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Molecular Interactions 2013 Liverpool

Molecular Interactions 2013 Liverpool. PSICQUIC & PSICQUIC-view 2.5/2.6/2.7. Review of new implementation based on MITAB2.7 (2.6/2.5) Reference implementation updated and released – SOLR and Lucene implementations Usage of columns discussed to try and standardize across resources.

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Molecular Interactions 2013 Liverpool

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  1. Molecular Interactions 2013Liverpool

  2. PSICQUIC & PSICQUIC-view 2.5/2.6/2.7 • Review of new implementation based on MITAB2.7 (2.6/2.5) • Reference implementation updated and released – SOLR and Lucene implementations • Usage of columns discussed to try and standardize across resources

  3. PSICQUIC & PSICQUIC-view 2.5/2.6/2.7 Future plans • Add ability to Sort • SOLR indexing allows faceting - enable users to restrict/filter searches based on facets • Update SOAP with new Rest protocols • Organise websites by database ‘types’ • IMEx data • Internally-curated • Imported data • Text-mining/predicted

  4. PSICQUIC -XML • Lukasz Salwinski has XML based reference implementation (alpha) • User directly queries record store, minimizes LOSSY transformation stages as transformation done on indexing • Needs to enable additional download formats but all PSI formats already available • Needs to test and gather statistics on query time and indexing • Can deal with multi-protein complexes

  5. Clustering • To cluster or to merge? • Sufficient to continue to cluster based on MITAB2.5 columns • Continue to rely on identifiers for clustering – keeping isoforms and PRO chains as separate entities

  6. Clustering Jose Villaveces - Demo of tool developed at Max Planck to enable clustering and scoring on the fly using PSICQUIC – library required update to cope with ever-increasing datasize Manuel Bernal Llinares– experience of working with MITAB2.7 – documentation needs improving, and sample code

  7. JAMI • Single JAVA API which operates over both MITAB and XML – ends requirement for redundant development • Initial test-cases – development of Syntax checker and file enricher using web-services • Code available for review and input

  8. Protein complexes • Birgit Meldal (EBI) – encyclopaedia of stable reference complexes • Kim van Roey (EMBL) – annotation of transient complexes • Colin Combes (U Edinburgh) – complex viewer • Sylvie Ricard-Blum (MatrixDB) – extracellular matrix requires complexes as an annotation object Several shortfalls of XML2.5 schema identified as a result of this work

  9. XML3.0 • Need to properly describe complexes – knowledge rather than data so ‘experiment’ now not required • Need to model ‘protein groups’ – enable capture of AP-MS expts. • Opportunity to remove/deprecate unused items compromising parsing • Opportunity to improve capture of additional biology in systematic manner

  10. XML3.0 • Specification needs to be written • Prototype to be prepared • Circulate both for criticism and feedback!!!

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