Molecular Interactions – HUPO Proteomics Standards Initiative (original) (raw)

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. This we aim to achieve by presenting our data in a common standard data format (PSI-Mi XML/MITAB). As a result of this, data can be downloaded from multiple sources and easily combined using a single parser

To this end we have developed :

Data standard guidelines

• IMEx – International Molecular Interaction Exchange consortium
• **MIMIx **– the Minimum Information about a Molecular Interaction experiment guidelines to assist the scientist in reporting and submitting interaction data and in manuscript preparation (Full text)
• MIAPAR – the Minimum Information about a Protein Affinity Reagent to assist the scientist in describing reagent, such as antibodies used as protein identification tools (full text).
• **MIABE**– Minimum Information About a Bioactive Entity guidelines to assist the scientist in reporting and submitting drug-target data (Full text)

Data exchange formats

• PSI-MI XML (miXML) 2.5 data interchange format (the deprecated version 1.0 is still available here, with some details on how to convert files from 1.0 into 2.5 version)
  • XSD Schema and auto-generated schema documentation.
  • PSI-XML 2.5 specifications and guidelines
  • PSI-PAR Representation of Protein Affinity Reagents (PARs) in the PSI-MI XML format
• PSI-MI XML (miXML) 3.0 data interchange format
  • XSD Schema and auto-generated schema documentation.
  • The paper is available to read.
• PSI-MI TAB (miTab) (v2.5, v2.6, v2.7 and v2.8) data interchange format, a common tab delimited format.

Controlled vocabularies

• PSI-MI CV the controlled vocabularies for annotating the data in combination with the PSI-MI XML format
• OLS (Ontology Lookup Service) is a centralized query interface for ontology and controlled vocabulary lookup. It provides a web interface, a webservice and can also be installed and run locally.
• Notes on how to adapt the PSI-MI XML2.5 formats and CV terms to annotate cooperative binding such as allosteric events, illustrated with a detailed example are available at http://PSI-MI-CooperativeInteractions.embl.de/. This is not necessary using PSI-MI XML3.0 format.

Tools

• IMEx central application/webservice to centrally register publications and assign IMEx ids.
• PSI-MI online validator tool can be used to validate the syntax, controlled vocabulary terms and semantic (compliant to IMEx rules, MIMIx guidelines, …). The current version of the PSI-MI validator based on JAMI (Java framework for Molecular Interactions) is able to validate both PSI-MITAB 2.5, 2.6 and 2.7 and PSI-XML 2.5.
  • A PSI-MI command line validator can be used in case of large XML files containing thousand of interactions. The source code is open source and can be checked out from here.
  • The PSI-MI validator Java API which can be extended to write your own validator. The validator framework is open source and can be checked out from here.
• PSICQUIC a web service to access interaction data provided by multiple resource around the world.
  • Registry of PSICQUIC services. More information about how to access the registry programmatically can be found here.
  • MIQL: the molecular interactions query language
  • PSICQUIC View is a web application that can browse, search and download molecular interactions from all PSICQUIC webservices.
  • Cytoscape PSICQUIC plugin 3.3 provides support for PSICQUIC web service. Version of the plugin for Cytoscape 2.8 can be found here.
  • Data Distribution Best Practices: guidelines for Data Providers about how to format molecular interactions in PSICQUIC
  • The data enricher is a tool that can enrich molecular interaction data stored in standard formats using different webservices (uniprot for proteins, OLS for controlled vocabulary terms, ChEBI for biochemical entities, …)
  • Java Reference implementation based on LUCENE which can index MITAB 2.5. The source code can be checked out from here. More information about how to install/run this reference implementation can be found here.
  • Java Reference implementation based on SOLR which can index MITAB 2.5, 2.6 and 2.7 (recommended). The source code can be checked out from here. More information about how to install/run this reference implementation can be found here.
  • Default PSICQUIC Java clients are provided but other examples with other languages can be found as well (perl, python).
• JAMI is a Java framework for Molecular Interactions. The framework should provide default interfaces for molecular interactions. It is aimed at parsing/writing PSI-MITAB and PSI-XML 2.5 files and load the objects in a common framework so developing applications on top of the standard formats should be easier for developers.
  • JAMI core interfaces and default implementations source code.
  • PSI-MI XML parser (implements JAMI interfaces) source code.
  • PSI-MITAB parser (implements JAMI interfaces) source code.
  • JAMI to html view writer source code.
• Standard format parsers
  • Java
    * PSI-XML 2.5 parser and writer. Some examples on how to use the Java parsers/writers can be found here.
    * PSI-MITAB 2.5, 2.6 and 2.7 parser and writer.
    * Parser and writer based on a simple Java API representing BinaryInteraction objects.
    * Parser and writer based on Calimocho API. This API represents interactions as a Row in a Document. A Row would be a list of Fields and each Field is a map of key/value pairs.
• Format converters
  • Java
    * PSI-XML 2.5 to RDF/BioPax converters.
    * PSI-MITAB 2.5, 2.6, 2.7 to PSI-XML 2.5 converters. These converters can also be used to convert PSI-XML 2.5 to PSI-MITAB 2.5, 2.6 and 2.7 and are in the same library as the PSI-MITAB parsers and writers.
    * PSI-MITAB 2.5, 2.6, 2.7 to XGMML (cytoscape format) converters.
  • XSLT transformation
    * PSI-XML 2.5 to HTML view
    * MIF25_compact.xsl : conversion from the expanded to the compact form of the PSI 2.5 format.
    * MIF25_expand.xsl : conversion from the compact to the expanded form.
    * MIF25_view.xsl : conversion from xml into “draft” html.
• Scoring systems
  • PSISCORE : PSISCORE is a new approach for confidence scoring of molecular interactions. It relies on standardized data formats and a decentralized client-server architecture, where multiple scoring servers can be used to assess various qualitative aspects of protein interactions.
    * PSISCOREweb : Web-based client for the PSI confidence scoring system
  • Miscore : Miscore is a score for molecular interactions designed to calculate annotation evidence based on common and minimum curated information reporting a molecular interaction experiment.
• Grouping/merging redundant interactions
  • Micluster (Mimerge) : It is a service to regroup multiple interaction evidences of a unique pair of interactors in a single MITAB line.
• Indexing and searching
  • Java
    * Library to index MITAB 2.5 in LUCENE based on MIQL 2.5 fields specification. This library also provides classes to query the LUCENE index and return the results in a BinaryInteraction object
    * Library to index MITAB 2.5, MITAB 2.6 and MITAB 2.7 in SOLR based on MIQL 2.7 fields specification and calimocho tab parser.
    * Library to query and search binary interaction in a PSICQUIC SOLR index. It also provides some scripts to index MITAB 2.5, 2.6 or 2.7 based on SPRING batch framework
• Visualization
  • Cytoscape.js : A JavaScript graph library for analysis and visualisation
  • Cytoscape : Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
• Databases
  • IMEx : The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort.
  • PathGuide : Pathguide is a registry of more than 300 biological pathway and molecular interaction resources.

Data submission

• Data producers are encouraged to deposit data in an IMEx database as an part of the publication process. Further details available here.

Getting involved

If you would like to contribute to the work of the molecular interaction group, or just to receive the occasional email when a new version of a format becomes available, please contact us on psi-mi@ebi.ac.uk and we’ll add you to the mailing list.