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Medical Ontologies: An Overview. Barry Smith http://ifomis.de. Three levels of ontology. formal (top-level) ontology dealing with categories employed in every domain: object, event, whole, part, instance, class 2) domain ontology , applies top-level system to a particular domain
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Medical Ontologies: An Overview Barry Smith http://ifomis.de
Three levels of ontology • formal (top-level) ontology dealing with categories employed in every domain: • object, event, whole, part, instance, class • 2) domain ontology, applies top-level system to a particular domain • cell, gene, drug, disease, therapy • 3) terminology-based ontology • large, lower-level system • Dupuytren’s disease of palm, nodules with no contracture http:// ifomis.de
Three levels of ontology • formal (top-level) ontology dealing with categories employed in every domain: • object, event, whole, part, instance, class • 2) domain ontology, applies top-level system to a particular domain • cell, gene, drug, disease, therapy • 3) terminology-based ontology • large, lower-level system • Dupuytren’s disease of palm, nodules with no contracture http:// ifomis.de
Three levels of ontology • formal (top-level) ontology dealing with categories employed in every domain: • object, event, whole, part, instance, class • 2) domain ontology, applies top-level system to a particular domain • cell, gene, drug, disease, therapy • 3) terminology-based ontology • large, lower-level system • Dupuytren’s disease of palm, nodules with no contracture http:// ifomis.de
Three levels of ontology • formal (top-level) ontology dealing with categories employed in every domain: • object, event, whole, part, instance, class • 2) domain ontology, applies top-level system to a particular domain • cell, gene, drug, disease, therapy • 3) terminology-based ontology • large, lower-level system • Dupuytren’s disease of palm, nodules with no contracture http:// ifomis.de
IFOMIS • Institute for Formal Ontology and Medical Information Science • Leipzig • http://ifomis.de • philosophers and medical informaticians attempting to build and test a Basic Formal Ontology for applications in biomedical and related domains http:// ifomis.de
IFOMIS • use basic principles of philosophical ontology • for quality assurance and alignment of biomedical ontologies http:// ifomis.de
Compare: • pure mathematics (theories of structures such as order, set, function, mapping) employed in every domain • applied mathematics, applications of these theories = re-using the same definitions, theorems, proofs in new application domains • physical chemistry, biophysics, etc. = adding detail http:// ifomis.de
Three levels of ontology ????? • formal (top-level) ontology = • medical ontology has nothing like the technology of definitions, theorems and proofs provided by pure mathematics • 2) domain ontology • = UMLS Semantic Network, GALEN CORE • 3) terminology-based ontology • = UMLS, SNOMED-CT, GALEN, FMA http:// ifomis.de
Strategy • Part 1: Provide an overview of medical ontologies and of the top-level ontologies which they implicitly define • Part 2: Show how principles of classification and definition derived from top-level ontology can help in quality assurance of terminology-based ontologies and in ontology alignment • Parts 3 and 4: IFOMIS Collaboration with L&C http:// ifomis.de
part of the UMLS Semantic Network http:// ifomis.de
UMLS Semantic Network • entity event • physical conceptual • object entity http:// ifomis.de
UMLS Semantic Network • entity event • physical conceptual • object entity http:// ifomis.de
conceptual entity • Organism Attribute • Finding • Idea or Concept • Occupation or Discipline • Organization • Group • Group Attribute • Intellectual Product • Language http:// ifomis.de
Conceptual Entity • Idea or Concept • Functional Concept • Qualitative Concept • Quantitative Concept • Spatial Concept • Body Location or Region • Body Space or Junction • Geographic Area • Molecular Sequence • Amino Acid Sequence • Carbohydrate Sequence • Nucleotide Sequence http:// ifomis.de
Fairfax County • is an Idea or Concept http:// ifomis.de
Why is Fairfax County a Conceptual Entity for UMLS-SN? • UMLS-SN Spatial Concepts share the following characteristics: • a) they are extended in space • b) their boundaries are determined not by any underlying physical discontinuities but rather by human fiat. • The referent of ‘Fairfax County’ satisfies these conditions, • but so also does hand, which is not classified by UMLS as a conceptual entity. http:// ifomis.de
