1. Pubcrawler

6. Semantic Web  “The Semantic Web will bring structure to the meaningful content of Web pages, creating an environment where software agents roaming from page to page can readily carry out sophisticated tasks for users.”

7. Semantic Web  Two major components: Agents-software designed to execute searches without direction from a human. Agents-software designed to execute searches without direction from a human. Flexible - server down, look for alternate resource.Flexible - server down, look for alternate resource. Persistent - works without supervision, as needed.Persistent - works without supervision, as needed. Ontology- structured language Ontology- structured language

8. Ontology   That department of metaphysics which investigates and explains the nature and essential properties and relations of all beings, as such, or the principles and causes of being. Webster's Revised Unabridged Dictionary

9. Ontology  Structured, hierarchical, controlled vocabulary that describes the concepts or knowledge regarding a particular domain.

10. Why develop an ontology?   To share common understanding of the structure of information. everyone agrees that the terms of the ontology describe the domain of knowledge http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

11. Why develop an ontology?   To share common understanding of the structure of information.   To allow reuse of domain knowledge. Ontologies describing gene functions can be combined with an ontology describing the sequence of genes. http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

12. Why develop an ontology?   To share common understanding of the structure of information.   To allow reuse of domain knowledge.   To make domain assumptions explicit. Dehydrogenases ARE enzymes. http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

13. Why develop an ontology?   To share common understanding of the structure of information.   To allow reuse of domain knowledge.   To make domain assumptions explicit.   Separate domain knowledge from operational knowledge. Domain knowledge about the function of enzymes from the reaction mechanisms of enzymes. http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

14. Why develop an ontology?   To share common understanding of the structure of information.   To allow reuse of domain knowledge.   To make domain assumptions explicit.   Separate domain knowledge from operational knowledge.   Analyze domain knowledge. Formalizing knowledge into defined relationships of an ontology permits computer science to help analyze data. http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

15. Ontology  Describes the concepts or knowledge regarding a particular domain.  An ontology is comprised of Classes Classes concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product - Function of a gene product - Subclasses may exist-- enzyme Subclasses may exist-- enzyme

17. Ontology  An ontology is comprised of Classes Classes concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product - Function of a gene product - Subclasses may exist-- enzyme Subclasses may exist-- enzyme Properties of the classes Properties of the classes specific propertiesspecific properties dehydrogenase dehydrogenase

19. Ontology  An ontology is comprised of Classes Classes concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product - Function of a gene product - Subclasses may exist-- enzyme Subclasses may exist-- enzyme Properties of the classes Properties of the classes specific propertiesspecific properties dehydrogenase dehydrogenase Restrictions on the properties Restrictions on the properties only certain classes of dehydrogenases existonly certain classes of dehydrogenases exist

21. Ontology  Typically, instances of the domain are kept separate from the ontology. Liver alcohol dehydrogenase is an instance. Liver alcohol dehydrogenase is an instance. Combining an ontology with specific instances is a knowledge base (as distinct from a database). Combining an ontology with specific instances is a knowledge base (as distinct from a database).

22. Taxonomy

23. Taxonomy  Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo sapiens

24.  * Gorilla  * Gorilla gorilla (gorilla)  * Gorilla gorilla beringei (mountain gorilla)  * Gorilla gorilla gorilla (lowland gorilla)  * Gorilla gorilla graueri  * Homo  * Homo sapiens (human)  * Homo sapiens neanderthalensis  * Pan (chimpanzees)  * Pan paniscus (pygmy chimpanzee)  * Pan troglodytes (chimpanzee)  * Pan troglodytes schweinfurthii  * Pan troglodytes troglodytes  * Pan troglodytes vellerosus  * Pan troglodytes verus  * Pongo  * Pongo pygmaeus (orangutan)  * Pongo pygmaeus abelii (Sumatran orangutan)  * Pongo pygmaeus pygmaeus (Bornean orangutan)  * Pongo sp.

25. Gene Ontology

26. From: Karen Christie, Ceri Van Slyke and Petra Fey

27. Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey

28. Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey

29. Gene Ontology Apoptosis

30. Utility: Microarray, want to know all genes involved in Apoptosis. Determine fold change in gene expression for all genes involved in Apoptosis. Report all genes, involved in apoptosis, that change at least 2 fold.

31. MeSH Ontology  Medical Subject Headings -provides indexing for PubMed.  Can be used to generate complex queries in a simple fashion.

32. Do not need to remember all these terms

34. Food

35. Fruits Vegetables Meats

36. Food Fruits Oranges ApplesPears Vegetables Meats

37. Food Fruits Oranges ApplesPears System would “know” that apples, oranges and pairs are all fruits, AND that they are edible. Vegetables Meats

38. Food Fruits Oranges ApplesPears Vegetables Meats Chicken “Know” that chicken is not a fruit

39. Food Fruits Oranges ApplesPears Vegetables Meats Chicken Additional subclasses

40. Food Fruits Oranges ApplesPears Vegetables Meats Chicken Additional subclasses Instances