IDMP Ontology Release 0.4.0
IDMP Ontology Release 0.4.0
Ontology Development in Details
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.
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New Competency Question Answering - the primary additions in Q2 involved UC3 - Therapeutic Indications. See UC3: Use Case Therapeutic Indication 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.
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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.
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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.
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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.
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Usability – see the detailed GitHub revisions for usability related revisions.
Qualitative Comparison To Previous Release
Overview
Three new ontologies were added:
- StatisticalMeasures
- ISO11238-Substances-DeprecatedElements
- StructuredCollections
The following ontologies were changed:
| Ontology Short Name | New Resources | Deleted Resources | Modified Resources |
|---|---|---|---|
| AmlodipineExample | 9 | 4 | 14 |
| ChangeManagement | 0 | 0 | 1 |
| Documents | 0 | 0 | 1 |
| EasternEuropeGovernmentEntitiesAndJurisdictions | 0 | 0 | 2 |
| EUGovernmentEntitiesAndJurisdictions | 0 | 0 | 3 |
| EuropeanUnionClinicalTrialsRegister | 0 | 0 | 1 |
| ISO11238-RegistrationAuthorities | 6 | 0 | 2 |
| ISO11238-Substances | 155 | 9 | 53 |
| ISO11239-PharmaceuticalDoseForms | 18 | 0 | 4 |
| ISO11615-MedicinalProducts | 42 | 0 | 42 |
| ISO11616-PharmaceuticalProducts | 2 | 0 | 1 |
| Organisations | 0 | 0 | 2 |
| PartiesAndSituations | 0 | 0 | 1 |
| ProductsAndServices | 0 | 0 | 20 |
| QlairaExample | 74 | 74 | 1 |
| QuantitiesAndUnits | 1 | 0 | 1 |
| RegistrationAuthorities | 0 | 0 | 4 |
| RegulatoryAgencies | 0 | 0 | 2 |
| SubstancesProductsOrganisationsReferentials | 0 | 0 | 1 |
| TerlipressinExample | 2 | 2 | 13 |
| WesternEuropeGovernmentEntitiesAndJurisdictions | 0 | 0 | 1 |
Details
idmp_different_axioms_for_same_subjects.txt
idmp_different_ontologies_in_repository_versions.xlsx
idmp_different_resources_in_ontology_revisions.xlsx
Deprecated Resources
The following 13 resources are considered as deprecated in 0.4.0.
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/RegulatoryContext-FoodAndDrugAdministrationPatentExclusive
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/ActiveIngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/AdjuvantRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/ExcipientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/InactiveIngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/IngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/SubstanceConstituency
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/hasActiveIngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/hasIngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/ProductConstituency
https://spec.pistoiaalliance.org/idmp/ontology/META/ChangeManagement/Specification
https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/L001
https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/Montenegrin
What's Changed
- IDMP-466 - PhP and MI are disjoint classes by @ElisaKendall in #333
- explicit json diff on failed unit test by @tw-osthus in #337
- IDMP-512 - Need the concept of an ordered collection to define polymers by @ElisaKendall in #339
- IDMP-483 - Complete the set of optional fields from Annex L: for Substance and Chemical Substance (excluding the reference information from Figure 16) by @ElisaKendall in #336
- IDMP-525 - Release the ISO 11615 Medicinal Products Ontology by @ElisaKendall in #343
- bugfix for #344 by @tw-osthus in #345
- Fix URL link by @aliariff in #352
- IDMP-514 - Review and Correct the target role for GSRS "Active Moiety (Exclusivity)" used in Aripiprazole Lauroxil by @ElisaKendall in #342
- IDMP-510 - Moiety has no restrictions for "moiety identifier" and "moiety name" by @ElisaKendall in #348
- BugFix-346 - Ontology StructuredCollections.rdf by @ElisaKendall in #349
- IDMP-531 - Add concepts for WHO case/demo e.g., release characteristics by @ElisaKendall in #357
- GSRS: Avoid obsolete triples by @aliariff in #359
- IDMP-528 - The definition of physical substance in the ISO 11238 ontology should correspond to the precise wording from paragraph 3.84 by @ElisaKendall in #351
- IDMP-527 - Revise the CMNS/ProductsAndServices ontology to reflect the latest discussions with GS1 by @ElisaKendall in #364
- IDMP-538 - Complete the definition of pharmaceutical dose form for the WHO demonstration by @ElisaKendall in #361
- IDMP-549 - Augment the definition of pharmaceutical dose form with two additional properties by @ElisaKendall in #366
- IDMP-304 - Complete the set of roles corresponding to the table in ISO/TS 20443, pages 112-113 (ingredient roles) by @ElisaKendall in #370
- Update GSRS transformation script for Active Moiety (Exclusivity) by @aliariff in #358
- IDMP-541 - Connect Manufactured Item and Pharmaceutical Product via Transformation by @ElisaKendall in #372
- IDMP-542 - Add script to retrieve all EDQM lists by @aliariff in #373
- IDMP-540 - Complete the set of optional fields from Annex L: for Substance and Chemical Substance for Modification (Figure 15) by @tw-osthus in #375
- IDMP-539 Complete the set of optional fields from Annex L: for Substance and Chemical Substance for Figure 14 Information model for structure and isotope by @tw-osthus in #377
- IDMP-417: Add test for GSRS by @aliariff in #374
- IDMP-561 - Augment the IDMP ontologies to cover therapeutic indications by @tw-osthus in #379
- IDMP-395 - Check definition for 'marketing authorization holder' by @ElisaKendall in #381
- IDMP-522 - Complete the set of optional fields from Annex L: for Substance and Chemical Substance for Reference Information (Figure 16) by @ElisaKendall in #355
- IDMP-581 The MedDRA individuals for the Amlodipine Example cause punning by @tw-osthus in #386
- Legal punning in d9ececf commit in master by @ElisaKendall in #390
- Add uuids to catalog files by @mereolog in #389
- IDMP-550 - Document the modelling pattern for Marketing Authorization by @ElisaKendall in #392
Full Changelog: master_v0.3.0...master_v0.4.0
