Skip to content

IDMP Ontology Release 0.5.0
Compare
Choose a tag to compare
@mereolog mereolog released this 05 Oct 08:51
· 800 commits to master since this release
master_v0.5.0
3d1ef50
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

IDMP Ontology Release 0.5.0

Ontology Development in Details

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.

Qualitative Comparison To Previous Release

Overview

12 new ontologies were added:

  1. CellCeptExample
  2. CommonTerminologyCriteriaForAdverseEvents
  3. ISO1087-TerminologyScience*
  4. ISO1087-VocabularyForTermsAndDefinitions*
  5. ISO5218-RepresentationOfHumanSexes
  6. MedicalDictionaryForRegulatoryActivities
  7. MultipleVocabularyFacility*
  8. MVFtoSKOSMapping*
  9. NorthAmericanRegistrationAuthorities
  10. NorthAmericanRegulatoryAgencies
  11. PublicHealthInformationNetwork
  12. RolesAndCompositions*

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 changed:

Ontology Short Name Deleted Resources New Resources Modified Resources
AmlodipineExample 5 13 42
ChangeManagement 1 0  
DatesAndTimes* 0 9 8
Documents* 14 3 11
EUGovernmentEntitiesAndJurisdictions 0 0 2
EuropeanRegistrationAuthorities 0 2 10
EuropeanRegulatoryAgencies 0 0 5
EuropeanUnionClinicalTrialsRegister 0 0 18
GovernmentEntities 0 0 2
ISO11238-RegistrationAuthorities 62 0 4
ISO11238-Substances 3 72 160
ISO11615-MedicinalProducts 9 42 68
ISO21090-HarmonizedDatatypes 0 2 49
Organizations* 0 0 5
PartiesAndSituations* 9 1 30
ProductsAndServices 0 0 11
QlairaExample 1 0 48
QuantitiesAndUnits 3 5 20
RegistrationAuthorities 0 0 5
RegulatoryAgencies 0 0 4
StatisticalMeasures 0 0 6
SubstancesProductsOrganisationsReferentials 19 108 10
TerlipressinExample 0 3 29

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.

Details

idmp_different_ontologies_in_repository_versions.xlsx
idmp_different_resources_in_ontology_revisions.xlsx
idmp_different_axioms_for_same_subjects.txt

What's Changed

  • IDMP-599 Adding UC2-CQ1 Amlodipine to sparql and unit tests. by @stsilva-osthus in #414
  • IDMP-371 - Add RIM related SPOR Referentials: Shelf Life Type and Special Precautions for Storage by @ElisaKendall in #293
  • GitHub-278 - hasSimplifiedMolecularInputLineEntrySpecification is misleading and inconsistent by @ElisaKendall in #416
  • Update spor-organisations.rqg for ORG-code property by @konradkrebs1411 in #417
  • Update binding SPOR SMS by @aliariff in #421
  • IDMP-138 - Extension of Registration Authorities by @ElisaKendall in #230
  • IDMP-597 Revise therapeutic text by @tw-osthus in #397
  • Update spor-referentials.rqg by @konradkrebs1411 in #423
  • IDMP-615 UC3-CQ2 SPARQL query by @tw-osthus in #420
  • IDMP-614 add route of administration by @tw-osthus in #424
  • Update EDQM transformation by @konradkrebs1411 in #429
  • owl:sameAs added to ignored properties of test for deprecated properties by @mereolog in #427
  • IDMP-618 Augment Example Data for UC3 CQ 3 by @tw-osthus in #430
  • Mark out some OWL constraints as inappropriate for shaclisation by @mereolog in #415
  • IDMP-533 - Provide alignment/mapping for ISO "codedConcept" to the target IDMP-O Pattern for Reference Code Lists by @ElisaKendall in #426
  • GitHub-434 - cmns-ra:designates is equivalent to cmns-ra:isDesignatedBy by @ElisaKendall in #435
  • IDMP-633 - The definition of product role is too narrow by @ElisaKendall in #437
  • IDMP-636 - Extend the concept of structural representation in the ISO 11238 substances ontology to include molfile by @ElisaKendall in #443
  • improve competency questions by @MaFi2000 in #378
  • Update GSRS for Molfile and cleanup by @konradkrebs1411 in #446
  • IDMP-639 added other therapy specifics related by @tw-osthus in #447
  • Some missing unit tests added by @mereolog in #444
  • IDMP-642 - Integrate the latest revisions from the Commons ontologies, splitting parties and situations into two ontologies and renaming constituency to composition by @ElisaKendall in #450
  • IDMP-646 add CTCAE by @tw-osthus in #454
  • fix owl:class to owl:Class by @tw-osthus in #459
  • IDMP-650: Update SPOR URIs by @aliariff in #460
  • IDMP-533a - Provide alignment/mapping for ISO "codedConcept" to the target IDMP-O Pattern for Reference Code Lists by @ElisaKendall in #448
  • Fix to some typos in unit tests by @mereolog in #464
  • IDMP-GitHub-465 - idmp-spor:hasSPORTermDescription is language dependent by @ElisaKendall in #466
  • IDMP-647 moved MedDRA related concepts into separate ontology by @tw-osthus in #455
  • IDMP-635 - Augment the substance ontology with coverage for structurally diverse substances by @ElisaKendall in #441
  • IDMP-619 add UC3 CQ3 by @tw-osthus in #433
  • IDMP-650: Update SPOR URIs in EDQM by @aliariff in #461
  • Update unit_tests_run.yml to orchestrate cache rebuild by @mereolog in #467
  • GitHub-470 by @tw-osthus in #472
  • IDMP-641 add CDC - PHIN Race and Ethnicity with agencies by @tw-osthus in #451
  • IDMP-654 - Remove deprecated elements prior to 1.0 release by @ElisaKendall in #474
  • IDMP-655 - Revise the Commons ontologies and related changes for Commons 1.1 by @ElisaKendall in #476
  • Unit test extension for gsrs by @mereolog in #471
  • GitHub-478 fix namespace by @tw-osthus in #479
  • IDMP-643 add ISO 5128 representations of human sexes by @tw-osthus in #452
  • hasShelfLifeTimePeriod should expect a cmns-dt:Duration instead of cmns-dt:DatePeriod for medicinal products by @ElisaKendall in #483
  • Update IRIs in transformation scripts by @mereolog in #484
  • IDMP-656: Remove generated UUID in GSRS transformation by @aliariff in #477
  • IDMP-592 - Complete the preliminary modeling work required for Nucleic Acid, covering all detail provided in ISO 11238 by @ElisaKendall in #488
  • Some spelling typos fixed by @mereolog in #490
  • IDMP-638 add package item type by @tw-osthus in #489
  • IDMP-632 - Batch should be a subclass of Constituent rather than Product by @ElisaKendall in #486
  • IDMP-661 - Revise the Amlodipine example to match the current patterns for strength and reference strength by @ElisaKendall in #493
  • IDMP-662 - Revise the Terlipressin example to address hygiene issues by @ElisaKendall in #495
  • AboutIDMPDev-ReferenceIndividuals.rdf alignment with AboutIDMPDev.rdf by @ElisaKendall in #491

New Contributors

Full Changelog: master_v0.4.0...master_v0.5.0

Contributors

ElisaKendall, aliariff, and 5 other contributors
Assets 2
Loading