1. “Semantic Web” Applications in Bioinformatics Amr AL-Hossary M.B.B.Ch

2. Agenda Web & Semantic Web RDF & DRF Schema –Elements –Schema –Name space –Queries –Pain, Design Patters, And limits, Applications of SW in Bioinformatics

3. Web Today Documents for HUMANS Increasing dramatically Hard to process on semantic level –e.g. searching for “give her a ring” doesn’t return “engage her”. Solution (semantic web) –annotating definitions –abstract representation of classes & relations

4. What is the Semantic Web?

5. Myths about Semantic Web… is Top-Down needs ontologies at the beginning requires all information to be converted to RDF must be centralized handles only binary relations requires the entire graph to exist on one memory store

6. Truths A means of describing (a Web of) Data A system defining and incorporating semantics A mechanism for making statements on things A format for associating metadata A strategy for federating data systems (with or without triplestore)

7. Needs shared definitions of knowledge domains, i.e. ontologies, association of concepts to existing data, metadata information describing information sources and contents, search tools able to make the best use of this additional information.

8. RDF (Directed) graph data model Set of Binary relations (triples) –Subject Predicate Object NOT like DBMS: Absence of a relation does NOT mean it is not present. XML and RDF/OWL are inherently different –XML = thesaurus document structure –RDF = thesaurus document content

9. Recombinant Data Space RDF is about Graphs rather than statements Separate Graphs can be merged easily into one aggregate graph Graphs can be filtered and pivoted, without losing meaning

10. Works in Studied Sun of Recombinant Data Space Amr Medicine ZaynabAli Amr N U Abolhouda

11. Recombinant Data Space Amr Medicine ZaynabAli Abolhouda N U

12. Recombinant Data Space Amr Medicine Abolhouda N U

13. RDF Elements Resources R Properties P Literal Values L Assertions "R P L" or "R P R" Namespaces

14. RDF Schema RDF Schema (RDFS) is a vocabulary to create vocabularies... –Comparable to XML Schema or XML DTD –Used to standardize which “tags” the creator of a graph is allowed to use for annotating resources Introduces notions such as "Class" and "Subclass„ Helps define which relations a resource of a certain type may have

15. RDFS Namespace Elements X rdf:type rdfs:class –denotes that resource X is a class R rdf:type rdf:Property –denotes that resource R is a property R rdfs:domain X –denotes that the subject of R must be an X R rdfs:range Y –denotes that the object of R must be a Y

16. Cited from http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdfhttp://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf

17. Query Languages RDQL SERQL SPARQL (upcoming W3C Standard)

18. SPARQL Example PREFIX nettab SELECT ?x ?y ?z WHERE { ?x nettab:givesTalk ?z } Matching triple: Subject:http://www.nettab.org/tutorial-ns#hst Predicate: http://www.nettab.org/tutorial-ns#givesTalk Object: http://www.know-who.net/talks/nettab.ppt Cited from http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdfhttp://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf

19. RDF Limitation (& Design Patterns) N-ary Relations –It understands only Binary ralations –Amr Leads Pulse in 2009 Exceptions –Human RBCs are Unnucleated

20. Example Applications of Semantic Web in Bioinformatics

21. Vocabularies (Thesauri) Example Thesauri in Medicine –UMLS –SNOMED –MESH –Galen

22. OKKAM (for ENS)

23. Addison’s disease in medical vocabularies Synonyms –Addisonian syndrome –Bronzed disease –Addison melanoderma –Asthenia pigmentosa –Primary adrenal deficiency –Primary adrenal insufficiency –Primary adrenocortical insufficiency –Chronic adrenocortical insufficiency Eponym Symptoms Clinical Varieties

