Topic map conversion of Gene Ontology - Revision history

Akivela at 13:18, 26 July 2012

2012-07-26T13:18:22Z

Akivela at 11:37, 23 August 2011

2011-08-23T11:37:23Z

Akivela: /* Metrics */

2011-08-23T10:55:48Z

‎Metrics

Akivela: /* License */

2011-08-23T10:53:50Z

‎License

Akivela at 10:52, 23 August 2011

2011-08-23T10:52:10Z

Akivela: /* History */

2011-08-23T10:51:51Z

‎History

Akivela: /* Download topic map conversion of Gene Ontology */

2011-08-23T10:51:06Z

‎Download topic map conversion of Gene Ontology

Akivela: /* Download topic map conversion of Gene Ontology */

2011-07-14T10:12:35Z

‎Download topic map conversion of Gene Ontology

Akivela: /* Download topic map conversion of Gene Ontology */

2009-10-27T14:19:20Z

‎Download topic map conversion of Gene Ontology

Akivela at 14:15, 27 October 2009

2009-10-27T14:15:33Z

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 There are two versions available:
-* [http://www.wandora.org/wandora/download/other/go/gene_ontology_20110822.wpr Wandora project file] (13.7 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_huge.bat) to open topic map version of GO.
+* [http://www.wandora.org/download/other/go/gene_ontology_20110822.wpr Wandora project file] (13.7 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_huge.bat) to open topic map version of GO.
-* [http://www.wandora.org/wandora/download/other/go/gene_ontology_20110822.zip Single XTM dump] (15.1 MB, unzipped 154 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.
+* [http://www.wandora.org/download/other/go/gene_ontology_20110822.zip Single XTM dump] (15.1 MB, unzipped 154 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.
 Note: Gene Ontology hosted at OBO Foundry is updated frequently. Topic Map version provided here may be out of date. To get the latest version of Gene Ontology Topic Map we suggest you download latest OBO version of the Gene Ontology from [http://www.obofoundry.org OBO Foundry] and convert it to a Topic Map with Wandora's [[OBO flat file import|OBO Import]] feature.

← Older revision		Revision as of 11:37, 23 August 2011
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−	Wandora is also capable to view topic maps as scalable graph presentations. Example graph below views small fragment of GO's topic map conversion. Graph contains ~~only superclass~~-subclass associations (''is_a'' relations of GO). Also, the graph contains only '''cellular_component (GO:0005575)''' and it's ~~neighbours~~ to depth 3. All other relations and terms have been filtered out. Photoshop was used to add blue arrows and texts.	+	Wandora is also capable to view topic maps as scalable graph presentations. Example graph below views small fragment of GO's topic map conversion. Graph contains super-subclass associations (''is_a'' relations of GO). Also, the graph contains only '''cellular_component (GO:0005575)''' and it's neighbors to depth 2. All other relations and terms have been filtered out. Photoshop was used to add blue arrows and texts.

@@ Line 30: / Line 30: @@
 == Metrics ==
-Metrics were measured on layer '''gene_ontology_edit.obo''' of Wandora project file.
+Metrics were measured on layer '''gene ontology''' of Wandora project file.
-* Number of topics: 102889
+* Number of topics: 177301
-* Number of associations: 195990
+* Number of associations: 280198
-* Number of topic base names: 101738
+* Number of topic base names: 175814
-* Number of subject identifiers: 102897
+* Number of subject identifiers: 177309
 * Number of subject locators: 0
-* Number of occurrences: 75401
+* Number of occurrences: 148057
-* Number of distinct topic classes: 16
+* Number of distinct topic classes: 15
 * Number of distinct types of associations: 16
 * Number of distinct roles in associations: 20
-* Number of distinct players in associations: 102855
+* Number of distinct players in associations: 177265

@@ Line 66: / Line 66: @@
 The Gene Ontology database and vocabularies are public domain [http://wiki.geneontology.org/index.php/GO_FAQ#I.27d_like_to_integrate_the_GO_files_into_a_commercial_application._Do_I_need_a_licensing_agreement.3F]
-Wandora Team gives '''the topic map conversion of Gene Ontology (2008-09-15)''' to the public domain. [http://www.geneontology.org/GO.cite.shtml Gene Ontology's usage policy] applies also to the topic map version.
+Wandora Team gives '''the topic map conversion of Gene Ontology (2011-08-22)''' to the public domain. [http://www.geneontology.org/GO.cite.shtml Gene Ontology's usage policy] applies also to the topic map version.
 __NOTOC__

