1. Summary Issues and Suggestions Workshop on The Future of the UMLS Semantic Network NLM, April 8, 2005 Olivier Bodenreider Lister Hill National Center for Biomedical Communications Bethesda, Maryland - USA

2. Issues

3. 3 UMLS Semantic Network u Necessary complement to the Metathesaurus l Provides direct categorization to concepts (some of which would be orphans otherwise) u Best used in conjunction with the Metathesaurus u Used for l Natural Language Processing l Information retrieval l Knowledge discovery u Essentially stable

4. 4 Semantic types u Purposely limited to a small number of categories u Purposely emphasizes categories of major interest l e.g., Neoplastic Process l No attempt to anything JEPD u No explicit classificatory principles or properties l Textual (not formal) definitions l Introduction points for semantic relationships

5. 5 Semantic relations u Single-inheritance hierarchy u Class-class relations u Simply mirrored by inverses u Weakest reading possible: some-some l Sufficient for some applications (e.g., semantic interpretation, reporting and visualization of clinical information) l Too limited for reasoning

6. 6 Semantic groups u 15 collections of semantic types u Created for visualization purposes u Purposely non-ontological (not subtrees from the isa hierarchy of STs) u Based on common properties of (sometimes) otherwise heterogeneous semantic types

7. 7 Semantic categorization u Generally corresponds to isa (rarely is an instance of) u Convenient for extracting a class l Direct access: no traversal necessary l Bypasses hierarchies in vocabularies: not subject to questionable hierarchical relations

8. 8 Semantic type assignment (1) u Essentially manual (default based on source information, reviewed by Metathesaurus editors) u Complex and labor intensive u Multiple ST assignment sometimes required l Structure + role (chemicals) l Systematic polysemy u Guidelines l Usage notes l Prior categorization of similar concepts

9. 9 Semantic type assignment (2) u No constraints based on mandatory consistency between SN and Metathesaurus (e.g., ST of the child concept must be identical to or a descendant of ST of the parent concept) u No constraints based on ontological principles (e.g., disjunction between Entity and Event) u No constraints based on structural principles (e.g., allowable hybrid types)

10. 10 Systematic polysemy (splitting vs. lumping) u Metathesaurus (RxNorm) distinguishes between l Clinical drug (e.g., Acetaminophen) l Branded drug (e.g., Tylenol) u But does not systematically distinguish between l Prostatic adenoma (the tumor responsible for compressing the urethra) l Prostatic adenoma (the disease of which urinary problems are one manifestation) both contain acetaminophen as their active ingredient

11. 11 Finding u Role played by many different types u Necessarily some-some (rare exceptions) u Reified for convenience

12. 12 Overall constraints for changes u Finite amount of resources u Driven by usefulness

13. Suggestions

14. 14 SN and Metathesaurus u Issues in the SN cannot be dissociated from issues in the Metathesaurus u Inaccurate/inconsistent concept categorization l May be a bigger issue than issues identified in the SN n Relatively frequent n Impair semantic integration and semantic interpretation l Will not be solved solely be addressing issues in the SN

15. 15 SN vs. Biomedical ontology u Having a good (high-level) ontology of biomedicine is certainly desirable… u But it will be of little use if it is not linked to Metathesaurus concepts u Some ontological features (e.g., some-all) require a much finer granularity than that of the current semantic types

16. 16 Editing vs. Auditing u Auditing must be pursued, but… u Better editing environments are needed l Law: explicit classificatory principles and properties l Order: n Enforce SN/Meta consistency (use SN relations as a reference for Meta relations) n Restrict allowable combinations of STs u Quality assurance starts at the time of editing

17. 17 Source transparency vs. Anarchy (1) u All relations asserted by sources are recorded… (source transparency) u But need not be necessarily trusted u Similar to how synonymy is treated l Metathesaurus synonymy does not always follow source synonymy

18. 18 Source transparency vs. Anarchy (2) u Similar to how names lacking face validity are treated l Fully specified Metathesaurus names are created l Invalid names are made suppressible u Similarly for relations l Metathesaurus hierarchical relations should ignore some obviously non-hierarchical relations used to create hierarchies in source vocabularies l Suppressibility or Content View Flag (CVF)

19. Agenda

20. 20 Semantic types u Rename some types (face validity) u Extract explicit classificatory principles u Rearrange hierarchy as needed (e.g., Alga) u Revisit roles l Place under sortals when unique (e.g., Enzyme) l Create allowable hybrids (e.g., Steroid hormone)

21. 21 Semantic relations u Align with Metathesaurus relations (e.g., caused_by / due_to) u Multiple inheritance (?) u Two levels l Coarse class-class, some-some, with mirrored inverses to label the relation (and support semantic interpretation) l Finer non-symmetric class-class, some-all (?) to support reasoning

22. 22 ST assignment u Facilitated by improved editing environment u Driven by explicit classificatory principles and properties u Simplified by allowable hybrids u Constrained by coherence with SN relations (requires aligned relations and labeled Metathesaurus relations)