Henning Hermjakob - ProteomeBinders

Designing a Binder DatabaseProteomeBinders meeting Alpbach, March 2007Henning Hermjakob, Proteomics ServicesEuropean Bioinformatics Institute

ProteomeBinders mission statement• Establish a comprehensive infrastructure resource ofbinding molecules for detection of the human proteome,together with tools for their use and applications instudying proteome function and organisation.Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Initiatives for Proteome Binderdevelopment• EU ProteomeBinders• Swedish Human Protein Atlas• US NCI initiative• German Antibody factory• …• Many commercial providersHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Data types relevant for Proteome Binders• Molecular entities• Binders• Targets• Experimental data• Applications/Validation Protocols and outcomes• Systematic, for example Western• Specific: Publication by researcher X: Successful use of binder Y• Production parameters• …Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Data fragmentation• Difficult to access allrelevant data• Difficult tosynchroniseefforts…User**Commercial/BiocompareProteomeBindersHPANCIHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

The HUPO Proteomics Standards Initiative• Develop data format standards• Data representation and annotationstandards• Involve data producers, databaseproviders, software producers, publishers• Open community initiativeHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

HUPO PSI MI XML format• Community standard for Molecular Interactions• XML schema and detailed controlled vocabularies• Exchange format, not internal format• Jointly developed by major data providers:BIND, CellZome, DIP, GSK, HPRD, Hybrigenics, IntAct,MINT, MIPS, Serono, and others• Version 1.0 published in February 2004The HUPO PSI Molecular Interaction Format - A communitystandard for the representation of protein interaction data.Hermjakob et al, Nature Biotechnology 2004, 22, 176-183.• Version 2.5 (Released December 5, 2005)covers flexible molecule types, and parameters• http://psidev.sf.net/mi/rel25Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

PSI MI components• XML format• Controlled vocabulary• Implemented in databases(DIP, MINT, MIPS, IntAct)• Validation tools• Process for controlledvocabulary and schemamaintenance• Inter-database exchange(in progress)Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

PSI MI components• XML format• Controlled vocabulary• Implemented in databases(DIP, MINT, MIPS, IntAct)• Validation tools• Process for controlledvocabulary and schemamaintenance• Inter-database exchange(in progress)Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

PSI MI components• XML format• Controlled vocabulary• Implemented in databases(DIP, MINT, MIPS, IntAct)• Validation tools• Process for controlledvocabulary and schemamaintenance• Inter-database exchange(in progress)Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Working hypothesis:Binder-Target binding is a special case of molecularinteractionTargetPrESTModificationsExpressionACSeqAntigenBinding *ExperimentTypeSource*Binder inst.SpecificityScoreEvidenceMethodLabBinderconcentrationHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Requirements gathering• What are the use cases for data exchange betweenbinder resources and users?• Which data types and attributes are required in each ofthese use cases?• Detailed requirements gathering, feedback fromparticipants of ProteomeBinders• ProtemeBinders workshop St. Emillion, July 2006• ProtemeBinders Deliverable - doneHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Data model development• Mapping requirements to PSI MI data model• For all relevant data items, check if they can be consistentlymapped to the PSI MI data model• HUPO PSI workshop Washington, September 2006• ProtemeBinders workshop Cambridge, December 2006Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Current status• “Working hypothesis” confirmed:At least the core data for the ProtemeBinder use casescan be consistently mapped to the PSI MI 2.5 XMLschema• Detailed proposal for the extension of the PSI MIcontrolled vocabularies• To be discussed/approved at PSI meeting April 23-25, 2007, inLyon, France• Some controlled vocabularies specific toProteomeBinders need to be developed• Some schema extensions potentially required in the nextversion of the PSI MI schemaHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Next steps• Development of prototype ProteomeBinders productiondatabase• Capture detailed records on binder production, properties, andquality control• Existing IntAct molecular interaction database can be used asbasis for development• Development of prototype ProtemeBinders warehouse• Present summarised, processed user views, for example qualityassessments based on multiple independent experiments• Advanced tools, for example support for binder array designHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Perspective• Standard binder formatfacilitates data exchangebetween resources and users• Regular data exchange ofhigh level data betweenresources allows users toquickly get an overview ofavailable binders suitable forspecific task…User**Commercial/BioCompareProteomeBindersHPANCIHenning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007

Acknowledgements• Sandrine Palcy, U.Bordeaux• David Sherman, U.Bordeaux• David Gloriam, EBI• Sandra Orchard, EBI• Luisa Montecchi-Palazzi, EBI• Antoine de Daruvar, U.Bordeaux• All ProteomeBindersparticipants• All HUPO PSIparticipants• EU ProteomeBindersfunding• YOU!http://cbi.labri.fr/ProteomeBinders/bin/view/NA5/WebHomehttp://www.psidev.info/Henning HermjakobProteomics Services TeamProteomeBindersAlpbach meeting, March 2007