From dd23d8d86fbfe2b777c0f5a9e028e6823fe2b492 Mon Sep 17 00:00:00 2001 From: ialarmedalien Date: Fri, 17 May 2024 11:24:31 -0700 Subject: [PATCH] Fixing a number of minor linting errors. Updating prefixes. Removing some cruft. Adding credit metadata source." --- schema/kbase/linkml/credit_metadata.yaml | 283 +++++++++++------------ 1 file changed, 131 insertions(+), 152 deletions(-) diff --git a/schema/kbase/linkml/credit_metadata.yaml b/schema/kbase/linkml/credit_metadata.yaml index c976a6d..e8c01d2 100644 --- a/schema/kbase/linkml/credit_metadata.yaml +++ b/schema/kbase/linkml/credit_metadata.yaml @@ -6,8 +6,8 @@ version: 0.0.1-commonmeta prefixes: bioportal: https://bioportal.bioontology.org/ontologies/ biolink: https://w3id.org/biolink/vocab/ - kbcm: https://kbase.github.io/credit_engine/ - CRediT: https://credit.niso.org/contributor-roles/ + kbcms: https://kbase.github.io/credit_engine/ + crcr: https://credit.niso.org/contributor-roles/ Crossref: https://crossref.org/ DataCite: https://purl.org/datacite/v4.4/ DOI: http://identifiers.org/doi/ @@ -15,9 +15,9 @@ prefixes: JGI: https://data.jgi.doe.gov/search/ linkml: https://w3id.org/linkml/ ORCID: http://identifiers.org/orcid/ - OSTI: https://www.osti.gov/biblio/ + OSTI.ARTICLE: https://www.osti.gov/biblio/ ROR: http://identifiers.org/ror/ - RDFS: http://www.w3.org/2000/01/rdf-schema# + rdfs: http://www.w3.org/2000/01/rdf-schema# schema: http://schema.org/ xsd: http://www.w3.org/2001/XMLSchema# imports: @@ -25,7 +25,7 @@ imports: default_range: string default_curi_maps: - semweb_context -default_prefix: kbcm +default_prefix: kbcms classes: @@ -54,8 +54,8 @@ classes: - value: Person - value: Organization exact_mappings: - - DataCite:attributes.contributors[].name_type - - DataCite:attributes.creators[].name_type + - DataCite:attributes.contributors.name_type + - DataCite:attributes.creators.name_type contributor_id: slot_uri: schema:identifier @@ -66,14 +66,14 @@ classes: - value: ORCID:0000-0001-9557-7715 - value: ROR:01znn6x10 exact_mappings: - - DataCite:attributes.contributors[].name_identifiers[].name_identifier - - DataCite:attributes.creators[].name_identifiers[].name_identifier + - DataCite:attributes.contributors.name_identifiers.name_identifier + - DataCite:attributes.creators.name_identifiers.name_identifier # from: DataCite:attributes.contributors[].name_identifiers[].name_identifier_scheme == 'ORCID' # via: f"ORCID:{src.attributes.contributors[].name_identifiers[].name_identifier.replace('https://orcid.org/', '')}" narrow_mappings: - ORCID:contributor.orcidId - - OSTI:author.orcid_id - - OSTI:contributor.orcid_id + - OSTI.ARTICLE:author.orcid_id + - OSTI.ARTICLE:contributor.orcid_id - Crossref:message.project.funding.funder.name name: @@ -86,17 +86,17 @@ classes: required: true related_mappings: # these have the names comma-separated and inverted - - DataCite:attributes.creators[].name - - DataCite:attributes.contributors[].name + - DataCite:attributes.creators.name + - DataCite:attributes.contributors.name exact_mappings: - - JGI:organisms[].pi.name + - JGI:organisms.pi.name - ORCID:name close_mappings: - - OSTI:author - # from OSTI:author + - OSTI.ARTICLE:author + # from OSTI.ARTICLE:author # via: f"{src.author.first_name} {src.author.last_name}" - - OSTI:contributor - # from OSTI:contributor + - OSTI.ARTICLE:contributor + # from OSTI.ARTICLE:contributor # via: f"{src.contributor.first_name} {src.contributor.last_name}" given_name: @@ -106,8 +106,8 @@ classes: - value: Helena - value: Hubert George related_mappings: - - DataCite:attributes.contributors[].givenName - - DataCite:attributes.creators[].givenName + - DataCite:attributes.contributors.givenName + - DataCite:attributes.creators.givenName family_name: description: The family name(s) of the contributor. @@ -116,8 +116,8 @@ classes: - value: Bonham Carter - value: Wells related_mappings: - - DataCite:attributes.contributors[].familyName - - DataCite:attributes.creators[].familyName + - DataCite:attributes.contributors.familyName + - DataCite:attributes.creators.familyName affiliations: slot_uri: schema:affiliation @@ -126,23 +126,23 @@ classes: multivalued: true range: Organization related_mappings: - - DataCite:attributes.contributors[].affiliation[] + - DataCite:attributes.contributors.affiliation # from: DataCite:attributes.contributors[].affiliation[] # via: { # organization_name: src.attributes.contributors[].affiliation[].name # } - - DataCite:attributes.creators[].affiliation[] + - DataCite:attributes.creators.affiliation # from: DataCite:attributes.creators[].affiliation[] # via: { # organization_name: src.attributes.creators[].affiliation[].name # } - - JGI:organisms[].pi.institution + - JGI:organisms.pi.institution # from: JGI:organisms[].pi.institution # via: { # organization_name: src.organisms[].pi.institution #} narrow_mappings: - - OSTI:contributor.affiliation_name + - OSTI.ARTICLE:contributor.affiliation_name # via { organization_name: src.contributor.affiliation_name } contributor_roles: @@ -152,16 +152,16 @@ classes: # inlined_as_list: true multivalued: true exact_mappings: - - DataCite:attributes.contributors[].contributor_type - - DataCite:attributes.creators[].contributor_type + - DataCite:attributes.contributors.contributor_type + - DataCite:attributes.creators.contributor_type related_mappings: - - JGI:organisms[].pi + - JGI:organisms.pi # from: JGI:organisms[].pi # via: "DataCite:ProjectLeader" close_mappings: # TODO: mappings to CRediT/DataCite roles - ORCID:contributor.role - - OSTI:contributor.contributorType + - OSTI.ARTICLE:contributor.contributorType CreditMetadataEntry: @@ -232,8 +232,7 @@ classes: inlined_as_list: true multivalued: true examples: - - value: - - "Credit metadata generated automatically from DOI:10.13039/100000015" + - value: "This comment adds a lot of extra value!" content_url: description: The URL of the content of the resource. @@ -252,17 +251,26 @@ classes: - DataCite:attributes.contributors - DataCite:attributes.creators - ORCID:contributors - - OSTI:contributors - - OSTI:authors - - JGI:organisms[].pi + - OSTI.ARTICLE:contributors + - OSTI.ARTICLE:authors + - JGI:organisms.pi + + credit_metadata_source: + description: A list of CURIEs, URIs, or free text entries denoting the source of the credit metadata. + inlined_as_list: true + multivalued: true + examples: + - value: "https://figshare.com/articles/dataset/Blue_Hole_Metagenome-assembled_Genomes/12644081" + - value: "DataCite" + - value: DOI:10.13039/100000015 dates: description: A list of relevant lifecycle events for the resource. Note that these dates apply only to the resource itself, and not to the creation or update of the credit metadata record for the resource. inlined_as_list: true multivalued: true range: EventDate - examples: - - value: { date: 2022-05-10, event: available } + # examples: + # - value: { date: 2022-05-10, event: available } close_mappings: - DataCite:attributes.published # from DataCite:attributes.published @@ -270,14 +278,14 @@ classes: - DataCite:attributes.updated # from DataCite:attributes.updated # via { date: src.attributes.updated, event: 'updated' } - - DataCite:attributes.dates[] + - DataCite:attributes.dates # from DataCite:attributes.dates[] # via { date: src.attributes.dates[].date, event: src.attributes.dates[].dateType } - ORCID:publicationDate # from: ORCID:publicationDate # via { date: src.publicationDate, event: 'available' } - - OSTI:publication_date - # from: OSTI:publication_date + - OSTI.ARTICLE:publication_date + # from: OSTI.ARTICLE:publication_date # via { date: src.publication_date, event: 'available' } - Crossref:message.deposited # from: Crossref:message.deposited @@ -298,7 +306,7 @@ classes: close_mappings: - DataCite:attributes.funding_references - Crossref:Message.project.funding - - OSTI:awards + - OSTI.ARTICLE:awards identifier: slot_uri: schema:identifier @@ -315,14 +323,14 @@ classes: - DataCite:id # from: DataCite:id # via: f"DOI:{src.id}" - - JGI:organisms[].grouped_by + - JGI:organisms.grouped_by # from src.organisms[].grouped_by # via: src.organisms[].files[][src.organisms[].grouped_by] narrow_mappings: - - OSTI:osti_id - # from: OSTI:osti_id - # via: