IDMP Ontology Release 1.2.0

Ontology Development in Details

This quarter our focus was on bug fixing, usability, and simplification, in preparation for extensions supporting additional use cases in Q3. Analysis done over several weeks led to the conclusion that certain constructs, including some related to packaging, could be simplified for ease of use as well as to increase representation and reasoning efficiency. Because of the complexity involved not only in the ontology but in the IDMP standards, we are unwinding certain parts of the ontology incrementally rather than in a single issue. Simplification efforts will continue into Q3, when we will also be adding a number of new constructs. New work will involve fleshing out details for concepts needed for use cases such as the EMA PMS Data Alignment PoC, filling in gaps where there are missing attributes, for example, for some parts of the model.

Qualitative Comparison To Previous Release

Overview

No ontology was added or deleted.

The following ontologies were revised and/or extended:

Details

idmp_different_resources_in_ontology_revisions.xlsx

idmp_different_axioms_for_same_subjects.txt

What's Changed

• IDMP-GitHub-564 - Textual values for substance names by @ElisaKendall in #566
• IDMP-GitHub-567 - Two typos in reference to rdfs:subPropertyOf by @ElisaKendall in #568
• IDMP-GitHub-573 - Correct a wrong prefix for reference source by @ElisaKendall in #574
• IDMP-GitHub-571 - Simplify the licensing definitions in Commons to facilitate mapping to BFO by @ElisaKendall in #572
• hygiene tests added for prefLabels by @mereolog in #575
• IDMP-734 - Add skos:prefLabel to terms that have multilingual labels by @ElisaKendall in #570
• IDMP-720 - Few SHACL examples added for discussion by @mereolog in #563
• GitHub-589 - Improper references to IDMP resources by @ElisaKendall in #592
• IDMP-GitHub-584 - Loosen constraints on MVF Element to allow for mapping MEDdra terms to those in EMA SPOR and other vocabularies by @ElisaKendall in #585
• GitHub-590 - Missing disjointness axiom on starting material role by @ElisaKendall in #591
• GitHub-587 - "Broken" URLs in IDMPO literals by @ElisaKendall in #593
• GitHub-580: add mvf-trm:Term as parent class for MedDRA term by @tw-osthus in #581
• GitHub-863 - Possibly broken URLs in IDMP Prod literals by @ElisaKendall in #595
• GitHub-586 - Add the additional definitional material for substance from ISO 11238 to the current definition from Commons as annotations by @ElisaKendall in #597
• GitHub-583 - Possible ill-formed definition for MarketingStatusReasonCode by @ElisaKendall in #596
• GitHub-577 - Potentially vicious "circular" restrictions by @ElisaKendall in #600
• GitHub-601 - Modify the SPAR PO ontology to eliminate the SWRL Builtin statements which cannot be processed by certain reasoners by @ElisaKendall in #602
• GitHub-598 - Obsolete restriction on idmp-sub:Amount by @ElisaKendall in #603
• Additional hygiene test for obsolete restrictions by @mereolog in #604
• IDMP-682 - Investigate simplifying potential circularity in population characteristic by @ElisaKendall in #606
• IDMP-748 - Modify the packaging approach to make package roles individuals by @ElisaKendall in #609
• IDMP-738: Fix uri in GSRS transformation files by @aliariff in #610
• Update SPOR transformation files by @aliariff in #612
• Fix Warning in GitHub Actions CI by @aliariff in #611

Full Changelog: master_v1.1.0...master_v1.2.0

IDMP Ontology Release 1.1.0

Ontology Development in Details

In Q1 2024 there were two primary areas of work, including:

1. significant additions to cover details needed for representation of biologics – organisms, parts of organisms, the subset of the Linnean taxonomy needed for herbal substances, inheritance relationships between organisms, completion of the model with respect to target and target interaction, and related areas in the ISO 11238 Substance ontology, and
2. significant additions to cover gaps in the ISO 11615 model related to medicinal products, package items and other concepts required for the jurisdiction-agnostic UC4 – adding concepts representing attributes and relations that were not completely modeled for therapeutic indications, contraindications, and population characteristics; completing the definition of pharmaceutical product characteristic, completing details for manufactured item and package item, completing details related to pharmaceutical dose form and its subclasses (administrable, combined), and related restrictions on medicinal product, and adding missing attributes and relations such as ‘special measures’, pediatric use indicator, and monitoring indicator, as well as addressing other miscellaneous gaps and issues in restrictions in that part of the ontology for ISO 11615.

