183" }, - "hasAssertionSummary": { - "@id": "hasAssertionSummary" + "evidence_line_strength": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + }, + "@id": "sepio:0000132" }, - "hasEvidenceCategory": { + "has_evidence_category": { "@context": { "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" }, - "@id": "hasEvidenceCategory" + "@id": "has_evidence_category" }, - "hasEvidenceText": { - "@id": "hasEvidenceText" + "has_evidenceline_description": { + "@id": "braiankb:has_evidenceline_description" }, - "hasEvidenceSummary": { - "@id": "hasEvidenceSummary" + "has_annotation": { + "@id": "has_annotation" }, - "has_assertion_method": { - "@type": "@id", - "@id": "has_assertion_method" + "has_evidence_item": { + "@id": "has_evidence_item" }, - "has_data_annotation": { - "@id": "has_data_annotation" + "has_evidence_line": { + "@id": "has_evidence_line" }, - "is_associated_with": { - "@id": "is_associated_with" + "has_identifier": { + "@id": "has_identifier" }, - "used_in": { - "@type": "@id", - "@id": "used_in" + "member": { + "@id": "member" }, - "uses": { - "@type": "@id", - "@id": "uses" + "reference": { + "@id": "reference" + }, + "was_associate_with": { + "@id": "was_associate_with" + }, + "was_generated_by": { + "@id": "was_generated_by" }, "Activity": { "@id": "prov:Activity" @@ -86,26 +125,44 @@ "Agent": { "@id": "prov:Agent" }, + "Annotation": { + "@id": "oa:Annotation" + }, "Assertion": { - "@id": "sepio:Assertion" + "@id": "sepio:0000001" + }, + "CellAnnotation": { + "@id": "CellAnnotation" }, - "AssertionMethod": { - "@id": "eco:0000217" + "Document": { + "@id": "iao:0000310" }, - "AssertionSummary": { - "@id": "AssertionSummary" + "EvidenceItem": { + "@id": "sepio:0000149" }, - "DataAnnotation": { - "@id": "DataAnnotation" + "EvidenceLine": { + "@id": "sepio:0000002" }, - "Document": { - "@id": "sepio:Document" + "Group": { + "@id": "foaf:Group" + }, + "Identifier": { + "@id": "edam:data_0842" + }, + "OrcidIdentifier": { + "@id": "edam:data_4022" + }, + "Organization": { + "@id": "prov:Organization" + }, + "Person": { + "@id": "prov:Person" }, - "Evidence": { - "@id": "Evidence" + "PersonIdentifier": { + "@id": "edam:data_2118" }, - "EvidenceSummary": { - "@id": "EvidenceSummary" + "SoftwareAgent": { + "@id": "prov:SoftwareAgent" } } } diff --git a/models_py-autogen/assertion_evidence.py b/models_py-autogen/assertion_evidence.py index 2ae9fec24..aa5d3db8c 100644 --- a/models_py-autogen/assertion_evidence.py +++ b/models_py-autogen/assertion_evidence.py @@ -74,29 +74,41 @@ def __contains__(self, key:str) -> bool: 'name': 'assertion-evidence-schema', 'prefixes': {'bican': {'prefix_prefix': 'bican', 'prefix_reference': 'https://identifiers.org/brain-bican/vocab/'}, + 'braiankb': {'prefix_prefix': 'braiankb', + 'prefix_reference': 'http://example.org/braiankb/'}, 'brainkb': {'prefix_prefix': 'brainkb', 'prefix_reference': 'https://brainkb.org/'}, + 'datacite': {'prefix_prefix': 'datacite', + 'prefix_reference': 'http://purl.org/spar/datacite/'}, + 'dcterms': {'prefix_prefix': 'dcterms', + 'prefix_reference': 'http://purl.org/dc/terms/'}, 'eco': {'prefix_prefix': 'eco', 'prefix_reference': 'http://purl.obolibrary.org/obo/ECO_'}, + 'edam': {'prefix_prefix': 'edam', + 'prefix_reference': 'http://edamontology.org/'}, + 'foaf': {'prefix_prefix': 'foaf', + 'prefix_reference': 'http://xmlns.com/foaf/0.1/'}, + 'iao': {'prefix_prefix': 'iao', + 'prefix_reference': 'http://purl.obolibrary.org/obo/IAO_'}, 'linkml': {'prefix_prefix': 'linkml', 'prefix_reference': 'https://w3id.org/linkml/'}, + 'oa': {'prefix_prefix': 'oa', + 'prefix_reference': 'http://www.w3.org/ns/oa#'}, 'prov': {'prefix_prefix': 'prov', 'prefix_reference': 'http://www.w3.org/ns/prov#'}, + 'ro': {'prefix_prefix': 'ro', + 'prefix_reference': 'http://purl.obolibrary.org/obo/RO_'}, 'schema': {'prefix_prefix': 'schema', 'prefix_reference': 'http://schema.org/'}, 'sepio': {'prefix_prefix': 'sepio', 'prefix_reference': 'http://purl.obolibrary.org/obo/SEPIO_'}, + 'sio': {'prefix_prefix': 'sio', + 'prefix_reference': 'http://semanticscience.org/resource/SIO_'}, 'spdx': {'prefix_prefix': 'spdx', 'prefix_reference': 'http://spdx.org/rdf/terms#'}}, 'source_file': 'assertion_evidence.yaml', 'title': 'Assertion Evidence Schema'} ) -class AssertionType(str, Enum): - Positive = "Positive" - Negative = "Negative" - Inconclusive = "Inconclusive" - - class Categories(str, Enum): Behavioral = "Behavioral" Biomarker = "Biomarker" @@ -128,7 +140,7 @@ class Categories(str, Enum): CognitiveNeuroscience = "CognitiveNeuroscience" -class SignificanceLevel(str, Enum): +class EvidenceStrength(str, Enum): # P value less than 0.01 HighlySignificant = "HighlySignificant" # P value less than 0.05 @@ -141,182 +153,248 @@ class SignificanceLevel(str, Enum): Unknown = "Unknown" -class Significance(str, Enum): - Clinical = "Clinical" - NonClinical = "NonClinical" +class EvidenceDirection(str, Enum): + supporting = "supporting" + disputing = "disputing" + inconclusive = "inconclusive" + + + +class Activity(ConfiguredBaseModel): + """ + 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. