1. Introduction to Applied and Theoretical Ontology Barry Smith http://ontologist.com

3. The Challenge of Biomedical Research
Each (clinical, pathological, genetic, proteomic, pharmacological …) information system uses its own terminology and category system
But biomedical research demands the ability to navigate through all such information systems
How can we overcome the incompatibilities which become apparent when data from different sources is combined?

4. Database and terminology standardization
is desparately needed in medical and bioinformatics
to enable the huge amounts of existing data to be fused together automatically

5. Current standard solution
The Unified Medical Language System (UMLS)
a metathesaurus of some 100 source vocabularies:
SNOMED
ICD-10
MeSH – Medical Subject Headings
Foundational Model of Anatomy
LOINC (Logical Observation Identifiers Names and Codes)
Gene Ontology
HL7

6. compiled by US National Library of Medicine, Bethesda MD
UMLS Metathesaurus
> 1,800,000 Concepts
> 10,000,000 Relations
compiled by US National Library of Medicine, Bethesda MD

7. Problem
The Source Vocabularies contain bad coding

8. MeSH Organisms Plants Plant Components Plant Components, Aerial
                     Flowering Tops 
                      Flowers 
                        Pollen
Confusion of mass and count senses of ‘substance’

9. both_testes is_a testis
SNOMED
both_testes is_a testis

10. Problem The UMLS Source Vocabularies are Mutually Inconsistent

11. Representation of Blood in SNOMED
Blood is_a Tissue

12. Representation of Blood in MeSH
Blood is_a Bodily Fluid

13. How to make ONE SYSTEM out of different source terminologies?
Through the UMLS Semantic Network
134 Semantic Types
55 Links (is_a, part_of, etc.)
built by linguists for the sake of your health and well-being …

14. built by Saussurian linguists
AND MANDATED BY THE US FEDERAL GOVERNMENT
for the sake of your health and well-being …

17. UMLS Semantic Network entity event physical conceptual object entity
organism

18. Occupation or Discipline
conceptual entity
Organism Attribute
Finding
Idea or Concept
Occupation or Discipline
Organization
Group
Group Attribute
Intellectual Product
Language

19. Occupation or Discipline
conceptual entity
Organism Attribute
Finding
Idea or Concept
Occupation or Discipline
Organization
Group
Group Attribute
Intellectual Product
Language

20. 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

21. Bad Zwischenahn
is an Idea or Concept

22. 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

25. organism anatomical structure fully formed anatomical structure
entity
physical conceptual
object entity
organism anatomical structure
fully formed anatomical structure
body part, organ or organ component

26. entity
physical conceptual
object entity
idea or concept
functional concept
body system

27. Musculo-Skeletal System etc.
Body System
Circulatory System
Nervous System
Immune System
Musculo-Skeletal System
etc.

28. Your digestive system, according to UMLS, is a conceptual entity

29. GO: the Gene Ontology
3 large telephone directories of standardized designations for gene functions and products
designed to cover the whole of biology
model for
fungal ontology,
plant ontology,
drosophila ontology,
etc.

30. GO: the Gene Ontology
GO organized into 3 hierarchies via is_a and part_of

31. The intended meaning of part-of
as explained in the GO Usage Guide is:
« can be a part of »
GO axiom: flagellum part-of cell,
means: “a flagellum is part-of some cells”

32. GO divided into three disjoint term hierarchies
cellular component ontology
molecular function ontology
biological process ontology
flagellum, chromosome, cell
ice nucleation, binding, protein stabilization
glycolysis, death

33. GO divided into three disjoint term hierarchies
= no is_a and no part_of relations between them
How are functions and processes linked together?
cellular component ontology
molecular function ontology
biological process ontology

34. Definition of «Function»
UMLS Semantic Network:
Functional Concept =df A concept which is of interest because it pertains to the carrying out of a process or activity.
GO:
Molecular Function =df the action characteristic of a gene product.

35. UMLS brings clarity
On March 2003 all nodes in the Molecular Function ontology (except the root) had ‘activity’ added to their names
Function = activity

36. Confusion of Function and Activity
If function = activity (= functioning)
But then how deal with dormant/suppressed functions?