Qualitative Comparison To Previous Release

Overview

Three of the SPAR ontologies (related to library science, which we were not using) were deleted:

• frbr
• c4o
• datacite

The following ontologies were changed:

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-657 - add missing package item properties by @tw-osthus in #555
• IDMP-713 - Augment the ontology to incorporate additional information related to biologics by @ElisaKendall in #554
• IDMP-713a - Augment the ontology to incorporate additional information related to biologics by @ElisaKendall in #557
• IDMP-726 - Augment / revise the ontology to cover gaps w.r.t. ISO 11615 for UC4 by @ElisaKendall in #559

Full Changelog: master_v1.0.0...master_v1.1.0

IDMP Ontology Release 1.0.0

Ontology Development in Details

Over the last quarter, since the 0.5.0 release, the development team has focused on:

1. better coverage of the ISO 11238 Substances content.
2. better coverage of the ISO 11615 Medicinal Products content.
3. extending and improving examples to demonstrate how to use the ontologies in real-world applications.

We have also worked towards increased usability and flexibility, and augmented these two ontologies with additional metadata to improve understandability. Details, including additional references and the degree to which a given element complies with the ISO standard(s), were also added. 

In addition to adding new content, we have taken advantage of revisions to the OMG Commons Ontology Library v1.1 updates. Four additional ontologies have been added as formal standards at OMG, which are now dereferenceable from the OMG website. They include the Documents, Parties and Situations, Roles and Compositions, and Quantities and Units ontologies that IDMP-O depends on. We anticipate publication of another update to the Commons Library, including the other 5 ontologies that our main ISO standard ontologies depend on in mid-2024. See https://www.omg.org/spec/Commons/ for more information.

Also, in order to demonstrate how to extend labeling details as required by the ISO IDMP standards with tables or other rich document content, we've integrated a new family of ontologies from the library science community called the "SPAR Ontologies", or Semantic Publishing and Referencing Ontologies (see http://www.sparontologies.net/ and https://github.com/sparontologies for more information). These ontologies include a few issues which we are working with their development team to resolve, and are only used in examples as a consequence. Together with a new DocumentComponents ontology in IDMP, they address challenges for IDMP based regulatory reporting related to linking content embedded in documents, including rich tables, which are referenced as string values in the IDMP ISO documents. These are described under the quantitative view, below, among the 7 new ontologies listed. They are also described in examples at [Pattern: Citing and linking into reference documents - REVIEW]
(https://wiki.edmcouncil.org/display/IDMP/Pattern: Citing and linking into reference documents - REVIEW).

We removed one starting point example which may be reintegrated over the coming months if it is needed. It did not show enough new content to warrant integration in the 1.0 release.

Qualitative Comparison To Previous Release

Overview

One ontology was deleted:

1. CellCeptExample – incomplete example that may be added back later this year
   7 new ontologies were added:
2. c40 – Citation Counting and Context Characterisation Ontology (C4O)
3. datacite – covers the DataCite Metadata Schema Specification for citations
4. deo – Discourse Elements Ontology (DEO)
5. doco – Document Components Ontology (DoCo)
6. frbr – Essential FRBR in OWL2 DL Ontology (FRBR), which corresponds to the IFLA report on the Functional Requirements for Bibliographic Records (FRBR)
7. po – Pattern Ontology (PO)
8. DocumentComponents – an extension to the SPAR ontologies primarily focused on table content 

Except for the last one, all of them are SPAR ontologies.

The following ontologies were changed:

