Open Bio Ontologies

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Published November 22, 2022 | Version v0.1.55
Software Open

INCATools/ontology-access-kit: v0.1.55

Authors/Creators

  • 1. Lawrence Berkeley National Laboratory
  • 2. Harvard Medical School
  • 3. @TB-Modeling
  • 4. SIB Swiss Institute of Bioinformatics
  • 5. LBNL
  • 6. Leibniz-Institut für Katalyse e.V.
  • 7. Queen Mary University of London
  • 8. Lawrence Berkeley National Lab
  • 9. semanticly Ltd

Description

Enhanced ORCID validation

This release restricts the OAK OBO Ontology Metadata schema (https://incatools.github.io/ontology-access-kit/datamodels/ontology-metadata/index.html) to require the range of dcterms:contributor and dcterms:creator to be a valid ORCID, specifically:

  • the RDF, the value should be a resource with an orcid https (not http) URI
  • in the underlying sql database orcid https URLs are contracted to orcid: CURIEs

This release is timely as there is a new resource from @cthoyt, https://github.com/cthoyt/wikidata-orcid-ontology/, which provides an OWL ABox ontology of orcid instances. Note that direct joining only works if the exact same URIs are used in metadata.

The validator will now make use of regex patterns; as an example, try running:

alias cl='runoak -i sqlite:obo:cl`
cl validate -o cl-validate.tsv

A sample of the 2k results:

type subject severity instantiates predicate object object_str source info

http://www.w3.org/ns/shacl#PatternConstraintComponent|CL:0002638|ERROR|None|dcterms:contributor|None|None|None|Pattern violation: contributor = http://orcid.org/0000-0001-7258-9596 does not conform to orcid:\d{4}-\d{4}-\d{4}-\d{3}[0-9X]| |http://www.w3.org/ns/shacl#PatternConstraintComponent|CL:0017010|ERROR|None|dcterms:contributor|None|None|None|Pattern violation: contributor = http://orcid.org/0000-0003-2473-2313 does not conform to orcid:\d{4}-\d{4}-\d{4}-\d{3}[0-9X]| |http://www.w3.org/ns/shacl#PatternConstraintComponent|CL:0017011|ERROR|None|dcterms:contributor|None|None|None|Pattern violation: contributor = http://orcid.org/0000-0003-2473-2313 does not conform to orcid:\d{4}-\d{4}-\d{4}-\d{3}[0-9X]| |http://www.w3.org/ns/shacl#ClosedConstraintComponent|CL:0700009|ERROR|None|dce:contributor|None|None|None|Unknown pred (dce:contributor) = orcid:0000-0002-1773-2692 None| |http://www.w3.org/ns/shacl#ClosedConstraintComponent|CL:4030001|ERROR|None|dce:contributor|None|None|None|Unknown pred (dce:contributor) = orcid:0000-0002-1773-2692 None|

This tells us that CL is using some http ORCIDs, rather than https

(it also tells us CL is also incorrectly using some dce properties rather than dcterms)

What's Changed

Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.1.54...v0.1.55

Files

INCATools/ontology-access-kit-v0.1.55.zip

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Additional details

Related works

Is supplement to
https://github.com/INCATools/ontology-access-kit/tree/v0.1.55 (URL)