Sandra Orchard

EMBL-EBI

Molecular Interactions 2012-2013

Follow-up on San Diego

PSICQUIC – a success story: 25 services, 152 million interactions

but

Users 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 tools

1. 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 Diego

2 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 week

1. In depth summary of this year’s activities and issues arising

2. JAMI

3. Annotation of complexes

• Stable entities

• Transient complexes

• Can the current XML deal with complexes?

4. XML3.0

5. CV updates

IMEx Members= 248,753 interactionsFrom >6000 publications