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Molecular Interactions 2012-2013

Molecular Interactions 2012-2013. Sandra Orchard EMBL-EBI. Follow-up on San Diego. PSICQUIC – a success story: 25 services, 152 million interactions but Users need data summaries (clusters) – Jose/ Rafael

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Molecular Interactions 2012-2013

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  1. Molecular Interactions 2012-2013 Sandra Orchard EMBL-EBI

  2. Follow-up on San Diego PSICQUIC – a success story: 25 services, 152 million interactions but Users need • data summaries (clusters)– Jose/ Rafael • the ability to differentiate experimental data from predicted/text-mined and also primary data sources from imported/recycled We agreed to move to tagging individual records as resources upgrade to MITAB2.7- no advance made

  3. Follow-up on San Diego • Agreement on information which should be included in each field – Data Distribution Best Practice document • Need to build suite of tools 1. MITAB validator to ensure file is correctly formatted- Marine 2. Data enricher – takes the minimal information in the file and use web services (e.g. PICR, UniProt) to add more information in a consistent manner across multiple files – EBI student

  4. Follow-up on San Diego • Urgently need to develop PSICQUIC MITAB2.7 and eventually PSICQUIC XML identified Hackathon 28th May – 1st June 2012 • 10 developers from 7 different groups • BioJS, Cytoscape, DIP, InnateDB, IntAct, MatrixDB, MINT, MPIDB

  5. Follow-up on San Diego 2 working groups SOLR team: reference implementation • indexing MITAB 2.5, 2.6 and 2.7 using SOLR • MIQL 2.7 • XML indexing and PSICQUIC webservices improvements - publication under 2nd round review Client team: • PSICQUIC view visualization: table, network and search • Cytoscape plugin BioJS: An Open Source JavaScript Framework for Biological Data Visualization (PMID:23435069)

  6. Follow-up on San Diego - CVs • Allostery terms approved– terms added and manuscript on usage under review • More terms relating to transcription factor/gene binding requested – added • List of databases + search URLs + regexs could potentially be replaced by use of MIRIAM registry - not done yet • PTM terms finally obsoleted

  7. Issue highlighted in San Diego - segmentation of the tools/software PSI-MITAB 2.5, 2.6 and 2.7 PSI-XML 2.5 - PSICQUIC - Enricher - clustering and scoring - can be easily used for visualization/networking - MI-XML validator - can be used to exchange fully MIMIx/IMEx compliant data Need to unify our tools/software

  8. Proposed solution: common framework? PSICQUIC and indexing Semantic validator Data enricher Protein update Clustering and scoring JAMI Common API/framework (interfaces) Databases PSI-XML 2.5 PSI-MITAB 2.7 + Other formats

  9. Plans for this week • In depth summary of this year’s activities and issues arising • JAMI • Annotation of complexes • Stable entities • Transient complexes • Can the current XML deal with complexes? • XML3.0 • CV updates

  10. IMEx Members = 248,753 interactions From >6000 publications

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