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Activity', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', + 'slot_usage': {'was_associate_with': {'name': 'was_associate_with', + 'range': 'Agent', + 'slot_uri': 'prov:wasAssociatedWith'}}}) + + was_associate_with: Optional[Agent] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'was_associate_with', + 'domain_of': ['Activity'], + 'slot_uri': 'prov:wasAssociatedWith'} }) + ended_at_time: Optional[datetime ] = Field(None, description="""The prov:endedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity ended.""", json_schema_extra = { "linkml_meta": {'alias': 'endedAtTime', 'domain_of': ['Activity']} }) + started_at_time: Optional[datetime ] = Field(None, description="""The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started.""", json_schema_extra = { "linkml_meta": {'alias': 'startedAtTime', 'domain_of': ['Activity']} }) + + +class Agent(ConfiguredBaseModel): + """ + An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Agent', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', + 'slot_usage': {'has_identifier': {'domain_of': ['Agent'], + 'name': 'has_identifier', + 'range': 'Identifier', + 'slot_uri': 'edam:has_identifier'}}}) + + has_identifier: Optional[Identifier] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_identifier', + 'domain_of': ['Agent'], + 'slot_uri': 'edam:has_identifier'} }) +class Annotation(ConfiguredBaseModel): + """ + An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'oa:Annotation', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) + + pass + class Assertion(ConfiguredBaseModel): """ A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'sepio:Assertion', + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'sepio:0000001', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', - 'slot_usage': {'has_assertion_method': {'description': 'The ' - 'brainkb:hasAssertionMethod ' - 'property relates an ' - 'eco:Assertion to an ' - 'brainkb:AssertionMethod ' - 'that differentiates ' - 'different types of ' - 'assertions techniques ' - 'used while making an ' - 'assertion.', - 'name': 'has_assertion_method'}, - 'has_data_annotation': {'name': 'has_data_annotation', - 'range': 'DataAnnotation'}, - 'is_associated_with': {'description': 'The ' - 'brainkb:isAssociatedWith ' - 'property establishes ' - 'relationships between ' - 'different entities:it ' - 'links sepio:Assertion ' - 'to ' - 'brainkb:AssertionSummary, ' - 'indicating the ' - 'association between an ' - 'assertion and its ' - 'corresponding summary.', - 'name': 'is_associated_with', - 'range': 'AssertionSummary'}}}) - - has_assertion_method: Optional[AssertionMethod] = Field(None, description="""The brainkb:hasAssertionMethod property relates an eco:Assertion to an brainkb:AssertionMethod that differentiates different types of assertions techniques used while making an assertion.""", json_schema_extra = { "linkml_meta": {'alias': 'hasAssertionMethod', + 'slot_usage': {'has_annotation': {'name': 'has_annotation', + 'range': 'Annotation', + 'slot_uri': 'sio:000255'}, + 'has_evidence_line': {'description': 'A relationship between ' + 'an assertion or ' + 'proposition and an ' + 'evidence line used in ' + 'evaluating its validity.', + 'name': 'has_evidence_line', + 'range': 'EvidenceLine', + 'slot_uri': 'sepio:0000006'}, + 'was_generated_by': {'name': 'was_generated_by', + 'range': 'Activity', + 'slot_uri': 'prov:wasGeneratedBy'}}}) + + has_annotation: Optional[Annotation] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_annotation', + 'domain_of': ['Assertion'], + 'slot_uri': 'sio:000255'} }) + was_generated_by: Optional[Activity] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'was_generated_by', + 'domain_of': ['Assertion', 'EvidenceLine'], + 'slot_uri': 'prov:wasGeneratedBy'} }) + has_evidence_line: Optional[EvidenceLine] = Field(None, description="""A relationship between an assertion or proposition and an evidence line used in evaluating its validity.""", json_schema_extra = { "linkml_meta": {'alias': 'has_evidence_line', 'domain_of': ['Assertion'], - 'slot_uri': 