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!!!