f"OSTI:{src.osti_id}" - - OSTI:doi + - OSTI.ARTICLE:osti_id + # from: OSTI.ARTICLE:osti_id + # via: f"OSTI.ARTICLE:{src.osti_id}" + - OSTI.ARTICLE:doi - ORCID:doi # it should be possible to generate an URL from a curie - ORCID:url @@ -336,21 +344,21 @@ classes: All data published at KBase is done so under a Creative Commons 0 or Creative Commons 4.0 license. - examples: - - value: { id: "CC-BY-NC-ND-4.0" } - - value: { id: "MIT OR Apache-2.0" } - - value: { url: "https://jgi.doe.gov/user-programs/pmo-overview/policies/" } + # examples: + # - value: { id: "CC-BY-NC-ND-4.0" } + # - value: { id: "MIT OR Apache-2.0" } + # - value: { url: "https://jgi.doe.gov/user-programs/pmo-overview/policies/" } exact_mappings: - biolink:license related_mappings: - DataCite:attributes.rights_list - provider: - description: The provider of the resource. This can be a DOI registration agency or a repository. - range: ProviderType - examples: - - value: DataCite - - value: OP + # provider: + # description: The provider of the resource. This can be a DOI registration agency or a repository. + # range: Organization + # examples: + # - value: DataCite + # - value: OP publisher: description: The publisher of the resource. For a dataset, this is the repository where it is stored. @@ -359,7 +367,7 @@ classes: range: Organization narrow_mappings: - ORCID:url - - OSTI:site_url + - OSTI.ARTICLE:site_url related_identifiers: description: Other resolvable persistent unique IDs related to the resource. @@ -371,13 +379,13 @@ classes: - DataCite:attributes.related_identifiers - DataCite:attributes.alternate_identifiers - ORCID:externalIds - - OSTI:related_identifiers + - OSTI.ARTICLE:related_identifiers narrow_mappings: - ORCID:doi # from ORCID:doi # via: { id: f"DOI:{src.doi}" } - - OSTI:doi - # from: OSTI:doi + - OSTI.ARTICLE:doi + # from: OSTI.ARTICLE:doi # via: { id: f"DOI:{src.doi}"} resource_type: @@ -386,14 +394,14 @@ classes: range: ResourceType required: true exact_mappings: - # OSTI:DA is used for dataset - - OSTI:product_type + # OSTI.ARTICLE:DA is used for dataset + - OSTI.ARTICLE:product_type # ORCID:data-set - - OSTI:workType + - OSTI.ARTICLE:workType # see DataCite:attributes.types - DataCite:attributes.types.schema_org narrow_mappings: - - OSTI:dataset_type + - OSTI.ARTICLE:dataset_type examples: - value: dataset @@ -404,22 +412,22 @@ classes: range: Title required: true exact_mappings: - - DataCite:attributes.titles[] + - DataCite:attributes.titles - ORCID:title # from: ORCID:title # via: [{ title: src.title }] - - OSTI:title - # from: OSTI:title + - OSTI.ARTICLE:title + # from: OSTI.ARTICLE:title # via: [{ title: src.title }] - examples: - - value: - - title: Amaranthus hypochondriacus genome - - value: - - title: Геном амаранта ипохондрического - title_type: translated_title - - value: - - title: I know what genome you sequenced last summer - title_type: alternative_title + # examples: + # - value: + # - title: Amaranthus hypochondriacus genome + # - value: + # - title: Геном амаранта ипохондрического + # title_type: translated_title + # - value: + # - title: I know what genome you sequenced last summer + # title_type: alternative_title url: description: The URL of the resource. @@ -502,11 +510,11 @@ classes: slot_uri: schema:identifier description: Code for the grant, assigned by the funder exact_mappings: - - DataCite:attributes.funding_references[].award_number + - DataCite:attributes.funding_references.award_number - Crossref:message.award narrow_mappings: - - OSTI:award_doi - - OSTI:award_number + - OSTI.ARTICLE:award_doi + - OSTI.ARTICLE:award_number examples: - value: '1296' - value: CBET-0756451 @@ -516,7 +524,7 @@ classes: slot_uri: schema:name description: Title for the grant exact_mappings: - - DataCite:attributes.funding_references[].award_title + - DataCite:attributes.funding_references.award_title examples: - value: Metagenomic analysis of the rhizosphere of three biofuel crops at the KBS intensive site @@ -524,9 +532,9 @@ classes: slot_uri: schema:url description: URL for the grant exact_mappings: - - DataCite:attributes.funding_references[].award_url + - DataCite:attributes.funding_references.award_url close_mappings: - - OSTI:award_doi + - OSTI.ARTICLE:award_doi range: uriorcurie pattern: "^[a-zA-Z0-9.