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Molecular Interactions 2013Liverpool
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
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
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
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
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
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
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
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
XML3.0
• Specification needs to be written • Prototype to be prepared• Circulate both for criticism and feedback!!!
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