Molecular interactions. PSICQUIC and IntAct.
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Enabling Systems Biology. Bioinformatics Workshop April 13-14, 2011
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Molecular interactions. PSICQUIC and IntAct.
- 1. Enabling Systems Biology Bioinformatics Workshop April 13-14, 2011 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation Molecular interactions PSICQUIC and IntAct
- 2. Integration, standards and dissemination Uniprot Protein Sequences Reactome Pathways IntAct Interactions PRIDE Mass Spec DAS PSICQUIC EnCore Annotation Archive
- 3. sequence databases (INSDC) EMBL DDBJ NCBI interactions IMEx IntAct BIND DIP MINT … mass spec ProteomeXchange PRIDE PeptideAtlas GPMDB Tranche … Sharing infrastructures • Multiple repositories in a particular field Collaboration and data exchange More data coverage
- 4. 4 PSI-MI Data format Data distribution Control vocabulary Data submission Website Search Interactions Interaction details Interactors Molecular view Graph view Standard format Tools PSICQUIC PSI-MI CV Reporting guideline MIMIx Tools PSI-MI XML PSI-MITAB XML Java API MITAB Java API XMLMakerFlattener Semantic Validator RPsiXML (Bioconductor) PSI-MI XML files PSI Excel Sheet PSI Web Form Data Servers Registry Clients PSISCORE Servers Registry Clients
- 5. • Work group of the Proteomics Standards Initiative • Community coordination to ensure deposition of data in public repositories • Concentrating on … – Annotation and representation of published MI data – Accessibility of MI data to the user community PSI - Molecular Interactions Data format Data distribution Control vocabulary MIAPE Reporting guideline PSI-MI XML PSI-MITAB PSICQUIC MIMIxPSI-MI CV http://www.psidev.info/MI Scoring PSISCORE
- 6. PSI-MI format • Community standard for Molecular Interactions • Jointly developed by major data providers: BIND, CellZome, DIP, GSK, HPRD, Hybrigenics, IntAct, MINT, MIPS, Serono, U. Bielefeld, U. Bordeaux, U. Cambridge, and others • Collecting and combining data from different sources has become easier • Standardized annotation through PSI-MI ontologies • Tools from different organizations can be chained, e.g. IntAct data in Cytoscape. 6 psi-mi/xml25psi-mi/xml25 psi-mi/tab25psi-mi/tab25
- 7. PSI-MI Control vocabulary • Ontology browser: http://www.ebi.ac.uk/ontology-lookup
- 8. MIMIx • MIAPE document guideline for molecular interactions • 1. Manuscript information • 2. Experiment • 3. Interaction • 4. Confidence
- 9. Data distribution: PSICQUIC • Proteomics Standards Initiative Common QUery InterfaCe. • Community effort to standardise the way to access and retrieve data from Molecular Interaction databases. • Widely implemented by independent interaction data resources. • Based on the PSI standard formats (PSI-MI XML and MITAB) • Not limited to protein-protein interactions, also e.g. • Drug-target interactions • Simplified pathway data • A registry listing resources implementing PSICQUIC • Documentation: http://psicquic.googlecode.com
- 10. PSICQUIC Query Interactions PSICQUIC Registry PSI-MIMIQL Input Output PSICQUIC Service A PSICQUIC Service B PSICQUIC Service C User View Web Service System Data Provenance
- 11. PSICQUIC Registry • 16 sources • 16,358,233 interactions http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
- 12. PSICQUIC example: REST queries Bruno Aranda (baranda@ebi.ac.uk) http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/query/p53 http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/p53 http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/p53 1 2 3
- 13. PSICQUIC example: MIQL Bruno Aranda (baranda@ebi.ac.uk) • Molecular Interaction Query Language
- 14. PSICQUIC example: MIQL …/query/specie:rat …/query/brca AND rpa1 • Terms • Fields • Operands
- 17. 0.90 0.380.25 —0.63 0.45 0.71 0.40 0.11 PSICQUIC PSISCORE Query Interactions PSI-MI 0.90 0.380.25 —0.63 0.45 0.71 0.40 0.11 PSICQUIC Registry Confidence Scores PSI-MIMIQL PSISCORE Registry client Input Input Output Output PSICQUIC Service A PSICQUIC Service B PSISCORE Service D PSISCORE Service E PSICQUIC Service C User View Web Service System
- 18. PSISCORE registry • 4 sources • 14 scoring methods
- 19. PSISCORE client
- 20. EnVision: a PSICQUIC & PSISCORE client
- 21. IntAct • Freely available, open-source database system • Public repository of molecular interactions • Interactions manually curated and reviewed by experts • Interaction derived from literature or direct user submissions • Topic centric datasets (eg. Cancer, Chromatin, MSD…) • Analysis tools for interaction data • EBI database (part of the IMEx consortium and the PSI-MI) • Data updated every week: ftp://ftp.ebi.ac.uk/pub/databases/intact • Data formats available: http://www.ebi.ac.uk/intact
- 24. • Interactions by identification method • ~70% Y2H • ~25% Affinity purification • ~3% Physical data • ~2% Other methods IntAct statistics
- 25. UniProt Taxonomy PubMed Method (PSI-MI CV)Interaction details Complex ?Interactors IntAct: Search and results
- 26. IntAct: Search and results Export Custom columns Filters More results (PSICQUIC)
- 27. IntAct
Editor's Notes
- HUPO The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training. PSI The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification. PSI-Molecular Interactions Work group of the Proteomics Standards Initiative focused on Molecular Interactions IMEx The IMEx consortium is a group of major public interaction data providers sharing curation effort. IntAct Open source database system and analysis tools for molecular interaction data including information derived from literature curation or direct user submissions.
- The Molecular Interactions workgroup is concentrating on: improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser
- PSICQUIC Server (web service). Provide data from PSI-MITAB PSICQUIC Registry. Find data providers PSICQUIC Clients. Visualize data from different providers.
- Each line is a binary interaction evidence reported by a scientific publication Evidences are grouped by molecule pairs (allowing for subsequent filtering should you need to) Data can be downloaded in standard formats (see table header) Only 30 interactions per page for speedy loading One can customize the list of columns by clicking on the “Change Column Displayed”
- Each line is a binary interaction evidence reported by a scientific publication Evidences are grouped by molecule pairs (allowing for subsequent filtering should you need to) Data can be downloaded in standard formats (see table header) Only 30 interactions per page for speedy loading One can customize the list of columns by clicking on the “Change Column Displayed”