From 5f51a8ef2409ae630c10060a5f3e4c505da5a4fa Mon Sep 17 00:00:00 2001 From: puja-trivedi Date: Fri, 13 Dec 2024 19:22:36 +0000 Subject: [PATCH] Generate new version of the linkml model for assertion_evidence --- linkml-schema/assertion_evidence.yaml | 399 +++++++++++++----- .../gsheet_output/Classes.tsv | 32 +- .../gsheet_output/Prefixes.tsv | 5 +- .../gsheet_output/Relations.tsv | 23 +- .../gsheet_output/Slots.tsv | 28 +- .../gsheet_output/ValueSets.tsv | 103 +++-- 6 files changed, 410 insertions(+), 180 deletions(-) diff --git a/linkml-schema/assertion_evidence.yaml b/linkml-schema/assertion_evidence.yaml index 07f69b531..afc5f5dd5 100644 --- a/linkml-schema/assertion_evidence.yaml +++ b/linkml-schema/assertion_evidence.yaml @@ -12,6 +12,13 @@ prefixes: prov: http://www.w3.org/ns/prov# eco: http://purl.obolibrary.org/obo/ECO_ sepio: http://purl.obolibrary.org/obo/SEPIO_ + ro: http://purl.obolibrary.org/obo/RO_ + iao: http://purl.obolibrary.org/obo/IAO_ + sio: http://semanticscience.org/resource/SIO_ + datacite: http://purl.org/spar/datacite/ + foaf: http://xmlns.com/foaf/0.1/ + dcterms: http://purl.org/dc/terms/ + oa: http://www.w3.org/ns/oa# default_prefix: brainkb default_range: string enums: @@ -71,30 +78,148 @@ enums: permissible_values: Clinical: {} NonClinical: {} + EvidenceType: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + permissible_values: + SupportingEvidence: {} + DisputingEvidence: {} + InconclusiveEvidence: {} + ContributorType: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + permissible_values: + datacite:ContactPerson: + description: The main individual to contact regarding the resource + title: ContactPerson + datacite:DataCollector: + description: Person responsible for collecting data. + title: DataCollector + datacite:DataCurator: + description: Person responsible for managing and curating the data. + title: DataCurator + datacite:DataManager: + description: Person responsible for maintaining the data. + title: DataManager + datacite:Distributor: + description: Entity that distributes the data. + title: Distributor + datacite:Editor: + description: Person responsible for overseeing the content's editorial aspects. + title: Editor + datacite:HostingInstitution: + description: The institution hosting the data. + title: HostingInstitution + datacite:Producer: + description: Person or organization responsible for producing the data. + title: Producer + datacite:ProjectLeader: + description: Person who leads the project or study. + title: ProjectLeader + datacite:ProjectManager: + description: Person responsible for managing the project's administrative + aspects. + title: ProjectManager + datacite:ProjectMember: + description: Member of the project team. + title: ProjectMember + datacite:RegistrationAgency: + description: Agency responsible for registering the data. + title: RegistrationAgency + datacite:RegistrationAuthority: + description: Authority that oversees the registration process. + title: RegistrationAuthority + datacite:RelatedPerson: + description: Person related to the data or study, but not directly contributing. + title: RelatedPerson + datacite:Researcher: + description: Person who conducts the research. + title: Researcher + datacite:ResearchGroup: + description: A group of researchers working on the data or study. + title: ResearchGroup + datacite:RightsHolder: + description: Entity holding the rights to the data. + title: RightsHolder + datacite:Sponsor: + description: Entity sponsoring the data or research. + title: Sponsor + datacite:Supervisor: + description: Person supervising the research or project. + title: Supervisor + datacite:WorkPackageLeader: + description: Leader responsible for a specific work package in a project. + title: WorkPackageLeader 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. - 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. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - range: Assertion + was_associate_with: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema 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. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - range: AssertionMethod + has_cell_annotation: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + has_contributer: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + has_description: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + has_summary: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_expressed_in: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + has_evidence_line: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema is_associated_with: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - has_data_annotation: + is_described_by: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + output_of: 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 + and xsd:DateTime that allows one to specify the time when the activity ended. