1. Agenda Intro: Information management in Biology Information management engineering Formats and standards XML MAGE example Perspectives: the Semantic Web The semantic web Semantic Web and Biology Service Integration: web services Conclusions

2. Where do we are? We have good technologies for data management applications We have XML for data exchange But it's not enough... What about semantics in XML? How to exchange XML? How to interface the applications? Is it possible without IT specialists?

3. Ontologies

4. Examples of queries with ontologies ● “nails is-part-of elephant”? yes, because: – “has-legs” and “has-nails” are particular “has-parts” transitive relation – “is-part-of” is the inverse of “has-parts”

5. Ontologies Examples of queries with ontologies ● “giraffe is-eaten-by lion”? yes, because: – giraffe is-a herbivore => is-a animal lion is-a carnivore => lion eats animal => lion eats giraffe “is-eaten” is the inverse of “eats”

6. ArrayExpres s MIAMExpress RAD MAGE-ML data exchange Ontology instances propagated to submission/annotation web forms Curation of user defined terms, before inclusion in the ontology User defined terms collected via forms MGED Ontology BiomaterialDescriptio n Sex C C C C Gender documentation: Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender. used in individuals: female, hermaphrodite,male,mixed_sex,unknown_sexfemalehermaphroditemixed_sexunknown_sex MAGE and Ontologies

7. THE “ontology”: Gene Ontology

8. Semantic Web The Web is a huge repository of information Information is unstructured and without associated structured semantics We need to semantically structure the information We need to share semantic representations We need to “reason” over knowledge (inference) Ontologies and other semantic-aware formalisms + XML + standards + semantic-web engines + applications = Semantic Web

9. Semantic Web examples

10. Semantic Web: Annonzilla

12. Semantic Web examples

13. Friend of a Friend (FOAF), see also LinkedIn

14. RSS, possible future of PubMed and alike RSSOwl, try with feeds from: Nature, Bioinformatics, etc. RSSOwl, try with feeds from: Nature, Bioinformatics, etc.

15. Semantic Web, RDF, Bioinformatics

18. You may handle statements Subject/Property(or verb)/Object may reference public resources, identified by URIs (like Web pages) A given resource may flexibly be annotated by many statements Meaning of statements may be defined by other statements and higher languages (which still are RDF representable)

19. Semantic Web, RDF, Bioinformatics

21. Refer to the same resource The second doc extends the first one

22. Semantic Web, RDF, Bioinformatics

23. Semantic Web layered cake

24. URI: how to address thing on internet Unicode: the “alphabet” RDF-S, OWL: ontologies, define the semantics of things SPARQ-L: to make semantic-aware queries Logic, proof, trust: deductions, logical “reasoning”, inference Unfortunately all this complexity is needed for...

25. ...this!

26. Metabolic Pathways Molecular Interaction Networks Signaling Pathways Main categories: Bioinformatics Semantic Web: BioPAX

27. species reactionmodifier

28. BioPAX Motivation Before BioPAXWith BioPAX Common format will make data more accessible, promoting data sharing and distributed curation efforts >150 DBs and tools Database Application User

29. BioPAX in action

31. Bioinformatics Semantic Web Several other in-progress examples GandrKB Flymine Microarrays annotations (my PhD...) FUGE (MAGE 2) YeastHUB (simple integration by means of RDF)...

32. Services Integration User Amazon Web site 3 rd parties catalogs Purchase Service CC service VISA Mastercard... 3 4 5 1 2,2b 6 7 8 9

33. Services Integration How to realize such services integration? Call remote code (RPC, J2EE) Code mobility (Java Applets, Agents) Exchange messages, use XML => SOAP and Web services How to discover services? Handily or Registers How to know that a service is about “book purchasing”? Up to user Ontologies! How to compose services? Up to user Reasoning!

34. Services Integration Bank Trading Agent Stock Exch Service http://www.stock.org/stock IBM http://www.stock.org/stock 34.5

35. Web services in Biology

37. myGRID and Taverna

40. Future of Web services? Give me the directions from A to B...

41. Future of Web services?

42. Agenda Intro: Information management in Biology Information management engineering Formats and standards XML MAGE example Perspectives: the Semantic Web The semantic web Semantic Web and Biology Service Integration: web services Conclusions

43. What should a biologist know? Bioinformatics integration is a complex task Must be done by informaticians and biologists, together As user, should have notion of general concepts: Models and architectures Object and relational models n-tiers systems Distributed systems, web services etc. As user/curator should be aware of knowledge representation issues The idea of standards, some standards The idea of ontology, some ontologies Should know about tools existence, try to use!

44. Thanks! Find this slides at: http://bioguest.btbs.unimib.it/~brandizi/master05