'brainkb:hasAssertionMethod'} }) - is_associated_with: Optional[AssertionSummary] = Field(None, description="""The brainkb:isAssociatedWith property establishes relationships between different entities:it links sepio:Assertion to brainkb:AssertionSummary, indicating the association between an assertion and its corresponding summary.""", json_schema_extra = { "linkml_meta": {'alias': 'is_associated_with', 'domain_of': ['Assertion', 'Agent', 'Evidence']} }) - has_data_annotation: Optional[DataAnnotation] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_data_annotation', 'domain_of': ['Assertion']} }) - has_assertion_category: Optional[Categories] = Field(None, description="""The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to.""", json_schema_extra = { "linkml_meta": {'alias': 'hasAssertionCategory', + 'slot_uri': 'sepio:0000006'} }) + has_assertion_category: Optional[Categories] = Field(None, description="""The brainkb:hasAssertionCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the assertion belongs to.""", json_schema_extra = { "linkml_meta": {'alias': 'has_assertion_category', 'domain_of': ['Assertion'], - 'slot_uri': 'brainkb:hasAssertionCategory'} }) - has_assertion_text: Optional[str] = Field(None, description="""The brainkb:hasAssertionText property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.""", json_schema_extra = { "linkml_meta": {'alias': 'hasAssertionText', + 'slot_uri': 'brainkb:has_assertion_category'} }) + has_assertion_description: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_assertion_description', 'domain_of': ['Assertion'], - 'slot_uri': 'brainkb:hasAssertionText'} }) + 'slot_uri': 'brainkb:has_assertion_description'} }) + has_assertion_summary: Optional[str] = Field(None, description="""The brainkb:has_assertion_text property relates an eco:Assertion to an xsd:string, providing a textual excerpt of the assertion being made.""", json_schema_extra = { "linkml_meta": {'alias': 'has_assertion_summary', + 'domain_of': ['Assertion'], + 'slot_uri': 'brainkb:has_assertion_summary'} }) -class Document(ConfiguredBaseModel): - """ - A collection of information content entities intended to be understood together as a whole - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'sepio:Document', +class CellAnnotation(Annotation): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'brainkb:CellAnnotation', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) pass -class Activity(ConfiguredBaseModel): +class EvidenceItem(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'sepio:0000149', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', + 'slot_usage': {'reference': {'name': 'reference', + 'range': 'Document', + 'slot_uri': 'sepio:0000442'}}}) + + reference: Optional[Document] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'reference', + 'domain_of': ['EvidenceItem'], + 'slot_uri': 'sepio:0000442'} }) + + +class Document(EvidenceItem): """ - 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. + A collection of information content entities intended to be understood together as a whole """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Activity', + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'iao:0000310', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) - ended_at_time: Optional[datetime ] = Field(None, description="""The prov:endedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity ended.""", json_schema_extra = { "linkml_meta": {'alias': 'endedAtTime', 'domain_of': ['Activity']} }) - started_at_time: Optional[datetime ] = Field(None, description="""The prov:startedAtTime establishes the relationship between prov:Activity and xsd:DateTime that allows one to specify the time when the activity started.""", json_schema_extra = { "linkml_meta": {'alias': 'startedAtTime', 'domain_of': ['Activity']} }) + identifier: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'identifier', + 'domain_of': ['Document'], + 'slot_uri': 'datacite:identifier'} }) + reference: Optional[Document] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'reference', + 'domain_of': ['EvidenceItem'], + 'slot_uri': 'sepio:0000442'} }) -class Agent(ConfiguredBaseModel): +class EvidenceLine(ConfiguredBaseModel): """ - An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. + An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence. """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Agent', + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'sepio:0000002', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', - 'slot_usage': {'is_associated_with': {'description': 'The ' - 'brainkb:isAssociatedWith ' - 'property establishes ' - 'relationships between ' - 'different entities: it ' - 'connects prov:Agent to ' - 'prov:Activity, ' - 'reflecting the ' - 'involvement or ' - 'connection between an ' - 'agent and an activity.', - 'name': 'is_associated_with', - 'range': 'Activity'}}}) - - is_associated_with: Optional[Activity] = Field(None, description="""The brainkb:isAssociatedWith property establishes relationships between different entities: it connects prov:Agent to prov:Activity, reflecting the involvement or connection between an agent and an activity.""", json_schema_extra = { "linkml_meta": {'alias': 'is_associated_with', 'domain_of': ['Assertion', 'Agent', 'Evidence']} }) - - -class AssertionSummary(ConfiguredBaseModel): - """ - A summary is a brief statement or description of the main points, especially as a conclusion to a work about the assertion. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'brainkb:AssertionSummary', + 'slot_usage': {'has_evidence_item': {'description': 'A relation holding ' + 'between an evidence line ' + 'and an individual ' + 'information entity that ' + 'contributes to the ' + 'argument it represents.', + 'domain_of': ['EvidenceLine'], + 'name': 'has_evidence_item', + 'range': 'EvidenceItem', + 'slot_uri': 'sepio:0000084'}, + 'was_generated_by': {'domain_of': ['Assertion', 'EvidenceLine'], + 'name': 'was_generated_by', + 'range': 'Activity', + 'slot_uri': 'prov:wasGeneratedBy'}}}) + + has_evidence_item: Optional[EvidenceItem] = Field(None, description="""A relation holding between an evidence line and an individual information entity that contributes to the argument it represents.""", json_schema_extra = { "linkml_meta": {'alias': 'has_evidence_item', + 'domain_of': ['EvidenceLine'], + 'slot_uri': 'sepio:0000084'} }) + was_generated_by: Optional[Activity] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'was_generated_by', + 'domain_of': ['Assertion', 'EvidenceLine'], + 'slot_uri': 'prov:wasGeneratedBy'} }) + evidence_direction: Optional[EvidenceDirection] = Field(None, description="""A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).""", json_schema_extra = { "linkml_meta": {'alias': 'evidence_direction', + 'domain_of': ['EvidenceLine'], + 'slot_uri': 'sepio:0000183'} }) + evidence_line_strength: Optional[EvidenceStrength] = Field(None, description="""A relation describing the degree of support provided by an evidence line for a target assertion or proposition.""", json_schema_extra = { "linkml_meta": {'alias': 'evidence_line_strength', + 'domain_of': ['EvidenceLine'], + 'slot_uri': 'sepio:0000132'} }) + has_evidence_category: Optional[Categories] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_evidence_category', + 'domain_of': ['EvidenceLine'], + 'slot_uri': 'brainkb:has_evidence_category'} }) + has_evidenceline_description: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_evidenceline_description', + 'domain_of': ['EvidenceLine'], + 'slot_uri': 'braiankb:has_evidenceline_description'} }) + + +class Group(Agent): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'foaf:Group', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) - has_assertion_summary: Optional[str] = Field(None, description="""The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary to an xsd:string, providing a concise overview that differentiates various assertions. This summary encapsulates the core content of the assertion, allowing for easy identification and understanding of its essence.""", json_schema_extra = { "linkml_meta": {'alias': 'hasAssertionSummary', - 'domain_of': ['AssertionSummary'], - 'slot_uri': 'brainkb:hasAssertionSummary'} }) + has_identifier: Optional[Identifier] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_identifier', + 'domain_of': ['Agent'], + 'slot_uri': 'edam:has_identifier'} }) -class EvidenceSummary(ConfiguredBaseModel): - """ - A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'brainkb:EvidenceSummary', +class Identifier(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'edam:data_0842', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) - has_evidence_summary: Optional[str] = Field(None, description="""The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary to an xsd:string, providing a concise overview that differentiates various evidence. This summary encapsulates the core content of the evidence, allowing for easy identification and understanding of its essence.""", json_schema_extra = { "linkml_meta": {'alias': 'hasEvidenceSummary', - 'domain_of': ['EvidenceSummary'], - 'slot_uri': 'brainkb:hasEvidenceSummary'} }) + pass -class