24. Disease of Endocrine System Addison’s Disease SNOMED International Disease/Diagnosis Disease of the Adrenal Gland

25. Endocrine Disease Addison’s Disease MeSH Adrenal Gland Disease Adrenal Gland Hypofunction Disease

26. Endocrine Disorder Adrenal Disorder Corticoadrenal insufficiency Addison’s Disease AOD Adrenal Cortical Disorder

27. Endocrine Diseases Disorder of Adrenal Gland Hypoadrenalism Corticoadrenal insufficiency Adrenal Hypofunction Addison’s Disease Read Codes

28. Organizing concept Endocrine Diseases Adrenal Gland Diseases Hypoadrenalism Adrenal cortical hypofunction Adrenal Cortex Diseases Adrenal Gland Hypofunction Addison’s Disease SNOMED MeSH ADO Read Codes UMLS

29. UMLS vocabularies available in RDF/OWL NCI Thesaurus (OWL) –http://ncicb.nci.nih.gov/core/EVShttp://ncicb.nci.nih.gov/core/EVS Gene Ontology –http://www.geneontology.orghttp://www.geneontology.org Repository of biomedical ontologies (OBO, OWL) –http://www.bioontology.org/ncbo/faces/index.xhtmlhttp://www.bioontology.org/ncbo/faces/index.xhtml

30. User-defined Datatypes –Based on syntax used in Protégé –Semantics derived from XML Schema datatypes –For numbers: min, max, digits, fraction digits –For strings: length (min, max, equal), regular expression patterns –Class (Teenager complete restriction (age someValuesFrom (datatype(xsd:int minInclusive(“13”^^xsd:int) maxInclusive(“19”^^xsd:int)))))

31. Biological Pathway eXchange (BioPAX) Represent: –Metabolic pathways –Signaling pathways –Protein-protein, molecular interactions –Gene regulatory pathways –Genetic interactions Community effort: pathway databases distribute pathway information in standard format

34. cPath cPath is a database and software suite for storing, visualizing, and analyzing biological pathways

35. cPath Key Features Identifier mapping system e.g. proteins Scalable pathway data aggregation Simple web interface for browse and query Standard web service API for application communication 100% open source –Java, Tomcat, MySQL, Lucene, Struts, YUI Local installation and customization

36. iHOP (information Hyperlink Over Protein) Adding value via text mining

38. Pathway Commons

41. A Genome – Phenome Integrated Approach for Mining Disease-Causal Genes using Semantic Web Gudivada Ranga Chandra Email : gudx6u@cchmc.org Department of Biomedical Engineering/University of Cincinnati Division of Biomedical Informatics/ Cincinnati Children’s Hospital Medical Center

45. Questions?

46. References RDF standard and technologies (presentation) Heiko Stoermer, University of Trento, Italy –http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdfhttp://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf The Unified Medical Language System (UMLS) and the Semantic Web (presentation) Olivier Bodenreider, National Library of Medicine, USA –http://www.nettab.org/2007/slides/Tutorial_Bodenreider.pdfhttp://www.nettab.org/2007/slides/Tutorial_Bodenreider.pdf Semantic Web for Health Care and Life Science Interest Group: A Vision for Advancing Research Communities (presentation) Eric Neumann, Teranode Co., USA. –http://www.nettab.org/2007/slides/SemanticWeb_Neumann.pdfhttp://www.nettab.org/2007/slides/SemanticWeb_Neumann.pdf OKKAM web site –http://www.okkam.org/http://www.okkam.org/ Unified Medical Language System (UMLS) –http://www.nlm.nih.gov/research/umls/http://www.nlm.nih.gov/research/umls/ Biological Pathway eXchange (BioPAX) –http://www.biopax.org/http://www.biopax.org/ cPath: Demo Site –http://cbio.mskcc.org/cpath/http://cbio.mskcc.org/cpath/ iHOP (information Hyperlink Over Protein) –http://www.ihop-net.org/UniPub/iHOP/http://www.ihop-net.org/UniPub/iHOP/ Pathway Commons –http://www.pathwaycommons.org/pc/http://www.pathwaycommons.org/pc/