genepart_ofcell component • body systemconceptual_part_of • fully formed anatomical structure http:// ifomis.de
conceptual • entity • idea or concept • functional concept • body system http:// ifomis.de
But: • Gene or Genome is defined as: “A specific sequence … of nucleotides along a molecule of DNA or RNA …” • and • nucleotide sequence is_a conceptual entity http:// ifomis.de
entity • physical conceptual • object entity • idea or concept • functional concept • body system confusion of entity and concept http:// ifomis.de
Functional Concept: • Body system is_a Functional Concept. • but: • Concepts do not perform functions or have physical parts. http:// ifomis.de
This: is not a concept http:// ifomis.de
Problem: Confusion of Is_A and Has_Role • Physical Entity • Chemical Entity • Chemical Chemical • Viewed Viewed • Structurally Functionally http:// ifomis.de
Chemical Viewed Structurally vs. Chemical Viewed Functionally • reflects a distinction between types of classification – not between types of entity • compare a classificationof people into: • tall people, • people who play tennis, • people who look like flies from a distance • etc. http:// ifomis.de
Confusion of Is_A and Has_Role • Physical Object • Substance • Food Chemical Body Substance http:// ifomis.de
Roles • A box used for storage is not (ipso facto) a special kind of box • An animal belonging to the emperor is not a special kind of animal http:// ifomis.de
The Hydraulic Equation • BP = CO*PVR • arterial blood pressure is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR) http:// ifomis.de
Confusion of Ontology and Epistemology • blood pressure is an Organism Function, • cardiac output is a Laboratory or Test Result or Diagnostic Procedure • BP = CO*PVR thus asserts that • blood pressure is proportional either to a laboratory or test result or to a diagnostic procedure http:// ifomis.de
Disease History • is classified by UMLS under Health Care Activity • This runs together • the history or course of a disease on the side of the patient (ontology) • with • the act of eliciting that history (epistemology). http:// ifomis.de
Object vs. Process =Continuant vs. Occurrent • Continuant entities = endure through time • organisms, cells, molecules exist in full in every instant at which you exist at all • Occurrent entities (processes, events, activities, changes, histories) unfold themselves in time; • never exist in full in any single instant http:// ifomis.de
Dependent vs. Independent Entities • Dependent entities require support from other entities in order to exist: • there is no mass or shape without some body Independent entities are themselves the substrates for qualities, dispositions, motions, functions and other dependent entities http:// ifomis.de
entities • independent dependent occurrents • continuants continuants (always dependent) • ORGANISMS ROLES PROCESSES • CELLS FUNCTIONS HISTORIES • MOLECULES CONDITIONS LIVES (diseases) (courses of • diseases) http:// ifomis.de
entities • independent dependent occurrents • continuants continuants (always dependent) • ORGANISMS ROLES PROCESSES • CELLS FUNCTIONS HISTORIES • MOLECULES CONDITIONS LIVES (diseases) (courses of • diseases) classes instances http:// ifomis.de
A three-category ontology along these lines accepted by • DOLCE = first module of Semantic Web Wonderweb Foundational Ontologies Library • BFO = IFOMIS Basic Formal Ontology • UMLS-SN, GO http:// ifomis.de
GALEN • independent dependent occurrents • continuants continuants (always dependent) • GENERALISED MODIFIER GENERALISED • STRUCTURES + CONCEPT PROCESS • GENERALISED (features, • SUBSTANCES states, • roles) http:// ifomis.de
GALEN • independent dependent occurrents • continuants continuants (always dependent) • GENERALISED MODIFIER GENERALISED • STRUCTURES + CONCEPT PROCESS • GENERALISED (features, • SUBSTANCES states, • cell + sputum roles) http:// ifomis.de
GALEN • independent dependent occurrents • continuants continuants (always dependent) • GENERALISED MODIFIER GENERALISED • STRUCTURES + CONCEPT PROCESS • GENERALISED (features, • SUBSTANCES states, • roles) http:// ifomis.de
GALEN • independent dependent occurrents • continuants continuants (always dependent) • GENERALISED ASPECT GENERALISED • STRUCTURES + PROCESS • GENERALISED (features, • SUBSTANCES states, • roles) http:// ifomis.de
immune system is_a logical structure http:// ifomis.de
GALEN CORE (1996) • Phenomenon = those categories which can be observed http:// ifomis.de
GALEN CORE (1996) • Phenomenon = categories whose instances can be observed http:// ifomis.de
