Ontology Development

Summary

A number of significant extensions were added in the Q2 0.4.0 release, including (1) the ability to answer new competency questions, (2) integration of additional data sources as well as improved use of existing sources for better question answering / mapping, (3) increased coverage more generally of some areas of the ISO standards, (4) integration of new examples, and (5) refinements to improve usability and address user feedback. Some of the major changes made include the following.

1. New Competency Question Answering - the primary additions in Q2 involved UC3 - Therapeutic Indications. See /wiki/spaces/IDMP/pages/7244594 for details. Preliminary coverage was added in Q2, and additional competency questions will be supported in Q3. Note that one of the more important changes with respect to question answering is that we now use the competency questions and sample answers as part of regression testing. Three of our example ontologies will be continuously updated in order to fully support this testing and provide examples that can be used by the pharma participants as good examples for mapping purposes: Amlodipine, Terlipressin, and the EU Clinical Trials example, all of which are in GitHub under /EXT/Examples. 
2. Data Source Integration and Support – in Q2 we've added preliminary support for EDQM and have continued to improve mappings and support for GSRS and SPOR. Note that the IRIs in the SPOR data are not consistent with the guidelines for IRIs for use in RDF/OWL, so we have ongoing challenges there are representing the content on the Pistoia site as a work-around.
3. Increased Coverage of the ISO Standards – the main changes to the ontologies this quarter include completion of coverage of the forthcoming Annex L to the ISO 11238 implementation guide (ISO 19844) at the substance and chemical substance levels. We've also increased coverage of ISO 11615 with respect to ingredients and related concepts, which led to some of the renaming indicated by deprecated resources (which are mapped to their replacements). We also added some preliminary content for ISO 11239, Pharmaceutical Dose Forms, pending review of the revised standard once it is publicly available.
4. New Examples – The documentation includes a number of examples that are not covered in the ontology per se, but one new example ontology covers the Qlaira content from the EMA PMS Implementation Guide, Chapter 8. Existing examples have been extended as well, to include new content for testing the latest additions and updates in the ontologies.
5. Usability – see the detailed GitHub revisions for usability related revisions.

Deprecated Resources

The following 13 resources are considered as deprecated in 0.4.0.

Comparison with the 0.3.0 version of the IDMP Ontology

By the Numbers

Three new ontologies were added:

1. StatisticalMeasures
2. ISO11238-Substances-DeprecatedElements
3. StructuredCollections

The following ontologies were changed:

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