Changes between Version 1 and Version 2 of Interaction networks

Timestamp:

2008/02/11 19:58:49 (17 years ago)

Author:

baranda

Comment:

--

Interaction networks

@@ -5 +5 @@
 It already exists an standard exchange format: PSI-MI. Two possibilities:
 
- * PSI-MI XML
+ * [http://www.psidev.info/index.php?q=node/60 "PSI-MI XML"]
  * PSI-MI TAB  (tabulated)
    * [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README Standard]
@@ -15 +15 @@
 
  * [http://www.ebi.ac.uk/intact IntAct] (Bruno Aranda, EBI)
- * DIP (Lukasz Salwinski, UCLA)
+ * [http://dip.doe-mbi.ucla.edu/ DIP] (Lukasz Salwinski, UCLA)
  * [http://string.embl.de STRING] (Michael Kuhn)
  * ... (please add yourself)
@@ -35 +35 @@
 
 Note: 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 
-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).
+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).
 
- * Taverna
+ * Taverna client
  * !BioMoby
  * Check use-cases:
@@ -46 +46 @@
 It would be useful to have a common query language for interactions. Options:
 
- * [wiki:PSICQUIC] - we have agreed that the acronym is horrible :)
- * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - what is currently used in !IntAct.
+ * [wiki:PSICQUIC] - attempt to create a REST-based query language.
+ * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - this is what is currently used in !IntAct.
    * This option seems to be the simplest according to the participants in the group, and could be a starting point.
 
@@ -54 +54 @@
 Cytoscape, as active consumer, has a bunch of use cases that can be a starting point to discuss how interaction data could be mined/queried.
 
-=== Implementation of an Interaction DAS Server ===
+=== Interaction DAS Server ===
 
-Nothing specific has been said about this, but it was in the original agenda.
+Possibility: http://www.dasregistry.org/extension_interaction.jsp
+
+Problems: it does not comply neither with the PSI-MI specification nor with the DAS one.
+
+= Other Resources =
+
+[http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html "The minimum information required for reporting a molecular interaction experiment (MIMIx)"]
 
 = Important reminder =