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Enhancing Molecular Interactions Data: A Collaborative Success Story

This update explores the progress and challenges faced in improving molecular interactions data. Key topics covered include data summaries, differentiation of experimental data, developing PSICQUIC MITAB2.7, building tools for data validation and enrichment, and creating a common framework for tools/software unification.

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Enhancing Molecular Interactions Data: A Collaborative Success Story

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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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