molecular interactions 2012-2013
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Molecular Interactions 2012-2013. Sandra Orchard EMBL-EBI. Follow-up on San Diego. PSICQUIC – a success story: 25 services, 152 million interactions but Users need data summaries (clusters) – Jose/ Rafael - PowerPoint PPT PresentationTRANSCRIPT
Sandra OrchardEMBL-EBI
Molecular Interactions 2012-2013
Follow-up on San DiegoPSICQUIC – a success story: 25 services, 152 million interactions
butUsers 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
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 tools1. 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
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
Follow-up on San Diego2 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)
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
Issue highlighted in San Diego - segmentation of the tools/software
PSI-XML 2.5
- MI-XML validator- can be used to exchange fully MIMIx/IMEx compliant data
- PSICQUIC- Enricher- clustering and scoring- can be easily used for visualization/networking
PSI-MITAB 2.5, 2.6 and 2.7
Need to unify our tools/software
Proposed solution: common framework?
PSI-XML 2.5 PSI-MITAB 2.7 Databases + Other formats
Common API/framework (interfaces)
PSICQUIC and indexing
Semantic validator Data enricher
Protein updateClustering and scoring
JAMI
Plans for this week1. In depth summary of this year’s activities and
issues arising2. JAMI3. Annotation of complexes
• Stable entities• Transient complexes• Can the current XML deal with complexes?
4. XML3.05. CV updates
IMEx Members= 248,753 interactionsFrom >6000 publications