Changes between Version 42 and Version 43 of OpenBio

Timestamp:

2010/02/12 15:43:37 (15 years ago)

Author:

tkappler

Comment:

Perl and RDF

OpenBio

@@ -16 +16 @@
  * Christian Zmasek
  * Keun-Joon Park
+ * Thomas Kappler
 
 === RDF libraries in each language ===
@@ -30 +31 @@
   * SPARQLWrapper http://sparql-wrapper.sourceforge.net/
  * Perl
-  * RDF: generic RDF library
+  * RDF:Trine: generic, actively developed RDF library
+  * RDF::Redland: Perl wrapper for the C library Redland (librdf.org)
+  * List of modules and community at www.perlrdf.org
   * [http://search.cpan.org/dist/ONTO-PERL/ ONTO-PERL]: it might be used (it is, however, OBO-centric http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn042)
 
@@ -37 +40 @@
  * RDF reader (in)
  * RDF generator (out)
+ * SPARQL query helpers
 
-|| language || in || out||
-|| Ruby || ? || ? ||
-|| Python || o || ? ||
-|| Perl || o || ? ||
+|| language || in || out || query ||
+|| Ruby || ? || ? || ? ||
+|| Python || o || ? || ? ||
+|| Perl || o || o || o ||
 
 === Tools to manipulate RDF data ===
@@ -58 +62 @@
 
   * general:
-    * RDF --> JSON (for [http://couchdb.apache.org/ CoachDB], [http://www.mongodb.org/ mongoDB] etc.)
+    * RDF --> JSON (for [http://couchdb.apache.org/ CouchDB], [http://www.mongodb.org/ mongoDB] etc.)
+      * easy to do with RDF::Trine (Perl) as it supports RDF/JSON, not sure about performance, though.
   * biological:
     * Bio DB entries -> RDF (in [http://bioruby.org BioRuby] for [http://togows.dbcls.jp TogoWS], for example)
-    * OBO <-> RDF (used in [http://cellcycleontology.org Cell Cycle Ontology] because ".obo" file format is easy to read for human)
+    * OBO <-> RDF (used in [http://cellcycleontology.org Cell Cycle Ontology] because ".obo" file format is easy to read for human): now in ONTO-PERL.
   * Bio2RDF converters:
     * Perl http://bio2rdf.svn.sourceforge.net/viewvc/bio2rdf/trunk/src/util/perl
@@ -79 +84 @@
 || Ruby || o || o ||
 || Python || o || o ||
-|| Perl || ? || x ||
+|| Perl || o || x ||
 || Java || o || o ||
 || R || ? || ? ||
@@ -89 +94 @@
     * [wiki:4storeQuickPrimer]
   * client library for Ruby/Python/Java http://4store.org/trac/wiki/ClientLibraries
+  * Supports HTTP-based Sparql Protocol, so can be used from any language that can do GET requests. Wrapper implemented by RDF::Query for Perl.
  * Virtuoso
   * database server http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/
@@ -133 +139 @@
 
   * Can we have common interface for major biological SPARQL endpoints?
-  * Can we have nice SPARQL query builder?
+  * Can we have nice SPARQL query builder? (see below for OWL notes)
   * Convert retrieved results into language's object?
   * What about getting not only a tabular result but also a result displaying a graph (nodes + edges)? (See [http://www.semantic-systems-biology.org/biogateway/sparql-viewer/ BioGateway browser])
@@ -143 +149 @@
 
 
+=== Using OWL to support dynamic queries and exploration of RDF data ===
+
+This a short summary of a discussion on Friday, 2010-02-12.
+
+The plan is to work on a nice SPARQL query builder, as a joint effort between the Bio* communities. It could make use of an OWL ontology as a description of the data: it lists what things there are, and how they are related. These relations could be offered to the user, via a simple API to the programmer or even on a web page to the biologist.
+
+Erick pointed out the [http://www.co-ode.org/resources/reference/manchester_syntax/ Manchester OWL Syntax] as a possibly related effort.