Changes between Version 1 and Version 2 of Data_exchange

Timestamp:

2010/02/12 16:46:19 (15 years ago)

Author:

gmicklem

Comment:

--

Data_exchange

@@ -2 +2 @@
 Wednesday 10th February p.m. - Room 516
 
-Semantic Data Exchange
-
-Gos Micklem
-Richard Smith
-James Taylor
-Arek Kasprzyk
-Soichi Ogishima
-Brad Chapman
-Christian Zmasek
-Peter Cock
-Hideyuki Morita
-Ryosuke Ishiwata
-Kei Ono
-Shinobu Okamoto
-Alberto Labarga
-
-------------------------------------------------------------------------------
-Discussion on possibilities/need for improving data exchange between
-e.g. InterMine, Galaxy, BioMart, Cytoscape...
+''' Semantic Data Exchange'''
+
+ * Gos Micklem
+ * Richard Smith
+ * James Taylor
+ * Arek Kasprzyk
+ * Soichi Ogishima
+ * Brad Chapman
+ * Christian Zmasek
+ * Peter Cock
+ * Hideyuki Morita
+ * Ryosuke Ishiwata
+ * Kei Ono
+ * Shinobu Okamoto
+ * Alberto Labarga
+
+'''Discussion on possibilities/need for improving data exchange between
+e.g. InterMine, Galaxy, BioMart, Cytoscape...'''
 
 Would typing of arbitrary data exchange improve communication between
@@ -27 +26 @@
 
 
-Current situation:
+'''Current situation:'''
 
 It was felt that the current situation wasn't so bad: however it would
@@ -42 +41 @@
    needed>
 
-   Cytoscape (http://www.cytoscape.org)/BioMart: REST API used.  Perhaps SOAP would be better but
+   Cytoscape (http://www.cytoscape.org) & BioMart: REST API used.  Perhaps SOAP would be better but
    this still requires some development.  REST was fine for data
    retrieval.
@@ -141 +140 @@
 large-scale users/providers can start to comply.
 
-
-Data exchange conclusions:
-*** A namespace for file formats would be useful.
-
-*** A namespace for column of tabular data would be useful.  Could
+'''Data exchange conclusions:'''
+ * A namespace for file formats would be useful.
+
+ * A namespace for column of tabular data would be useful.  Could
     also be used to describe data in other formats e.g. XML, though
     this could be rather verbose.
-*** Investigate whether the above exist.
+ * Investigate whether the above exist.
     Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup)
     and/orLife Science Resource Name Project (http://www.lsrn.org)
     applicable ?
 
-*** At the moment namespaces for columns is probably more important
+ * At the moment namespaces for columns is probably more important
     than URIs for each data element in a column.
 
-Agreed that worthwhile to pass URIs to describe columns.  Agreed that
-arbitrary human-friendly names are also good.
-
-*** Agreed to dump all BioMart/ InterMine column headings out, find
+ * Agreed that worthwhile to pass URIs to describe columns.  Agreed that
+  arbitrary human-friendly names are also good.
+
+ * Agreed to dump all BioMart/ InterMine column headings out, find
     the common/commonly-used ones and work on naming.
 
 
 
-========== Discussion turned to genome builds:
+'''Discussion turned to genome builds:'''
 
 There is no-where to go to find out if entities/ coordinates come from
@@ -201 +199 @@
 version.
 
-Genome version summary:
-* Investigate whether is there a standard available for describing genome version *
-* Consider whether to base naming on ensembl genome/ annotation versions *
-
-
-
-=========== Thoughts on RDF:
+'''Genome version summary:'''
+ * Investigate whether is there a standard available for describing genome version
+ * Consider whether to base naming on ensembl genome/ annotation versions
+
+
+
+'''Thoughts on RDF:'''
 
 If everyone is expressing their data in RDF with a common underlying