Changes between Version 3 and Version 4 of VisualizationAndInteraction

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Timestamp:
2010/02/12 17:15:53 (9 years ago)
Author:
baranda
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  • VisualizationAndInteraction

    v3 v4  
     1=== Participants === 
     2 
     3 * Andrea Splendiani 
     4 * Keiichiro Ono 
     5 * Bruno Aranda 
     6 * Kyung-Hoon Kwon 
     7 * ... 
     8 
     9 
    110== Visualization == 
    211 
     
    2231== Molecular Interactions == 
    2332 
    24 We 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. 
     33We have been working in trying to make [http://psicquic.googlecode.com 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.  
    2534 
    26 http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS 
     35 * PSICQUIC: http://psicquic.googlecode.com 
     36 * PSICQUIC registry: http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS 
    2737 
    2838The 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. 
    2939 
    30 At 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. 
     40At the end of the 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 PSICQUIC reference implementation. 
    3141 
    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. 
     42At 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.  
     43 
     44To do: 
     45 
     46 * 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. 
     47 * Add all the data available in PSI-MI XML to the output. 
    3348 
    3449A test to import the output data into Cytoscape 2.7.0 beta 3 has been successfully done. 
    3550 
    36 === About other PSI formats === 
     51=== Note about other PSI formats === 
    3752 
    3853PSI-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.