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + alias: endedAtTime + range: datetime + started_at_time: + description: The prov:startedAtTime establishes the relationship between prov:Activity + and xsd:DateTime that allows one to specify the time when the activity started. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + alias: startedAtTime + range: datetime + class_uri: prov:Activity + Agent: + 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. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + class_uri: prov:Agent + 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 + attributes: + cell_annotation: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:cellAnnotation + alias: cellAnnotation + range: string + description: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:description + alias: description + range: string + 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 @@ -102,21 +227,37 @@ classes: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema slots: - has_assertion_method - - is_associated_with - - has_data_annotation + - has_cell_annotation + - has_contributer + - has_description + - has_summary + - is_expressed_in + - has_evidence_line 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. + has_cell_annotation: + range: CellAnnotation + has_contributer: + slot_uri: sepio:0000151 + range: Agent + has_description: + range: Description + has_summary: + slot_uri: brainkb:hasSummary range: AssertionSummary - has_data_annotation: - range: DataAnnotation - + is_expressed_in: + slot_uri: sepio:0000108 + any_of: + - range: Document + - range: Platform + 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 @@ -126,13 +267,6 @@ classes: 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 @@ -141,53 +275,30 @@ classes: 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 - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: sepio:Document - 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 - - attributes: - ended_at_time: - description: The prov:endedAtTime establishes the relationship between prov:Activity - and xsd:DateTime that allows one to specify the time when the activity ended. + 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 - alias: endedAtTime - range: datetime - started_at_time: - description: The prov:startedAtTime establishes the relationship between prov:Activity - and xsd:DateTime that allows one to specify the time when the activity started. + slot_uri: brainkb:hasAssertionText + alias: hasAssertionText + range: string + has_assertion_type: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - alias: startedAtTime - range: datetime - class_uri: prov:Activity - Agent: - 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. + range: AssertionType + class_uri: sepio:0000001 + AssertionSummary: + description: A summary is a brief statement or description of the main points, + especially as a conclusion to a work about the assertion. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema slots: - is_associated_with 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 - - 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. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - + 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. + slot_uri: brainkb:isAssociatedWith + range: Assertion attributes: has_assertion_summary: description: The brainkb:hasAssertionSummary property relates a brainkb:AssertionSummary @@ -199,11 +310,88 @@ classes: alias: hasAssertionSummary range: string class_uri: brainkb:AssertionSummary + AutomaticAssertion: + description: An assertion method executed automatically by machines without human + intervention. + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: AssertionMethod + class_uri: eco:0000203 + CellAnnotation: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Annotation + class_uri: brainkb:CellAnnotation + Description: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Annotation + class_uri: brainkb:Description + 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: Source + attributes: + id: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: datacite:identifier + range: uri + class_uri: iao:0000310 + 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: + - has_contributer + - has_summary + - is_described_by + - output_of + slot_usage: + has_contributer: + description: A relation between an information content entity and an agent + who made a contribution to its information content, or to its subsequent + modification or assessment. + slot_uri: sepio:0000150 + range: Agent + has_summary: + slot_uri: brainkb:hasSummary + range: EvidenceSummary + is_described_by: + slot_uri: sepio:0000178 + range: Document + output_of: + slot_uri: ro:0002353 + range: Activity + attributes: + has_evidence_category: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:hasEvidenceCategory + alias: hasEvidenceCategory + range: Categories + has_evidence_text: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:hasEvidenceText + alias: hasEvidenceText + range: string + has_evidence_type: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + slot_uri: brainkb:hasEvidenceType + alias: hasEvidenceType + range: EvidenceType + class_uri: sepio:0000002 EvidenceSummary: description: A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - + is_a: Annotation + slots: + - is_associated_with + 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.' + slot_uri: brainkb:isAssociatedWith + range: EvidenceLine attributes: has_evidence_summary: description: The brainkb:hasEvidenceSummary property relates a brainkb:EvidenceSummary @@ -215,42 +403,37 @@ classes: alias: hasEvidenceSummary range: string class_uri: brainkb:EvidenceSummary - AssertionMethod: - description: A means by which a statement is made about the entity + Group: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: eco:0000217 - DataAnnotation: + is_a: Agent + class_uri: foaf:Group + ManualAssertion: + description: An assertion method that involves human review. from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - - class_uri: brainkb:DataAnnotation - Evidence: + is_a: AssertionMethod + class_uri: eco:0000218 + Organization: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slots: - - used_in - - is_associated_with - 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 - + is_a: Group + class_uri: prov:Organization + Person: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Agent attributes: - has_evidence_category: - description: The brainkb:hasEvidenceCategory property relates brainkb:Evidence - and brainkb:Categories, specifying the classification or category that the - evidence belongs to. + contributer_type: from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasEvidenceCategory - alias: hasEvidenceCategory - 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. - from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema - slot_uri: brainkb:hasEvidenceText - alias: hasEvidenceText - range: string + slot_uri: datacite:contributerType + alias: contributerType + range: ContributerType + class_uri: prov:Person + Platform: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Source + class_uri: brainkb:Platform + SoftwareAgent: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + is_a: Agent + class_uri: prov:SoftwareAgent + Source: + from_schema: https://identifiers.org/brain-bican/assertion-evidence-schema + class_uri: dcterms:source diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv index 4e2bb737c..3b93718b0 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Classes.tsv @@ -1,11 +1,21 @@ -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 +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 +AutomaticAssertion AssertionMethod An assertion method executed automatically by machines without human intervention. eco:0000203 +CellAnnotation Annotation brainkb:CellAnnotation +Description Annotation brainkb:Description +Document Source A collection of information content entities intended to be understood together as a whole iao:0000310 +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 +EvidenceSummary Annotation A summary is a brief statement or description of the main points, especially as a conclusion to a work about the evidence. brainkb:EvidenceSummary +Group Agent foaf:Group +ManualAssertion AssertionMethod An assertion method that involves human review. eco:0000218 +Organization Group prov:Organization +Person Agent prov:Person +Platform Source brainkb:Platform +SoftwareAgent Agent prov:SoftwareAgent +Source dcterms:source \ 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..a404fb13f 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Prefixes.tsv @@ -8,4 +8,7 @@ schema http://schema.org/ brainkb https://brainkb.org/ prov http://www.w3.org/ns/prov# eco http://purl.obolibrary.org/obo/ECO_ -sepio http://purl.obolibrary.org/obo/SEPIO_ \ No newline at end of file +sepio http://purl.obolibrary.org/obo/SEPIO_ +ro http://purl.obolibrary.org/obo/RO_ +iao http://purl.obolibrary.org/obo/IAO_ +sio http://semanticscience.org/resource/SIO_ \ 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..5a9eafbea 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Relations.tsv @@ -1,12 +1,17 @@ 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 +> internal_separator: "|" +Activity was_associate_with Agent prov:wasAssociatedWith 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 +Assertion has_cell_annotation CellAnnotation +Assertion has_contributer Agent sepio:0000151 +Assertion has_description Description +Assertion has_summary AssertionSummary brainkb:hasSummary +Assertion is_expressed_in Document|Platform sepio:0000108 +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 +AssertionSummary is_associated_with Assertion brainkb:isAssociatedWith 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 +EvidenceLine has_contributer Agent sepio:0000150 A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment. +EvidenceLine has_summary