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Ontology and RadLex

Ontology and RadLex. Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org

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Ontology and RadLex

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  1. Ontology and RadLex Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org This work was funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.

  2. Problem: radiologist wondering if radiation therapy in chest is linked to Cauda Equina Syndrome in lower back.she needs data and information to find a solution- calls colleagues - sends emails - queries RadLex

  3. Problem: radiologist wondering if radiation therapy in chest is linked to Cauda Equina Syndrome in lower back.She needs data and information to find a solution- calls colleagues - sends emails - queries RadLex

  4. RadLex:A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

  5. RadLex:A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources direct result of the information age and information science

  6. Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination.

  7. Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination. retrieval and dissemination: the goal of information science

  8. Informatics:the science of data and information collection, categorization, management, storage, processing, retrieval, and dissemination. but goal depends upon accurate categorization and management

  9. Computers are dumb beasts: At this point,* they can mostly only accurately output what we accurately input. * Not ruling out the possibility of human-like thinking in the future

  10. So, a central informatics problem that hampers retrieval and dissemination is: incorrect thinking (IT) associated with categorization and management of data and information

  11. Can’t get the data and/or info:- radiologist gives up the search in frustration- cure is not found- suffering is not relieved** moral obligation to retrieve and disseminate data and information?

  12. To combat incorrect thinking (IT) and assist in the accurate categorization and management of data and information so that retrieval and dissemination is maximally possible:ontologies are used

  13. What is an ontology? • Philosophical Ontology • Domain Ontology • Formal Ontology

  14. Philosophical Ontology • “...I can fit wholesale evolution and a creating god into my ontology without contradiction.” • “...just because it has mental existence doesn’t mean it has ontological existence.”

  15. - Ontos (being, existence)+ Logos (word, account, explanation) - The study of what is, of the kinds and structures of objects, properties, events, processes, and relations in every area of reality - “The branch of Metaphysics that studies the nature of existence.”Random House College Dictionary

  16. PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

  17. Sub-types (children) should inherit all the features of the relevant type (parent) PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

  18. Sub-types (children) should inherit all the features of the relevant type (parent) Sub-types (children) should inherit all the features of the relevant type (parent) along with some differentia (distinguishing feature) A is_a B that/which Cs A is_a B that/which has Cs - rational animal (A) is_a living entity with sensation (B) that has the capacity for conscious thinking (C) PORPHYRIAN TREE Compare: Linnean Taxonomy and Periodic Table

  19. A is_a B that/which Cs A is_a B that/which has Cs • radiology (A) is_ascience (B) that deals with medical imaging so as to understand, diagnose… (C) • domain ontology is_a ontology that deals with a specific area, sphere, or portion of reality • - mouse trap is_a rodent trap which captures mice

  20. To a certain extent, all of us are Philosophical Ontologists in that we naturally and automatically categorize any and all things in reality so as to understand, explain, control, dominate, and navigate reality.

  21. What is an ontology? • Philosophical Ontology • Domain Ontology • Formal Ontology

  22. (2) Domain Ontology “...I’m working on an ontology for annelids.” “...the Gene Ontology has data on that HOX gene.”

  23. Representation of the entities and relations existing within a particular domain of reality such as biology, medicine, geography, ecology, or law • - Gene Ontology (GO) • - Foundational Model of Anatomy (FMA) • Environment Ontology (EnvO) • See http://www.obofoundry.org/

  24. - Opposed to ontology in the philosophical sense, which has all of reality as its subject matter - Ideally, provides a controlled, structured vocabulary to annotate data in order to make it more easily searchable by human beings and processable by computers

  25. ONTOLOGY:“a representational artifact, comprising a taxonomy as its main part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them.” ** Smith, B., Kusnierczyk, W., Schober, D., & Ceusters, W. (2006). Towards a reference terminology for ontology research and development in the biomedical domain. Proceedings of KR-MED 2006, 1, 1-14.

  26. Domain ontology contrasted with:- Database- Rule-Based Language - Thesaurus- Glossary- Catalogue- Inventory- Axiomatic Theory- Simple Taxonomy • Ontology hybrid of: • - Taxonomy • Various Relations • Axiomatic Rules of Inference

  27. Domain ontology contrasted with:- Database- Rule-Based Language - Thesaurus- Glossary- Catalogue- Inventory- Axiomatic Theory- Simple Taxonomy RadLex, as of now, is a thesaurus of terms, although confuses terms and entities those terms refer to…

  28. Basic Mouse Trap Classification Simple Taxonomy: is_a, sub-type relation

  29. Beginnings of Mouse Trap Domain Ontology

  30. Beginnings of MRI Test Ontology

  31. A Gene Ontology Example: Cytokinesis

  32. is_a ─ part_of ─ A Gene Ontology Example

  33. Part of a Scientific Experiment Ontology

  34. Part of a Scientific Experiment Ontology p/o = part_of  = is_a

  35. Now, it’s fine to have all of these domain ontologies attempting to classify and categorize data and information…But, there is so much data and information…

  36. Crazy and overwhelming, isn’t it?

  37. So, instead of using a STANDARD like the Periodic Table of Elements, people start classifying things their own different ways…this results in…

  38. SILO EFFECT

  39. SILO EFFECT

  40. PROBLEM:DE-SILOING all of this domain data and information so that it may be queried effectively, shared, and re-usedINTEROPERABILITY

  41. PROBLEM:DE-SILOING all of this domain data and information so that it may be queried effectively, shared, and re-usedINTEROPERABILITY

  42. SOLUTION:

  43. FORMAL ONTOLOGY:- Upper-level- Applicable to any domain

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