Changes between Version 1 and Version 2 of Interaction networks

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Timestamp:
2008/02/11 19:58:49 (11 years ago)
Author:
baranda
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  • Interaction networks

    v1 v2  
    55It already exists an standard exchange format: PSI-MI. Two possibilities: 
    66 
    7  * PSI-MI XML 
     7 * [http://www.psidev.info/index.php?q=node/60 "PSI-MI XML"] 
    88 * PSI-MI TAB  (tabulated) 
    99   * [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README Standard] 
     
    1515 
    1616 * [http://www.ebi.ac.uk/intact IntAct] (Bruno Aranda, EBI) 
    17  * DIP (Lukasz Salwinski, UCLA) 
     17 * [http://dip.doe-mbi.ucla.edu/ DIP] (Lukasz Salwinski, UCLA) 
    1818 * [http://string.embl.de STRING] (Michael Kuhn) 
    1919 * ... (please add yourself) 
     
    3535 
    3636Note: 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  
    37 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). 
     37generated 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). 
    3838 
    39  * Taverna 
     39 * Taverna client 
    4040 * !BioMoby 
    4141 * Check use-cases: 
     
    4646It would be useful to have a common query language for interactions. Options: 
    4747 
    48  * [wiki:PSICQUIC] - we have agreed that the acronym is horrible :) 
    49  * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - what is currently used in !IntAct. 
     48 * [wiki:PSICQUIC] - attempt to create a REST-based query language. 
     49 * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - this is what is currently used in !IntAct. 
    5050   * This option seems to be the simplest according to the participants in the group, and could be a starting point. 
    5151 
     
    5454Cytoscape, as active consumer, has a bunch of use cases that can be a starting point to discuss how interaction data could be mined/queried. 
    5555 
    56 === Implementation of an Interaction DAS Server === 
     56=== Interaction DAS Server === 
    5757 
    58 Nothing specific has been said about this, but it was in the original agenda. 
     58Possibility: http://www.dasregistry.org/extension_interaction.jsp 
     59 
     60Problems: it does not comply neither with the PSI-MI specification nor with the DAS one. 
     61 
     62= Other Resources = 
     63 
     64[http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html "The minimum information required for reporting a molecular interaction experiment (MIMIx)"] 
    5965 
    6066= Important reminder =