Changes between Version 3 and Version 4 of VisualizationAndInteraction

Timestamp:

2010/02/12 17:15:53 (15 years ago)

Author:

baranda

Comment:

--

VisualizationAndInteraction

@@ +1 @@
+=== Participants ===
+
+ * Andrea Splendiani
+ * Keiichiro Ono
+ * Bruno Aranda
+ * Kyung-Hoon Kwon
+ * ...
+
+
 == Visualization ==
 
@@ -22 +31 @@
 == Molecular Interactions ==
 
-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.
+We 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. 
 
-http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
+ * PSICQUIC: http://psicquic.googlecode.com
+ * PSICQUIC registry: http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
 
 The 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.
 
-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.
+At 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.
 
- 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.
+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. 
+
+To do:
+
+ * 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.
+ * Add all the data available in PSI-MI XML to the output.
 
 A test to import the output data into Cytoscape 2.7.0 beta 3 has been successfully done.
 
-=== About other PSI formats ===
+=== Note about other PSI formats ===
 
 PSI-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.