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This page sets out the criteria for reuse and identifies a number of candidates that may be considered for reuse for the IDMP MVP.

Criteria for Reuse

In order to make a reasonable judgement call on whether or not a consider a given ontology is suitable for reuse in an ontology, such as an IDMP ontology, that is intended for standardization the following criteria must be met:

  1. The ontology must MUST be publicly available and de-referenceable at its IRI (or planned/announced for near-term public release), either by a recognized international standards body, (e.g., ISO, Dublin Core, W3C, OMG, OASIS), or in a well-known ontology repository (such as the OBO Foundry, BioPortal, COLORE (University of Toronto), and the like).
  2. The ontology must should include a copyright statement and MUST include an indication of licensing, which must be open source and non-viral at a minimum. Preference for the MIT or CC by 4 licenses.
  3. The ontology must MUST be encoded in the W3C Web Ontology Language and conform with the OWL 2 Description Logics (DL) Profile or a more restrictive profile such as OWL 2 RL (see https://www.w3.org/TR/2012/REC-owl2-quick-reference-20121211/)
  4. The ontology must MUST conform with FAIR (findable, accessible, interoperable and reusable) policies as described in M.D. Wilkinson , M. Dumontier , Ij.J. Aalbersberg , G. Appleton , M. Axton , A. Baak , … & B. Mons . The FAIR guiding principles for scientific data management and stewardship. Scientific Data 3(2016), 160018. https://www.nature.com/articles/sdata201618.pdf. and refined in B. Mons , C. Neylon , J. Velterop , M. Dumontier , L.O. Bonino da Silva Santos & M.D. Wilkinson . Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services & Use 37 (2017), 49–56. https://content.iospress.com/download/information-services-and-use/isu824?id=information-services-and-use%2Fisu824.
  5. The ontology must MUST be well-documented (i.e., every element must class and property MUST have, at a minimum, a human-readable label and definition) and it must be syntactically correct (pass validation by the RDF Validator available at https://www.w3.org/RDF/Validator/, and by the EDM Council's RDF Serializer available at https://github.com/edmcouncil/rdf-toolkit) and logically consistent as demonstrated by at least one well-known reasoner, such as HermiT or Pellet.
  6. The ontology MUST NOT include a default IRI and MUST include an xml:base IRI.  Many ontologies posted to various repositories and other sites have a default IRI of the Web Ontology Language, for example, and actually modify the OWL language unwittingly. Tools such as Protege have been known to cause this without the knowledge of the authors, particularly in cases where the authors are new to working in OWL. Any ontology that does this is NOT acceptable for reuse in a standard.  If the ontology meets IDMP project requirements from a content perspective as well as the other criteria presented herein, we recommend reaching out to the authors and asking them to fix it.
  7. The ontology must MUST be actively maintained by an identifiable and active community of interest.  Any ontology that has not been revised within the last 12-18 months may not meet this requirement.
  8. The ontology must MUST be relatively self-contained and must not import any ontology that does not conform to 1-67, above. The ontology may reference, without importing, an ontology that does not conform to the criteria listed in 1-67, but only under limited circumstances and only if approved by the governance team.

These criteria do not provide any constraints on evaluating whether or not the content of an ontology is sufficiently fit for purpose to warrant reuse.  They simply state the absolute minimum criteria that must be met before consideration with respect to the content is appropriate.


Ontologies Considered for Reuse

Ontology IRIOntology DescriptionOntology SerialisationReuse PromoterReuse ProsReuse ConsReuse DecisionComment
Chemistry and Biology Ontologies






http://purl.obolibrary.org/obo/chebi.owlCHEBI - Chemical Entities of Biological Interestttl
  • well known
  • broadly reused
  • comprehensive

Just follow pattern(s):

  1. subclass hierarchy under CHEBI_24431 ("chemical entity")
THIS IS JUST A TEST/EXAMPLE RECOMMENDATION








Infrastructure and Metadata Ontologies






https://www.w3.org/TR/vocab-dcat-3/

DCAT - Data Catalog Vocabulary

The main item is DCAT - it's the W3C ontology for data catalogues, and we are close to a release of version 3.

This is a key component of several pieces of work on the development of FAIR data, including all of the EU Member States' efforts in open data,  industrial data spaces, and also catalogues of services etc.  It is also core to the DDI-CDI work that CODATA and the EOSC are involved in as part of CODATA's decadal programme of work.  Basically, it goes a long way to provide the "F".


Email from Pedro <pedro.win.stan@googlemail.com> to Gerhard Noelken.



https://www.omg.org/spec/COMMONS/Commons Ontology Library.rdf, .ttlElisa Kendall 
  • Meets all reuse criteria
  • Passes Hygiene testing
  • Provides building blocks needed for IDMP
  • Well-tested in FIBO and other OMG projects (MVF, API4KP at Mayo Clinic, etc.)
Published recentlyFull reuse








Citation Ontologies






https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903725/ (CiTo)CiTO, the Citation Typing Ontology?
  • Recommended in papers from the U.S. National Library of Medicine
  • Links to this ontology result in 404 errors
Do not reuse
http://bibliontology.com/ (BIBO)Bibliographic Ontology Specification.rdf
  • Has a following
  • Most recent revision was in November 2009
  • Some links to this ontology result in 404 errors
Do not reuse
https://sparontologies.github.io/fabio/current/fabio.html (FRBR)FaBiO, the FRBR-aligned Bibliographic Ontology.rdf, .ttl, JSON-LD, NT
  • Recommended by the Mayo Clinic
  • Well-documented
  • Comprehensive
  • Most recent revision was in 2019 (need to check that it is still maintained)
  • Under consideration for Reference Source / Reference Document reuse
See also https://www.ifla.org/current-ifla-standards/
https://sparontologies.github.io/frbr/current/frbr.htmlEssential FRBR in OWL2 DL.rdf
  • Recommended by the Mayo Clinic
  • Well-documented
  • Relatively compact
  • Most recent revision was in 2018 (need to check that it is still maintained)
  • Under consideration for Reference Source / Reference Document reuse


Reuse Types

Reuse DecisionComment
Do not reuse
Just follow pattern(s)
Partial reuseE.g., we use a single resource without importing the whole ontology
Full reuse owl:imports