← Older revision		Revision as of 10:52, 23 August 2011
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−	[http://www.geneontology.org Gene Ontology] is a controlled vocabulary used to describe gene and gene product attributes in any organism. Gene Ontology is an ongoing developed of [http://www.geneontology.org/GO.consortiumlist.shtml The GO Consortium]. Topic map conversion is based on OBO flat file version (dated ~~2009~~-10-27) of the Gene Ontology hosted by the [http://www.obofoundry.org OBO Foundry]. Gene Ontology was converted to topic map with Wandora's [[OBO flat file import\|OBO Import]] feature.	+	[http://www.geneontology.org Gene Ontology] is a controlled vocabulary used to describe gene and gene product attributes in any organism. Gene Ontology is an ongoing developed of [http://www.geneontology.org/GO.consortiumlist.shtml The GO Consortium]. Topic map conversion is based on OBO flat file version (dated 2011-08-22) of the Gene Ontology hosted by the [http://www.obofoundry.org OBO Foundry]. Gene Ontology was converted to topic map with Wandora's [[OBO flat file import\|OBO Import]] feature.

	== Download topic map conversion of Gene Ontology ==		== Download topic map conversion of Gene Ontology ==

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 == History ==
 * 2009-10-27 Synchronizing the topic map conversion with original OBO flat file ontology.
 * 2008-09-15 Synchronizing the topic map conversion with original OBO flat file ontology.

@@ Line 3: / Line 3: @@
 == Download topic map conversion of Gene Ontology ==
-There are three versions available:
+There are two versions available:
 * [http://www.wandora.org/wandora/download/other/go_20091027.wpr Wandora project file] (9.18 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_large.bat or wandora_huge.bat) to open topic map version of GO.

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-[http://www.geneontology.org Gene Ontology] is a controlled vocabulary used to describe gene and gene product attributes in any organism. Gene Ontology is an ongoing developed of [http://www.geneontology.org/GO.consortiumlist.shtml The GO Consortium]. Topic map conversion is based on OBO flat file version (dated 2008-09-15) of the Gene Ontology hosted by the [http://www.obofoundry.org OBO Foundry]. Gene Ontology was converted to topic map with Wandora's [[OBO flat file import|OBO Import]] feature.
+[http://www.geneontology.org Gene Ontology] is a controlled vocabulary used to describe gene and gene product attributes in any organism. Gene Ontology is an ongoing developed of [http://www.geneontology.org/GO.consortiumlist.shtml The GO Consortium]. Topic map conversion is based on OBO flat file version (dated 2009-10-27) of the Gene Ontology hosted by the [http://www.obofoundry.org OBO Foundry]. Gene Ontology was converted to topic map with Wandora's [[OBO flat file import|OBO Import]] feature.
 == Download topic map conversion of Gene Ontology ==
@@ Line 5: / Line 5: @@
 There are three versions available:
-* [http://www.wandora.org/wandora/download/other/gene_ontology_20080915.wpr Wandora project file] (8.4 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_large.bat or wandora_huge.bat) to open topic map version of GO.
+* [http://www.wandora.org/wandora/download/other/go_20091027.wpr Wandora project file] (8.4 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_large.bat or wandora_huge.bat) to open topic map version of GO.
-* [http://www.wandora.org/wandora/download/other/gene_ontology_20080915.xtm.zip Single XTM dump] (9.2 MB, unzipped 154 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.
+* [http://www.wandora.org/wandora/download/other/go_20091027.xtm.zip Single XTM dump] (9.2 MB, unzipped 154 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.
-−
-* [http://www.wandora.org/wandora/download/other/gene_ontology_20080915.ltm.zip Single LTM dump] (7.1 MB, unzipped 38.1 MB). This version is a general topic map file usable in any topic map application supporting LTM file format.
 Note: Gene Ontology hosted at OBO Foundry is updated frequently. Topic Map version provided here may be out of date. To get the latest version of Gene Ontology Topic Map we suggest you download latest OBO version of the Gene Ontology from [http://www.obofoundry.org OBO Foundry] and convert it to a Topic Map with Wandora's [[OBO flat file import|OBO Import]] feature.
@@ Line 15: / Line 13: @@
 == History ==
 * 2008-09-15 Synchronizing the topic map conversion with original OBO flat file ontology.
 * 2008-03-04 Added SI base '''http://www.wandora.org''' to Wandora schema topics. Added LTM version of Gene Ontology topic map.