2. 1 Introduction to (Geo)Ontology Barry Smith http://ontology.buffalo.edu/smith

3. 2

4. 3 natural language labels to make the data cognitively accessible to human beings and algorithmically tractable to computers

5. 4 compare: legends for maps

6. 5 common legends allow (cross-border) integration

7. 6 ontologies are legends for data

8. 7 compare: legends for diagrams

9. 8 legends help human beings use and understand complex representations of reality help human beings create useful complex representations of reality help computers process complex representations of reality

10. 9 computationally tractable legends help human beings find things in very large complex representations of reality

11. 10 maps may be correct by reflecting topology, rather than geometry

12. 11 two kinds of annotations

13. 12 names of types

14. 13 names of instances

15. 14 First basic distinction type vs. instance (science text vs. diary) (human being vs. Tom Cruise)

16. 15 Ontology types Instances

17. 16 Ontology = A Representation of Types

18. 17 An ontology is a representation of types We learn about types in reality from looking at the results of scientific experiments in the form of scientific theories experiments relate to what is particular science describes what is general

19. 18 where in the body ? where in the cell ? what kind of organism ? what kind of disease process ?

20. 19 to yield: distributed accessibility of the data to humans reasoning with the data cumulation for purposes of research incrementality and evolvability integration with clinical data Creating broad-coverage semantic annotation systems for biomedicine

21. 20 The Gene Ontology

22. 21

23. 22

24. 23 The Idea of Common Controlled Vocabularies MouseEcotope GlyProt DiabetInGene GluChem sphingolipid transporter activity

25. 24 The Idea of Common Controlled Vocabularies MouseEcotope GlyProt DiabetInGene GluChem Holliday junction helicase complex

26. 25 what cellular component? what molecular function? what biological process?

27. 26 Michael Ashburner

28. GEO.OBO biological samples populations, epidemics speciation, evolutionary processes in space and time museum artifacts 27