RDF based on Integration of Pathway Database and Gene OntologySNU OOPSLA LAB.

2005DongHyuk Im

ContentsIntroductionPathway DatabaseEnzyme DatabaseGene OntologyRelated WorksOur ApproachSupporting FunctionData Transformation Integration of KEGG, Enzyme, Gene OntologyQuerying using SeRQL

Pathway?Most chemical reaction mechanisms are translated from a compound(substrate) to a compound(product) by enzyme acting Importanceto comparison and analyze pathways in order to understand the process of creating compounds and the evolutive relevance between organismsDrug Discovery

PathwayMap : Glycolysis / Gluconeogenesis Map : Aquifex aeolicus

Enzyme DatabaseEC numberRecommended nameAlternative names(if any)Catalytic activityCofactors (if any)Pointers to the SWISS-PORT entrie(s) that correspond to the enzyme (if any)Pointers to disease(s) associated with a deficiency of the enzyme (if any)

Enzyme HierarchyFour levelsEC numberEx) 1.1.1.1 is a member of the top level group [1]The leftmost number identifies the highest level[2.4.2.3] [2.4.2.4](sibling) : similar reactions in pathway

[*][1][2][3][2.1][2.2][2.3][2.2.1][2.2.2][2.2.3][2.2.2.1][2.2.2.2][2.2.2.3]

Gene Ontology

KEGG

KEGG To computerize all aspects of cellular functions in terms of the pathway of interacting molecules or genesTo maintain gene catalogs for all organisms and link each gene product to a pathway componentTo organize a database of all chemical compounds in the cell and link each compound to a pathway componentTo develop computational technologies for pathway comparison, reconstruction, and analysis

Why RDF Integration?Pathway data model : DAGRDF is a good model for representing pathwayRDF data model : DAGNeed integration of multiple knowledge sources available from internet : one of the major problems in biologistsRDF is a good model for same standardEnzyme, GO : hierarchy structureRDF is a good model for representing hierarchy structure GO annotation is importantEnzymes(proteins) in certain pathway need GO annotation

Related WorksKEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res. YeastHub: a semantic web case for integrating data in the life science domain, 2005, BioinformaticsLIGAND: database of chemical compounds and reactions in biological pathways, 2002, Nucleic Acids Res.Gene Ontology: tool for the unification biology, the Gene Ontology Consortium, 2000, Nature Genetics.

Our Systems SupportingKEGG Search compoundPath predictionSearch EnzymeOur systems function to addIntegration Query (pathway+enzyme+GO)Relaxation Query using GO hierarchySearching pathway using enzyme information

Search CompoundsCompound : C00668target

Pathway Prediction ToolcompoundRelaxation query using enzyme hierarchy

Search EnzymeEnzyme : 5.3.1.9

From Pathway to Gene OntologySelect enzyme

Data Translation for IntegrationKGML DataXSLTKEGG RDF DataEnzyme RDF DataGO RDF DataGENOS StorageAdding GO IDXSLT : http://www.w3.org/2005/02/13-KEGG/

KEGG RDF Data(1/2)

Gene entryEnzyme entryCompound entryNo information

KEGG RDF Data(2/2)

RelationReaction

How to Process KEGG PathwayProblemGENOS(Sesame) does not support multiple graphKEGG data consists of multiple documentsEx) map00010.rdf, aae00010.rdf SolutionUsing namespace, we can distinguish mapsWhen Storing pathway data, pathways map name is added as a namespace in resource table of GENOS

Processing Pathway Data

..

conflictresourcestable of GENOStriples tableof GENOS

IDNameSpaceLocalname12Glycolysis/3aae#00010_14aq_18656aae#00020_178map#00010_19.

SubjectPredicateObject368

Integrating DatabasesEnzyme numberGO ID

Relaxation Querying using SeRQLE1.*E1.*C1C2E1SELECT C1,C2 FROM Path_EXP WHERE E1 LIKE 1.*" Dewey orderEx. 1.1 and 1.2 are childrens of 1use PrefixSeRQLsubclassofsubclassof

Considering Performance

aae:aq_018path:aae03010aae:aq_020path:aae03010aae:aq_021path:aae00400....eco:b1236path:eco00052eco:b1236path:eco00500eco:b1236path:eco00520.KEGG : Pathway ListGenesMapusing genes_index

ScheduleImplementation (~11/30)Integrated DatabasesQuery Processor for pathwaySimple UI (Web :JSP)Complete Paper (~12/10)