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Ontological analysis of the semantic types

B I O M E D I C A L O N T O L O G Y. Ontological analysis of the semantic types. Anand Kumar MBBS, PhD I FOMIS, University of Saarland, Germany. Biological Entity classification using Realism. Anatomic Structure (Organ system, Organ…). Independent Biological

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Ontological analysis of the semantic types

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  1. B I O M E D I C A L O N T O L O G Y Ontological analysis of the semantic types Anand KumarMBBS, PhD IFOMIS, University of Saarland, Germany.

  2. Biological Entity classification using Realism Anatomic Structure (Organ system, Organ…) Independent Biological Continuant (FMA: Material Anatomic Entity) Body Substance Biological Entity Biological Occurants (processes, events, actions) Biological Continuants Dependent Anatomical Continuant (FMA: Immaterial Anatomical entity – point, space, surface, line) Dependent Biological Continuant Dependent Physiological Continuant (function)

  3. B I O M E D I C A L O N T O L O G Y Market, product and service Market: Producer/Service provider; Customer; Interest and motivation of customer; Resources Products: Goods and Services Need: Basic forces which drive customers to take action and engage in exchanges Difference between current state and desired state Want: Specific ways of satisfying a basic need Market segmentation Niche products Competitors

  4. B I O M E D I C A L O N T O L O G Y Events which are not events Behavior: Social behavior, Individual behavior Molecular Biology Research Technique Biological function: Physiological function: Organism function, Organ or Tissue function, Cell function, Molecular function Pathologic function: Disease or syndrome, Experimental model of disease

  5. B I O M E D I C A L O N T O L O G Y Concepts which are not concepts Spatial concept: Body slope or region, Body space or junction, Geographic area, Molecular sequence Conceptual entity: Organism attribute: Clinical atrribute Conceptual entity: Finding: Laboratory or test result, Sign or symptom Chemical: Chemical viewed structurally, Chemical viewed functionally

  6. B I O M E D I C A L O N T O L O G Y Epistemology within Ontology Finding: Sign or symptom Should not be mixed into ontology per se Finding vs. Disease or syndrome Many, many semantic types can have parallel findings Obesity - BMI, Finding Hypertension – Systolic/Diastolic pressure, Finding

  7. B I O M E D I C A L O N T O L O G Y Jointly exhaustive and Pairwise disjoint Single child Plant:Algae Mammal: Human Occupation or discipline: Biomedical occupation or disease Manufactured object: Medical device Medical device: Drug delivery device Pharmacologic substance: Antibiotic Organism attribute: Clinical attribute Functional concept: Body system Research activity: Molecular biology research technique Organism function: Mental process Molecular function: Genetic function

  8. B I O M E D I C A L O N T O L O G Y Jointly exhaustive and Pairwise disjoint Anatomic structure and organism: problem of granularity Intellectual product: Regulation or law, classification Manufactured object: Medical device, Research device, Clinical drug Organization: Health Care related organization, Professional soceity, Self-help or relief organization Conceptual entity: Organism attribute, Finding, Idea or concept, Occupation of discipline, Organization, Group, Group attribute, Intellectual product, Language Laboratory Procedure, Diagnostic Procedure, Therapeutic or preventive procedure

  9. B I O M E D I C A L O N T O L O G Y Sources and UMLS SN UMLS took many of its SN classes from original sources Some sources given preference over other Read Code - Region as parent of anatomical entity Medical Entities Dictionary - Chemical viewed functionally - Biologically active substance UMLS influences new Thesaurus/Ontology UMLS SN influence on NCI Thesaurus Neoplasm by morphology: Mucinous neoplasm Neoplasm: Neoplasm by morphology Mucinous neoplasm semantic_type Neoplastic process Chain of responsibility

  10. B I O M E D I C A L O N T O L O G Y Growth strategy (Mullins, Walker and Boyd) Current market, Current product: Market penetration strategy Increase market share: Increase frequency of usage, Increase quantity used, New applications New market, Current product: Market development strategy Geographic extension, Target new segments Current market, New product: Product development strategy Product improvement, Product-line extension, New products New market, New product: Diversification strategy Vertical integration, Concentric diversification, Conglomerate

  11. B I O M E D I C A L O N T O L O G Y Suggestions Correct certain mistakes Do not cover mistakes of Semantic types by modifying relations between them Carefully evaluate the sources (Digital anatomist, now FMA) Modularize, if needed (ICD10 vs. Snomed CT) Commit much less if resources are untenable Expand luxuriously if resources are present Enlighten Electronic Health Record standardizations (New NLM - HL7 contract, Snomed CT, LOINC) Follow shifting interests of current customers (EHRs, Bio)

  12. B I O M E D I C A L O N T O L O G Y Ontological analysis of the semantic types Anand KumarMBBS, PhD IFOMIS, University of Saarland, Germany.

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