Changes between Version 1 and Version 2 of VisualizationAndInteraction

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Timestamp:
2010/02/12 16:11:39 (9 years ago)
Author:
andrea
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  • VisualizationAndInteraction

    v1 v2  
    1919 
    2020Francois also illustrated the use of RelFinder, which is promising, under specific cirumstances (performant endpoint and "local enough" selections) 
     21 
     22== MOLECULAR INTERACTIONS == 
     23 
     24We have been working in trying to make PSICQUIC output RDF/XML. PSICQUIC is a standard that defines a common way to access Molecular Interaction resources (IntAct, MINT, BioGrid, iRefIndex, MatrixDB, Reactome x2, MPIDB, ChEMBL), reaching more than 1.7 milion interactions. 
     25 
     26http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS 
     27 
     28The approach taken has been to try to make PSICQUIC services return BioPAX Level 3 data. As the underlying data is PSI-MI XML, a converter has been created using JENA. 
     29 
     30At the end of biohackathon, PSICQUIC is able to return RDF data in a variety of formats (RDF/XML, N3, n-triples, etc). This may be a feature of the next release of the reference implementation. 
     31 
     32 At the moment PSICQUIC is returning part of all the information available, but it is a matter of continue implementing the converter to return the rest of data. Currently, the data returned contains interactions, its participants and cross-references for the participants. The ID of the interactions use IntAct URIs from uniprot (e.g. http://purl.uniprot.org/intact/EBI-12345), so in the future this will be changed in order to return the corresponding URI for all the different services depending on the original data source. 
     33 
     34A test to import the output data into Cytoscape 2.7.0 beta 3 has been successfully done. 
     35 
     36ABOUT OTHER PSI FORMATS 
     37 
     38PSI-MI XML is one of the PSI (Proteomics Standards Initiative) formats. There are other standard formats to manage mass spectrometry data (mzML), data analysis (analysisML) or sample preparations (spML). These may be converted to RDF equivalent formats in the future. Next month is taking place the PSI Meeting in Seoul, where this may be discussed.