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

• More possible typos in annotations fixed by @mereolog in #499
• Spellcheck automation as a GitHub action by @mereolog in #500
• IDMP-665 - Update the Qlaira example to use the proper IRIs for the SPOR details by @ElisaKendall in #503
• IDMP-863 - Complete the definition of protein substances by @ElisaKendall in #504
• IDMP-659 - add package components, medical device and characteristics by @tw-osthus in #498
• fix wrong rdf:type on classifier instance by @tw-osthus in #510
• IDMP-673 - Complete the minimal set of required fields from Annex L for Polymers by @ElisaKendall in #509
• GitHub-511 - dmp-sub:SubstanceNameClassifier-CommonName has incomplete definition by @ElisaKendall in #516
• GitHub-505 - Non-classifying, but just denoting, classifiers by @ElisaKendall in #514
• IDMP-674 - Exclude shelf life type and special precautions for storage from the SPOR ontology in advance of regeneration of the SPOR lists and vocabulary elements by @ElisaKendall in #518
• IDMP-634 - Remove the default code for ingredient and active ingredient by @ElisaKendall in #520
• IDMP-640 add characteristics for target populations by @tw-osthus in #453
• IDMP-675 - Complete the minimal set of required fields from Annex L for Mixtures by @ElisaKendall in #522
• GitHub-512 - idmp-mprd:hasSpecialStorageConditions has wrong range by @tw-osthus in #527
• GitHub-525 - hasSPORTermDescription is an ObjectProperty by @tw-osthus in #526
• Idmp 670 by @konradkrebs1411 in #524
• IDMP-645 add SPAR ontologies and an extension by @tw-osthus in #468
• Fixed URLs by @konradkrebs1411 in #529
• Spellcheck ignores reified languages by @mereolog in #534
• Fix to underspecified examples hygiene test by @mereolog in #533
• GitHub-501 - ISO non-compliant definitions by @ElisaKendall in #528
• Add and modify catalog files in subfolders by @mereolog in #539
• GitHub-538 - remove functional from properties by @tw-osthus in #540
• IDMP-616 enhance Amlodipine example by @tw-osthus in #482
• IDMP-678 - apply GSRS pattern for substances and substance names by @tw-osthus in #536
• IDMP-677 - Add missing macro content for ISO 11615 by @ElisaKendall in #531
• IDMP-677a - Add missing macro content for ISO 11615, addressing remaining gaps by @ElisaKendall in #542
• IDMP-679 - Remove the CellCept example prior to the 1.0 release by @ElisaKendall in #544
• Update spor-substances.rqg by @konradkrebs1411 in #546
• IDMP-322 - ISO11238: Document the ISO IDMP conformance level as annotations in the IDMP-O where deviations exist by @ElisaKendall in #548
• IDMP-383 - ISO11615: Document the ISO IDMP conformance level as annotations in the IDMP-O where deviations exist by @ElisaKendall in #550

Full Changelog: master_v0.5.0...master_v1.0.0

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:

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 https://github.com/edmcoun...

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.

1. 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.

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.

Qualitative Comparison To Previous Release

Overview

Three new ontologies were added:

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

The following ontologies were changed:

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 https://github.com/edmc...

IDMP Ontology Release 0.3.0

Ontology Development in Details

This quarter the development team made significant progress in several key areas, including:

• Augmenting the ontologies to incorporate concepts and relationships needed to support Use Case 2 (UC-2), relating regulatory reporting requirements to the manufacturing side of the business, e.g., packaging concepts
• Refactoring some of our original work to address areas where shortcuts had been taken for Phase 1, such as to better address the relationship between products and their ingredients
• Refactoring to distinguish substance and product specifications from their physical counterparts
• Adding initial support for molecular entities, including molecules and atoms

The work also involved revising our original set of competency questions and adding new ones for UC-2 as well as increasing support for mappings to EMA SPOR. We also added a new example from the EMA PMS Implementation Guide, Chapter 8, for Qlaira. This particular example, which is mapped to SPOR, is important because the same medicinal product includes several pharmaceutical products.

Qualitative Comparison To Previous Release

Overview

One new ontology was added: QlairaExample.

No ontology was removed.

The following existing ontologies were changed:

Details

idmp_different_ontologies_in_repository_versions.xlsx
idmp_different_resources_in_ontology_revisions.xlsx
idmp_different_axioms_for_same_subjects.txt
(Tha last file is a json file - to see its contents use a json editor, e.g., https://jsonviewer.stack.hu)

Deprecated Resources

The following resources were deprecated and may be deleted in v0.4.0 release:
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/ProductConstituency
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/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

