OBO flat file import - Revision history

Akivela: /* Post-processing the OBO imported Topic Map */

2011-03-10T10:49:38Z

‎Post-processing the OBO imported Topic Map

Akivela: /* is_a */

2010-04-23T18:24:21Z

‎is_a

Akivela: /* is_a */

2010-04-23T18:23:54Z

‎is_a

Akivela at 19:17, 16 April 2010

2010-04-16T19:17:06Z

Akivela: /* Conversion details */

2008-07-21T10:12:22Z

‎Conversion details

Akivela: /* Conversion details */

2008-05-22T07:04:34Z

‎Conversion details

Akivela: /* Conversion details */

2008-05-10T10:39:36Z

‎Conversion details

Akivela: /* Conversion details */

2008-05-10T10:39:18Z

‎Conversion details

Akivela: /* is_a */

2008-05-08T18:14:14Z

‎is_a

Akivela at 18:12, 8 May 2008

2008-05-08T18:12:45Z

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 == Post-processing the OBO imported Topic Map ==
-OBO ontology should use '''is_a''' and '''part_of''' relations consistently and without conflicts (See [http://www.geneontology.org/GO.usage.shtml#truePathRule True Path Rule]). Such usage ensures OBO ontology has only a limited set of root terms. Root term of '''is_a''' relations is a superclass of every other term. Root term of '''part_of''' relations has no enclosing terms. Finding such root topics is important as they are convenient starting points to browse the ontology. However, Wandora doesn't automatically search and mark such term topics but leaves this to the Wandora user. To find root topics of '''superclass-subclass''' associations
+OBO ontology should use '''is_a''' and '''part_of''' relations consistently and without conflicts (True Path Rule). Such usage ensures OBO ontology has only a limited set of root terms. Root term of '''is_a''' relations is a superclass of every other term. Root term of '''part_of''' relations has no enclosing terms. Finding such root topics is important as they are convenient starting points to browse the ontology. However, Wandora doesn't automatically search and mark such term topics but leaves this to the Wandora user. To find root topics of '''superclass-subclass''' associations
 * Open any topic containing such association.

← Older revision		Revision as of 18:24, 23 April 2010
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	=== is_a ===		=== is_a ===

−	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph viewed in Wandora (except blue arrows and labels) containing few '''is_a''' aka '''superclass-subclass''' relations of the Gene Ontology.</dd>	+	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph viewed by Wandora (except blue arrows and labels) containing few '''is_a''' aka '''superclass-subclass''' relations of the Gene Ontology.</dd>

← Older revision		Revision as of 18:23, 23 April 2010
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	=== is_a ===		=== is_a ===

−	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph containing few '''is_a''' aka '''superclass-subclass''' relations of the Gene Ontology.</dd>	+	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph viewed in Wandora (except blue arrows and labels) containing few '''is_a''' aka '''superclass-subclass''' relations of the Gene Ontology.</dd>

← Older revision		Revision as of 19:17, 16 April 2010
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−	Wandora's OBO flat file import feature converts [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file] ontology to a topic map and merges converted topic map to Wandora. Import begins with menu option '''File > Import > OBO import...'''. Wandora accepts also ~~dropped~~ OBO ~~files~~. If OBO file is dropped to layer stack, new layer is created for the imported file.	+	Wandora's OBO flat file import feature converts [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file] ontology to a topic map and merges converted topic map to Wandora. Import begins with menu option '''File > Import > OBO import...'''. Wandora accepts also OBO file drops. If OBO file is dropped to layer stack, new layer is created for the imported file.

	OBO flat file format is used mainly in bioinformatics to store and share ontologies related to biosciences. OBO flat file format was initially developed for [http://www.geneontology.org/ The Gene Ontology]. However, there exists over 60 public ontologies in OBO format today. These ontologies can be browsed and downloaded at [http://www.obofoundry.org Open Biological Ontologies Foundry].		OBO flat file format is used mainly in bioinformatics to store and share ontologies related to biosciences. OBO flat file format was initially developed for [http://www.geneontology.org/ The Gene Ontology]. However, there exists over 60 public ontologies in OBO format today. These ontologies can be browsed and downloaded at [http://www.obofoundry.org Open Biological Ontologies Foundry].

