Changes between Version 9 and Version 10 of Interaction networks

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Timestamp:
2008/02/14 12:55:46 (10 years ago)
Author:
baranda
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  • Interaction networks

    v9 v10  
    3030 
    3131 * !IntAct already provides a very simple SOAP based web service (http://www.ebi.ac.uk/~intact/devsite/remote/binarysearch_ws.html) 
     32 
    3233 * NCBI Entrez Gene has meta-database of interactions (MINT, !BioGrid, and BIND), but access to these dataset is hard due to API design. 
    3334 
     
    4849   * Get interaction or partners not only using Uniprot IDs (the primary identifiers for interactors used in !IntAct) 
    4950  
     51Note: during the week, a common WSDL for interaction web services has been defined, so this section will be accomplish by implementing such a service. 
     52 
    5053=== Define a common Interaction Query Language === 
    5154 
     
    5356 
    5457 * [wiki:PSICQUIC] - attempt to create a REST-based query language. 
    55  * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - this is what is currently used in !IntAct. 
    56    * This option seems to be the simplest according to the participants in the group, and could be a starting point. 
     58   * A common WSDL, based on the original ideas of PSICQUIC and new requirements, will be defined in the BioHackathon 
     59 * [http://lucene.apache.org Lucene] based searches over PSI-MI tab files - this is what is currently used in !IntAct. 
     60   * This option is really powerful. A method allowing queries will be part of the common WSDL. However, it is not clear if all providers will implement this method (!IntAct will, well, it is actually using it :) ) 
    5761 
    5862=== Define specific use-cases === 
     
    6569 
    6670Problems: it does not comply neither with the PSI-MI specification nor with the DAS one. 
     71 
     72Due to time constraints, no effort will be dedicated in the BioHackathon to this. 
    6773 
    6874= Other Resources = 
     
    8288   * The methods should be in the default exchange format (PSI-MI XML).  
    8389   * Problem: This means dealing with potentially huge files (about 30 Mb for 2000 interactions, and databases such as IntAct contain 100000+ and increasing exponentially). 
    84       * Solution: unknown (using URIs?)  
     90      * Solution: unknown ~~(using URIs?)~~ (comment from Day 4: pagination of the results will be implemented in the first version) 
    8591 
    8692== Day 3 == 
     
    8995 * PSI-MI Reader should be modifed to read more details in the object.  (Currently, some of the details are skipped.) 
    9096 * Need to add a switch to import minimal dataset (graph information only.  No attributes) or full detail. 
     97 
     98== Day 4 == 
     99=== PSICQUIC - Common Web Service interface for all Interaction providers === 
     100A initial set of methods have been defined and can be seen in the latest WSDL attachments. 
     101Basically, the result of the search methods will return !EntrySet (MIF) or MITAB format, dependending on the return type format parameter passed to the method. Some metadata about the query will be returned too (e.g. total results, first result index, block size, expirationDate...). 
     102The PSIMITAB format will be output by the methods wrapped in very simple XML (mitab-1.0.xml schema attached), that defines rows and columns instead of returning just plain strings that need to be parsed.