Ontology Development

Summary

Major accomplishments in the 0.5.0 release range from significant improvements in representation of controlled vocabularies, including but not limited to EMA SPOR vocabularies, to extensions in a number of areas related to the ISO 11238 Substances and ISO 11615 Medicinal Products ontologies.

The revised model for controlled vocabularies extends the Object Management Group's (OMG) Commons Ontology Library with the OMG Multiple Vocabulary Facility (MVF) ontologies, designed specifically to support controlled vocabularies, taxonomies, and nomenclature representation based on ISO 1087. The Commons Ontology Library was also updated to incorporate ontologies that have been revised or added in the 1.1 revision of that standard.

Several controlled vocabularies were added in addition to better support for EMA SPOR, including support for MedDRA vocabularies, Common Terminology Criteria for Adverse Events, ISO 5218 vocabulary for the representation of human sexes, and content from the Public Health Information Network. Content related to the US and EU regulatory agencies and repositories was also extended and US-specific content moved to a new North American module rather than in the main ISO Regulatory Agencies ontology, which ultimately will be limited to international bodies and repositories such as the WHO.

Additional content related to ISO 11238 includes complete coverage for nucleic acids and structurally diverse substances, as well as for more basic concepts such as properties of substances that apply to multiple kinds of substances. Updates to the ISO 11615 Medicinal Products ontology include support for therapeutic indications as well as packaging related details. Most examples were extended to cover the new content and the CellCeptExample was added to support additional competency questions.

Deprecated Resources

All deprecated resources, see Release Notes 0.4.0, were removed in preparation for the IDMP-O 1.0 release.

Comparison with the 0.4.0 version of the IDMP Ontology

Quantitative View

12 new ontologies were added:

Ontologies marked with '*' are OMG-related, either Commons Ontology Library v1.1 or Multiple Vocabulary Facility (MVF).  As noted above, the ISO11238-Substances-DeprecatedElements ontology, which was managed independently in order to facilitate elimination, was deleted.

The following ontologies were revised and/or extended:

Ontologies marked with '*' are OMG-related, modified as part of the Commons Ontology Library v1.1 release.  Note that certain OMG-specific ontologies were simplified, although some of the content, such as the concepts related to regulatory reporting, will come back in a separate ontology in the 1.2 revision of the Commons library. Elements that were eliminated from the Quantities and Units ontology were renamed to reflect the fact that they actually define scalar quantities. An upcoming addition to the library will cover arrays, tensors, and vectors as well as the related tensor and vector quantities, and a reference library of over 700 units will be generated from the new OMG SysML v2 library of quantities and units. We look forward to being able to use that, given that it is OWL DL compliant, which the QUDT ontology is not, and other ontologies for units tend to be incomplete.

Detailed View

In order to see the differences in axioms use the GitHub release comparison or IDMP viewer 'Compare versions' functionality:

See below an example of some differences in the description of idmp-sub:Substance