AssertionMethod(ConfiguredBaseModel): - """ - A means by which a statement is made about the entity - """ - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'eco:0000217', +class Organization(Group): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Organization', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) + + has_identifier: Optional[Identifier] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_identifier', + 'domain_of': ['Agent'], + 'slot_uri': 'edam:has_identifier'} }) + + +class Person(Agent): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:Person', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', + 'slot_usage': {'member': {'name': 'member', + 'range': 'Organization', + 'slot_uri': 'foaf:member'}}}) + + member: Optional[Organization] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'member', 'domain_of': ['Person'], 'slot_uri': 'foaf:member'} }) + has_identifier: Optional[Identifier] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_identifier', + 'domain_of': ['Agent'], + 'slot_uri': 'edam:has_identifier'} }) + + +class PersonIdentifier(Identifier): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'edam:data_2118', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) pass -class DataAnnotation(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'brainkb:DataAnnotation', +class OrcidIdentifier(PersonIdentifier): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'edam:data_4022', 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) pass -class Evidence(ConfiguredBaseModel): - linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema', - 'slot_usage': {'is_associated_with': {'description': 'The ' - 'brainkb:isAssociatedWith ' - 'property establishes ' - 'relationships between ' - 'different entities: it ' - 'associates eco:Evidence ' - 'with ' - 'brainkb:EvidenceSummary, ' - 'signifying the ' - 'connection between ' - 'evidence and its ' - 'summarized ' - 'representation.', - 'name': 'is_associated_with', - 'range': 'EvidenceSummary'}, - 'used_in': {'name': 'used_in'}}}) - - used_in: Optional[Assertion] = Field(None, description="""The eco:used_in property establishes a relationship between eco:Evidence and eco:Assertion, indicating that the evidence is utilized to support the corresponding assertion.""", json_schema_extra = { "linkml_meta": {'alias': 'used_in', 'domain_of': ['Evidence']} }) - is_associated_with: Optional[EvidenceSummary] = Field(None, description="""The brainkb:isAssociatedWith property establishes relationships between different entities: it associates eco:Evidence with brainkb:EvidenceSummary, signifying the connection between evidence and its summarized representation.""", json_schema_extra = { "linkml_meta": {'alias': 'is_associated_with', 'domain_of': ['Assertion', 'Agent', 'Evidence']} }) - has_evidence_category: Optional[Categories] = Field(None, description="""The brainkb:hasEvidenceCategory property relates brainkb:Evidence and brainkb:Categories, specifying the classification or category that the evidence belongs to.""", json_schema_extra = { "linkml_meta": {'alias': 'hasEvidenceCategory', - 'domain_of': ['Evidence'], - 'slot_uri': 'brainkb:hasEvidenceCategory'} }) - has_evidence_text: Optional[str] = Field(None, description="""The brainkb:hasEvidenceText property relates an eco:Evidence to an xsd:string, providing a textual excerpt of the evidence supporting the assertion.""", json_schema_extra = { "linkml_meta": {'alias': 'hasEvidenceText', - 'domain_of': ['Evidence'], - 'slot_uri': 'brainkb:hasEvidenceText'} }) +class SoftwareAgent(Agent): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'prov:SoftwareAgent', + 'from_schema': 'https://identifiers.org/brain-bican/assertion-evidence-schema'}) + + has_identifier: Optional[Identifier] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'has_identifier', + 'domain_of': ['Agent'], + 'slot_uri': 'edam:has_identifier'} }) # Model rebuild # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Assertion.model_rebuild() -Document.model_rebuild() Activity.model_rebuild() Agent.model_rebuild() -AssertionSummary.model_rebuild() -EvidenceSummary.model_rebuild() -AssertionMethod.model_rebuild() -DataAnnotation.model_rebuild() -Evidence.model_rebuild() +Annotation.model_rebuild() +Assertion.model_rebuild() +CellAnnotation.model_rebuild() +EvidenceItem.model_rebuild() +Document.model_rebuild() +EvidenceLine.model_rebuild() +Group.model_rebuild() +Identifier.model_rebuild() +Organization.model_rebuild() +Person.model_rebuild() +PersonIdentifier.model_rebuild() +OrcidIdentifier.model_rebuild() +SoftwareAgent.model_rebuild()