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Advancements in PSICQUIC Implementation: Enhancing Molecular Interaction Data Management

The review discusses the recent updates to PSICQUIC and PSICQUIC-view, focusing on MITAB2.7 implementation enhancements. Key advancements include sorting abilities, improved SOLR indexing for better search faceting, and updated SOAP services to REST protocols. The document highlights the organization of databases by type, clustering strategies for protein complexes, and the necessity for improved XML schema in version 3.0. Additionally, it emphasizes the need for user feedback on new features and tools designed to streamline data usage and processing in molecular interactions.

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Advancements in PSICQUIC Implementation: Enhancing Molecular Interaction Data Management

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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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