• single substance has max 1 molecular structure is wrong by @ElisaKendall in #280
• Fix to ISO conformance level test by @mereolog in #282
• IDMP-243 - stereochemisty by @tw-osthus in #279
• IDMP-GitHub-284 - Notes on certain classes for structure, molecular structure, and stereochemistry are needed by @ElisaKendall in #285
• IDMP-398 - Add concept for Marketing Status (SPOR RMS) by @ElisaKendall in #290
• Competency questions split to one query per file by @mereolog in #297
• Add more cleanup instructions for SPOR OMS transformation by @aliariff in #287
• Update SPOR OMS Transformation by @aliariff in #288
• IDMP-385: Update URI pattern by @aliariff in #300
• IDMP-393 & IDMP-408: Add SPOR RMS Transformation by @aliariff in #286
• IDMP 400 - GitHub action for competency questions run as unit tests by @mereolog in #304
• IDMP-405 - Refactor the substance class hierarchy to differentiate actual physical substances from classifiers for substances by @ElisaKendall in #303
• Update config files by @patrycjamia in #298
• All competency questions run as unit tests by @mereolog in #309
• IDMP-416 - Update Amlodipine Example (RDF file) by @ElisaKendall in #311
• IDMP-415 - Update Terlipressin Example for reference strength (RDF) by @ElisaKendall in #313
• IDMP-435 - Create classes for SSG1, SSG2, SSG3, SSG4 by @ElisaKendall in #317
• IDMP viewer config files are updated by @mereolog in #318
• Idmp 462: UC1 CQ Update by @stsilva-osthus in #322
• IDMP-465 - Integrate revised manufactured item and packaging strategy for UC-2 by @ElisaKendall in #321
• IDMP-436: Update SPOR SMS Transformation regarding SSG1 and SSG3 by @aliariff in #327
• IDMP-473 - Integrate the Qlaira Example into our Test Suite by @ElisaKendall in #324
• IDMP-433: Add idmp-sub:hasMoiety by @aliariff in #314
• Idmp 462 Use Case 2 Competency Questions by @stsilva-osthus in #326
• IDMP-479 - Further clean-up is needed to address remaining issues with the Qlaira example by @ElisaKendall in #329
• New cqs added as unit tests by @mereolog in #330

New Contributors

• @tw-osthus made their first contribution in #279

Full Changelog: master_v0.2.0...master_v0.3.0

Summary

This was a short quarter for us, as the Phase II project did not really get started in earnest until mid-November. The changes made during this period fell into several categories:
• Commons ontology revisions – including alignment of those that have been released by the Object Management Group (OMG) with the formal specification and extension of the products and services ontology to incorporate GTINs, UPCs, and SKUs, and add organizations and in particular, government organizations together with jurisdictions for the EU (others will follow in 2023)
• ISO IDMP ontology revisions – addressing some of the issues that came up during meetings in Boston, a very preliminary ontology for SPOR-related controlled vocabularies, the addition of some of the concepts required to answer competency questions related to UC-2, bridging the gap between regulatory and manufacturing, the addition of metadata annotations to enable clearer identification of deviations from the ISO standards in the ontologies, and additional restructuring needed to provide better semantics for substance-related concepts (which deviate from what is in the ISO standards, including new annotations)
• Revision of the UC-1 SPARQL queries to align with the changes made to the ontologies
• Revision of the GSRS transformation scripts to simplify them and align with changes to the ontologies
• New mappings and transformations to support SPOR reference data (OMS and SMS)
• New hygiene tests as a part of the infrastructure to address potential performance issues, including a new report to summarize deviations from the ISO standards using the new metadata annotations
• Governance and Infrastructure configuration updates

Detailed Description

Category: Commons Ontology Library (CMNS)

Summary: This quarter, 11 of the ontologies included in the current CMNS ontologies were published as a formal standard by the Object Management Group (OMG). The current library in use by the IDMP project includes an additional 9 ontologies that we will work on standardizing at OMG in 2023 along with a subset of the jurisdictions that we hope to complete and promote at OMG by the end of this year. Most of them were originally part of the Financial Industry Business Ontology (FIBO), and well tested in that context. They are all quite general useful for many ontology projects in addition to the IDMP effort. We will be revising FIBO and other projects to leverage the same version of these ontologies that we promote at OMG, and will incorporate any new insights that come from the other projects that use them as appropriate.
Changes to the ontologies that are not yet standardized by OMG, incorporated this quarter, include extension of the products and services ontology to incorporate GTINs, UPCs, and SKUs, the addition of small ontologies for organizations and in particular, government organizations, a small locations ontology, and 7 new jurisdiction-specific ontologies covering the EU, United Kingdom, and Western Asia, as some countries in Western Asia are members of the Council of Europe. These jurisdiction-specific ontologies and others that we have yet to generalize from FIBO are needed to represent the various regulatory agencies required for IDMP.