EvidenceSummary brainkb:hasSummary +EvidenceLine is_described_by Document sepio:0000178 +EvidenceLine output_of Activity ro:0002353 +EvidenceSummary is_associated_with EvidenceLine brainkb:isAssociatedWith 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 diff --git a/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv b/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv index 8448840c8..f36b8c1af 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/Slots.tsv @@ -1,12 +1,18 @@ - 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 Alias BICAN UUID Aliases Definition Nullable Multivalued Permissible Values Data Type Data Examples Min Value Max Value Unit Statistical Type Subsets Notes +> class attribute alias slot_uri 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 +Annotation cell_annotation cellAnnotation brainkb:cellAnnotation FALSE string +Annotation description description brainkb:description FALSE string +Assertion has_assertion_category hasAssertionCategory brainkb:hasAssertionCategory 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_method hasAssertionMethod brainkb:hasAssertionMethod 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 +Assertion has_assertion_text hasAssertionText brainkb:hasAssertionText 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 +Assertion has_assertion_type FALSE AssertionType +AssertionSummary has_assertion_summary hasAssertionSummary brainkb:hasAssertionSummary 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 +Document id datacite:identifier FALSE uri +EvidenceLine has_evidence_category hasEvidenceCategory brainkb:hasEvidenceCategory Categories +EvidenceLine has_evidence_text hasEvidenceText brainkb:hasEvidenceText FALSE string +EvidenceLine has_evidence_type hasEvidenceType brainkb:hasEvidenceType FALSE EvidenceType +EvidenceSummary has_evidence_summary hasEvidenceSummary brainkb:hasEvidenceSummary 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 +Person contributer_type contributerType datacite:contributerType ContributerType \ 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..50458f92e 100644 --- a/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv +++ b/linkml-schema/source_assertion_evidence/gsheet_output/ValueSets.tsv @@ -1,40 +1,63 @@ -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 +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 +EvidenceType SupportingEvidence +EvidenceType DisputingEvidence +EvidenceType InconclusiveEvidence +ContributorType datacite:ContactPerson ContactPerson The main individual to contact regarding the resource datacite:ContactPerson +ContributorType datacite:DataCollector DataCollector Person responsible for collecting data. datacite:DataCollector +ContributorType datacite:DataCurator DataCurator Person responsible for managing and curating the data. datacite:DataCurator +ContributorType datacite:DataManager DataManager Person responsible for maintaining the data. datacite:DataManager +ContributorType datacite:Distributor Distributor Entity that distributes the data. datacite:Distributor +ContributorType datacite:Editor Editor Person responsible for overseeing the content's editorial aspects. datacite:Editor +ContributorType datacite:HostingInstitution HostingInstitution The institution hosting the data. datacite:HostingInstitution +ContributorType datacite:Producer Producer Person or organization responsible for producing the data. datacite:Producer +ContributorType datacite:ProjectLeader ProjectLeader Person who leads the project or study. datacite:ProjectLeader +ContributorType datacite:ProjectManager ProjectManager Person responsible for managing the project's administrative aspects. datacite:ProjectManager +ContributorType datacite:ProjectMember ProjectMember Member of the project team. datacite:ProjectMember +ContributorType datacite:RegistrationAgency RegistrationAgency Agency responsible for registering the data. datacite:RegistrationAgency +ContributorType datacite:RegistrationAuthority RegistrationAuthority Authority that oversees the registration process. datacite:RegistrationAuthority +ContributorType datacite:RelatedPerson RelatedPerson Person related to the data or study, but not directly contributing. datacite:RelatedPerson +ContributorType datacite:Researcher Researcher Person who conducts the research. datacite:Researcher +ContributorType datacite:ResearchGroup ResearchGroup A group of researchers working on the data or study. datacite:ResearchGroup +ContributorType datacite:RightsHolder RightsHolder Entity holding the rights to the data. datacite:RightsHolder +ContributorType datacite:Sponsor Sponsor Entity sponsoring the data or research. datacite:Sponsor +ContributorType datacite:Supervisor Supervisor Person supervising the research or project. datacite:Supervisor +ContributorType datacite:WorkPackageLeader WorkPackageLeader Leader responsible for a specific work package in a project. datacite:WorkPackageLeader \ No newline at end of file