= Overview = == Exchange format == It already exists an standard exchange format: PSI-MI. Two possibilities: * [http://www.psidev.info/index.php?q=node/60 "PSI-MI XML"] * PSI-MI TAB (tabulated) * [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README Standard] * Expanded (!IntAct) - Additional columns to the standard, containing information like bait-prey, types, cross-references... == Service Providers == Service providers at the Hackathon * [http://www.ebi.ac.uk/intact IntAct] (Bruno Aranda, EBI) * [http://dip.doe-mbi.ucla.edu/ DIP] (Lukasz Salwinski, UCLA) * [http://string.embl.de STRING] (Michael Kuhn) * ... (please add yourself) == Service consumers == * [htt://www.cytoscape.org Cytoscape] (Keichiro Ono) * ... (please add yourself) = Existing Web Services = == !IntAct Web service == * !IntAct already provides a very simple SOAP based web service (http://www.ebi.ac.uk/~intact/devsite/remote/binarysearch_ws.html) * NCBI Entrez Gene has meta-database of interactions (MINT, !BioGrid, and BIND), but access to these dataset is hard due to API design. = Existing Clients = * Please visit [http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients this] page for Cytoscape clients and its visualizations. = Objectives = === Improve the existing !IntAct web service === Note: the !IntAct web service is in fact a web service that searches on a PSI-MI TAB file that contains all the interactions present at !IntAct. All the (java) code generated at !IntAct is open-source and licensed under the Apache Commons License 2.0. It means that this web service implementation could be used over any PSI-MI TAB file (not just the !IntAct ones). * Taverna client * !BioMoby * Check use-cases: * Get interaction or partners not only using Uniprot IDs (the primary identifiers for interactors used in !IntAct) === Define a common Interaction Query Language === It would be useful to have a common query language for interactions. Options: * [wiki:PSICQUIC] - attempt to create a REST-based query language. * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - this is what is currently used in !IntAct. * This option seems to be the simplest according to the participants in the group, and could be a starting point. === Define specific use-cases === Cytoscape, as active consumer, has a bunch of use cases that can be a starting point to discuss how interaction data could be mined/queried. === Interaction DAS Server === Possibility: http://www.dasregistry.org/extension_interaction.jsp Problems: it does not comply neither with the PSI-MI specification nor with the DAS one. = Other Resources = [http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html "The minimum information required for reporting a molecular interaction experiment (MIMIx)"] = Important reminder = This is a wiki. Please, participate with your thoughts/additions/comments! :)