Category: ISO IDMP Ontologies

Summary: Shortly after the initial Phase I release closed, the ontology team met with some of our stakeholders in Boston for workshops after the Pistoia Alliance conference. Several questions came up during those discussions, some of which led to Jira issues that we have addressed since. One of those was that IDMP ontology users were generally confused by the way ingredients were modeled in the ontology, which has been refined with this release.
Another issue was that a number of our stakeholders understood the need to model various concepts differently in the ontology from their more relational representation in the IDMP standards, but wanted a way to highlight those differences and report them back to the ISO working group as potential areas for enhancement in the standards. A new ontology that provides annotations for various ways that an IDMP ontology might differ from the relevant ISO standard was added to the META partition, and we have initiated incorporation of those annotations where they are appropriate. We will perform a comprehensive review in Q1 to ensure that we have annotated all such deviations properly and using a new reporting capability discussed below under hygiene testing can run the report at any time to highlight the deviations for our users and to forward to ISO TC 215 as appropriate.
Yet another issue that was discussed in Boston had to do with the simplistic way jurisdictions were modeled in the Phase I ontology. We initiated work to address this in Q4 for the EU by (1) including EU-specific governments and jurisdictions in Commons as mentioned above, and (2) moving the EU-specific regulatory agencies and registration authorities from the current ISO 11238 Registration Authorities ontology to a couple of new jurisdiction-specific ontologies in a new European Jurisdiction partition of the ISO category. We expect to continue moving and expanding on the number and nature of regulatory agencies and registration authorities for other jurisdictions following a similar pattern over the coming months until we have good coverage for the rest of the planet. Jurisdictions are divided based on the United Nations’ M49 codes for continents and the countries that are located in those continents, as well as based on ISO 3166 countries and country subdivisions.
One of the main areas of work this quarter was the addition of the mapping to SPOR. Most of that work involved the mapping and transformations discussed below, though we added a new, small starting point ontology to capture some of the SPOR-specific controlled vocabularies. More of these will be added over the coming months.
Finally, we initiated work on changes to the ontologies to support our next set of competency questions related to bridging the gap between manufacturing and the regulatory areas of the pharmaceutical industry, as well as continuing a bit of restructuring of substance related concepts to provide more scientifically oriented semantics than is reflected in the ISO standards. The concepts that no longer conform to the standards are annotated using the new metadata annotations defined for that purpose.

Category: Competency Questions (SPARQL Queries)

Summary: The primary changes made over the last several weeks involved streamlining the existing queries and revising them to reflect the latest revisions to the ontologies. Several additional queries were added to better reflect what is needed to answer the questions and to provide examples that the various pharma companies can use as examples for internal query and mapping efforts.

Category: Mappings and Transformations

Summary: This quarter a significant effort was focused on the preliminary integration of the IDMP ontologies with data from the European Commission’s SPOR repository. This includes support for reference data from several SPOR repositories. Some preliminary work to generate content reflecting various SPOR-specific controlled vocabularies was included as a part of this initial effort, which will be aligned with the ontology as the vocabularies are mapped more completely in 2023. In addition to SPOR integration, the GSRS transformation scripts were updated to simplify them and align with changes to the ontologies.

Classes being deprecated

The classes listed below are now deprecated and are likely to be deleted soon:
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/ISO11615-MedicinalProducts/hasActiveIngredientRole
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/hasIngredientRole

What's Changed - By Pull Request

• IDMP-GitHub-MaturityAlignment - Maturity Levels to About File Contents Alignment by @ElisaKendall in #220
• Update config file by @patrycjamia in #221
• IDMP-298 - Rename IngredientRole to Ingredient, including its subclasses by @ElisaKendall in #223
• IDMP-CMNS-1.0 - Revise the Commons Ontology Library per OMG updates by @ElisaKendall in #226
• IDMP-356: Simplify GSRS transformation scripts by @aliariff in #233
• Fix typo by @aliariff in #234
• IDMP-326 - Add the concept of a Global Trade Item Number (GTIN) by @ElisaKendall in #231
• IDMP-235: Fix ChemblDatabase URI by @aliariff in #235
• Sync GSRS transformation files by @aliariff in #237
• Fix GSRS script for result generation by @aliariff in #236
• IDMP-GitHub-228 - Nameless substances by @ElisaKendall in #242
• Cq updates mvp.01 by @stsilva-osthus in #218
• IDMP-305 - Update Ontology with jurisdiction concepts as discussed in Boston workshop by @ElisaKendall in #240
• Update config by @patrycjamia in #245
• IDMP-366: Add RIM related IDMP concept: Packaged Medicinal Product by @ElisaKendall in https://github.com/edmcounc...

Release Summary

This release provides the very first draft of the IDMP Ontology together with a set of competency questions related to our first use case.

For this release we focused on substance identification at various stages of product life-cycle. We managed to develop the data architecture capable to answer the eight competency questions which concerns the use case whereby substances are identified in clinical trials as active ingredients of medicinal products:

What's Changed

All pull requests for this release can be found here.

(New) Contributors

• @mereolog made their first contribution in #1
• @ElisaKendall made their first contribution in #9
• @trojczak made their first contribution in #73
• @stsilva-osthus made their first contribution in #82
• @patrycjamia made their first contribution in #120

Full Changelog: https://github.com/edmcouncil/idmp/commits/0.1