37. How are the ontologies related?
Function = “the action characteristic of a gene product.”
Process = “phenomenon marked by changes that lead to a particular result, mediated by one or more gene products”

38. Result:
constant coding errors result from lack of clear principles as concerns what basic notions like ‘function’, ‘process’, ‘part’ mean

39. Examples of GO Molecular Functions
anti-coagulant (defined as: “a substance that retards or prevents coagulation”)
enzyme (defined as: “a substance that catalyzes”)
structural molecule (defined as: “the action of a molecule that contributes to structural integrity”)

40. Problems with Bioinformatics Terminology Systems
Circular definitions
Confusion of use and mention
Confusion of concepts and objects
Confusion of concepts and classes
Confusion of terms and objects
Confusion knowledge with what is known
Simple stupidity
… all of which lead to poor coding

41. These problems are derived
1. from the drive for rapid population of bioinformatics databases
-- for funding bodies quantity overwhelms quality (KR mentality: quick and dirty)
2. from ignorance of the basic principles of ontology (and logic)
3. from relativism/reductionism of linguists

43. The problem
Different communities of medical researchers use different and often incompatible category systems in expressing the results of their work

44. The solution “ONTOLOGY” Remove “Ontology Impedance”
But what does “ontology” mean?

45. Two alternative readings
Ontologies are oriented around terms or concepts = currently popular IT conception
Ontologies are oriented around the entities in reality = traditional philosophical conception, embraced also by IFOMIS

46. Ontology as a branch of philosophy
seeks to establish
the science of the kinds and structures of objects, properties, events, processes and relations in every domain of reality

47. Ontology a kind of generalized chemistry or zoology
(Aristotle’s ontology grew out of biological classification)

48. world’s first ontologist
Aristotle
world’s first ontologist

49. World‘s first ontology (from Porphyry’s Commentary on Aristotle’s Categories)
Porphyry‘s Tree Ca. 1514

50. Linnaean Ontology

51. Ontology is distinguished from the special sciences
it seeks to study all of the various types of entities existing at all levels of granularity

52. and to establish how they hang together to form a single whole (‘reality’ or ‘being’)

53. different concept/terminology systems

54. need not interconnect at all
for example they may relate to entities of different granularity

55. we cannot make incompatible terminology-systems interconnect
just by looking at concepts,
or knowledge or language

56. we cannot make incompatible terminology-systems interconnect
by staring at the terminology systems themselves

57. to decide which of a plurality of competing definitions to accept
we need some tertium quid

58. we need, in other words,
to take the world itself into account

59. = basic formal ontology
BFO
= basic formal ontology

60. BFO
ontology is defined not as the ‘standardization’ or ‘specification’ of conceptualizations
(not as a branch of knowledge or concept engineering)
but as an inventory of the entities existing in reality

61. The BFO framework
will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications

62. BFO not a computer application
but a Reference Ontology
(something like old-fashioned metaphysics)

63. Reference Ontology
a theory of a domain of entities in the world

64. BFO not just a system of categories but a formal theory
with definitions, axioms, theorems
designed to provide the resources for reference ontologies for specific domains
of sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force

65. Proposed solution distinguish two separate tasks:
- the task of developing computer applications capable of running in real time
the task of developing an expressively rich framework of a sort which will allow us to resolve incompatibilities between definitions
and formulate intuitive and reliable principles for database curation

66. Reference Ontology a theory of the tertium quid – called reality –
needed to hand-callibrate database/terminology systems

67. Methodology Get ontology right first
(realism; descriptive adequacy; rather powerful logic);
solve tractability problems later

68. The Reference Ontology Community
IFOMIS (Leipzig)
Laboratories for Applied Ontology (Trento/Rome, Turin)
Foundational Ontology Project (Leeds)
Ontology Works (Baltimore)
Ontek Corporation (Buffalo/Leeds)
Language and Computing (L&C) (Belgium/Philadelphia)

69. Domains of Current Work
IFOMIS Leipzig: Medicine, Bioinformatics
Laboratories for Applied Ontology
Trento/Rome: Ontology of Cognition/Language
Turin: Law
Foundational Ontology Project: Space, Physics
Ontology Works: Genetics, Molecular Biology
Ontek Corporation: Biological Systematics
Language and Computing: Natural Language Understanding

70. THE END