-_]+:\\S" examples: @@ -537,35 +545,6 @@ classes: description: The funder for the grant or award range: Organization - # funder_id: - # # grant.funder = { identifier: funder_id, name: funder_name } - # slot_uri: schema:identifier - # description: Persistent unique identifier for the funder in the format : - # exact_mappings: - # - DataCite:attributes.funding_references[].funder_identifier - # - Crossref:message.project.funding.funder.id.id - # range: uriorcurie - # pattern: "^[a-zA-Z0-9.-_]+:\\S" - # examples: - # - value: DOI:10.13039/100000015 - # - value: ISNI:0000000405337147 - # - value: ROR:04xm1d337 - - # funder_name: - # # grant.funder = { identifier: funder_id, name: funder_name } - # slot_uri: schema:name - # description: Common name for the funder - # required: true - # exact_mappings: - # - DataCite:attributes.funding_references[].funder_name - # - Crossref:message.project.funding.funder.name - # - OSTI:sponsoring_organization - # - OSTI:award.funder_name - # examples: - # - value: Joint Genome Institute - # - value: National Science Foundation - # - value: US DOE Office of Science (SC), Biological and Environmental Research (BER) - License: description: License information for the resource. @@ -606,8 +585,8 @@ classes: - value: ISNI:0000000123423717 - value: CrossrefFunder:100000015 exact_mappings: - - DataCite:attributes.contributors[].affiliation.affiliation_identifier - - DataCite:attributes.creators[].affiliation.affiliation_identifier + - DataCite:attributes.contributors.affiliation.affiliation_identifier + - DataCite:attributes.creators.affiliation.affiliation_identifier range: uriorcurie pattern: "^[a-zA-Z0-9.-_]+:\\S" @@ -616,10 +595,10 @@ classes: description: Common name of the organization; use the name recommended by ROR if possible. required: true exact_mappings: - - DataCite:attributes.contributors[].affiliation.name - - DataCite:attributes.creators[].affiliation.name - - OSTI:research_organization - - JGI:organisms[].pi.institution + - DataCite:attributes.contributors.affiliation.name + - DataCite:attributes.creators.affiliation.name + - OSTI.ARTICLE:research_organization + - JGI:organisms.pi.institution examples: - value: KBase - value: Lawrence Berkeley National Laboratory @@ -650,17 +629,17 @@ classes: - value: HGNC:7470 exact_mappings: - DataCite:attributes.identifier.value - - DataCite:attributes.alternate_identifiers[] + - DataCite:attributes.alternate_identifiers # from: DataCite:attributes.alternate_identifiers[] # via: f"{src.attributes.alternate_identifiers[].alternate_identifier_type}:{src.attributes.alternate_identifiers[].alternate_identifier}" - - DataCite:attributes.related_identifiers[] + - DataCite:attributes.related_identifiers # from: DataCite:attributes.related_identifiers[] # via: f"{src.attributes.related_identifiers[].related_identifier_type}:{src.attributes.related_identifiers[].related_identifier}" - - DataCite:attributes.identifiers[] + - DataCite:attributes.identifiers # from: DataCite:attributes.identifiers[] # via: f"{src.attributes.identifiers[].identifier_type}:{src.attributes.identifiers[].identifier}" related_mappings: - - OSTI:site_url + - OSTI.ARTICLE:site_url range: uriorcurie pattern: "^[a-zA-Z0-9.-_]+:\\S" @@ -668,7 +647,7 @@ classes: slot_uri: schema:description description: Description of that entity. exact_mappings: - - OSTI:description + - OSTI.ARTICLE:description examples: - value: Amaranthus hypochondriacus genome - value: This data analysis workflow demonstrates how to process a metagenome to identify viruses using VirSorter. Then, provides taxonomic classification using vConTACT2. @@ -679,7 +658,7 @@ classes: For example, when a PermanentID class is used to represent objects in the CreditMetadata field 'related_identifiers', the 'relationship_type' field captures the relationship between the CreditMetadata and this ID. range: RelationshipType exact_mappings: - - DataCite:attributes.related_identifiers[].relation_type + - DataCite:attributes.related_identifiers.relation_type Title: @@ -809,60 +788,60 @@ enums: meaning: DataCite:Other title: other description: Any person or institution making a significant contribution to the development and/or maintenance of the resource, but whose contribution does not "fit" other controlled vocabulary for contributorType. Could be a photographer, artist, or writer whose contribution helped to publicize the resource (as opposed to creating it), a reviewer of the resource, someone providing administrative services to the author (such as depositing updates into an online repository, analysing usage, etc.), or one of many other roles. - CRediT:conceptualization: - meaning: CRediT:conceptualization + crcr:conceptualization: + meaning: crcr:conceptualization title: conceptualization description: Ideas; formulation or evolution of overarching research goals and aims. - CRediT:data-curation: - meaning: CRediT:data-curation + crcr:data-curation: + meaning: crcr:data-curation title: data curation description: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. - CRediT:formal-analysis: - meaning: CRediT:formal-analysis + crcr:formal-analysis: + meaning: crcr:formal-analysis title: formal analysis description: Application of statistical, mathematical, computational, or other formal techniques to analyze or synthesize study data. - CRediT:funding-acquisition: - meaning: CRediT:funding-acquisition + crcr:funding-acquisition: + meaning: crcr:funding-acquisition title: funding acquisition description: Acquisition of the financial support for the project leading to this publication. - CRediT:investigation: - meaning: CRediT:investigation + crcr:investigation: + meaning: crcr:investigation title: investigation description: Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection. - CRediT:methodology: - meaning: CRediT:methodology + crcr:methodology: + meaning: crcr:methodology title: methodology description: Development or design of methodology; creation of models. - CRediT:project-administration: - meaning: CRediT:project-administration + crcr:project-administration: + meaning: crcr:project-administration title: project administration description: Management and coordination responsibility for the research activity planning and execution. - CRediT:resources: - meaning: CRediT:resources + crcr:resources: + meaning: crcr:resources title: resources description: Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools. - CRediT:software: - meaning: CRediT:software + crcr:software: + meaning: crcr:software title: software description: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. - CRediT:supervision: - meaning: CRediT:supervision + crcr:supervision: + meaning: crcr:supervision title: supervision description: Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team. - CRediT:validation: - meaning: CRediT:validation + crcr:validation: + meaning: crcr:validation title: validation description: Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. - CRediT:visualization: - meaning: CRediT:visualization + crcr:visualization: + meaning: crcr:visualization title: visualization description: Preparation, creation and/or presentation of the published work, specifically visualization/data presentation. - CRediT:writing-original-draft: - meaning: CRediT:writing-original-draft + crcr:writing-original-draft: + meaning: crcr:writing-original-draft title: writing, original draft description: Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation). - CRediT:writing-review-editing: - meaning: CRediT:writing-review-editing + crcr:writing-review-editing: + meaning: crcr:writing-review-editing title: writing, review and/or editing description: Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision -- including pre- or post-publication stages. reachable_from: @@ -1148,7 +1127,7 @@ enums: meaning: Crossref:Replaces title: replaces Unknown: - meaning: Relationship type is unknown + # meaning: Relationship type is unknown title: unknown reachable_from: source_ontology: bioportal:DATACITE-VOCAB