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 Next chapters describe conversion details of OBO terms, instances and type definitions. It is assumed the readed is familiar with Topic Maps and [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file format].
-Long version of conversion details can be found in paper Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish)
+Long version of conversion details can be found in paper Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). ([http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf English Abstract]).
 == Converting OBO terms ==

← Older revision		Revision as of 07:04, 22 May 2008
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	Next chapters describe conversion details of OBO terms, instances and type definitions. It is assumed the readed is familiar with Topic Maps and [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file format].		Next chapters describe conversion details of OBO terms, instances and type definitions. It is assumed the readed is familiar with Topic Maps and [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file format].
		+
		+	Long version of conversion details can be found in paper Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish)

	== Converting OBO terms ==		== Converting OBO terms ==

@@ Line 13: / Line 13: @@
 OBO import creates a root topic for each namespace. Root topic is named '''obo (namespace)''' where '''namespace''' is a name of the namespace. Root topic is associated to a collection of namespace related meta-topics:
-* '''category (namespace)''' collects all subsets specified in the OBO file. Subset is a named category of terms in OBO file. Subset is defined in OBO file header with tag '''subsetdef'''. If namespace doesn't define any categories then collecting '''category (namespace)''' will not be created.
+* '''category (namespace)''' collects all subsets specified in the OBO file. Subset is a named category of terms in OBO file. Subset is defined in OBO file header with tag '''subsetdef'''. If namespace doesn't define any categories then collecting '''category (namespace)''' is not created.
 * '''header (namespace)''' is a header topic collecting OBO header properties. Each header property is stored as a text occurrences with a type generated using header tag name.
 * '''term (namespace)''' collects all OBO terms in given namespace. OBO term is an instance of the '''term (namespace)''' topic.

← Older revision		Revision as of 18:14, 8 May 2008
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	=== is_a ===		=== is_a ===

−	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph containing few is_a aka superclass-subclass relations of the Gene Ontology.</dd>	+	<dd>is_a relationships are converted to superclass-subclass associations with standard roles given in [http://www.topicmaps.org/xtm/index.html topic map specification]. Below is an example graph containing few '''is_a''' aka '''superclass-subclass''' relations of the Gene Ontology.</dd>

@@ Line 1: / Line 1: @@
 Wandora's OBO flat file import feature converts [http://www.geneontology.org/GO.format.obo-1_2.shtml OBO flat file] ontology to a topic map and merges converted topic map to Wandora. Import begins with menu option '''File > Import > OBO import...'''. Wandora accepts also dropped OBO files. If OBO file is dropped to layer stack, new layer is created for the imported file.
-OBO flat file format is used mainly in bioinformatics to store and share ontologies related to biosciences. OBO flat file format was initially developed for [http://www.geneontology.org/ The Gene Ontology]. However, there exists over 60 different and public ontologies in OBO format today. These ontologies can be browsed and downloaded at [http://www.obofoundry.org Open Biological Ontologies Foundry].
+OBO flat file format is used mainly in bioinformatics to store and share ontologies related to biosciences. OBO flat file format was initially developed for [http://www.geneontology.org/ The Gene Ontology]. However, there exists over 60 public ontologies in OBO format today. These ontologies can be browsed and downloaded at [http://www.obofoundry.org Open Biological Ontologies Foundry].
 As an example of OBO import we have converted [[Topic map conversion of Gene Ontology|the Gene Ontology to a topic map]]. Below is a screenshot of Wandora with Gene Ontology topic map open. Addition to OBO import, Wandora is also capable to export topic map back to OBO flat file format. Read more at [[OBO flat file export]] and [[OBO round trip]].