OboInOwl:Main Page - Revision history

Nigam: /* OBO Converter Protege tab: */

2008-09-16T18:47:38Z

OBO Converter Protege tab:

Nigam: /* OBO Converter Protege tab: */

2008-09-16T17:24:19Z

OBO Converter Protege tab:

Dilvan: /* OBO Converter Protege tab: */

2008-02-15T21:52:53Z

OBO Converter Protege tab:

Dilvan: /* OBO Converter Protege tab: */

2008-02-15T21:51:47Z

OBO Converter Protege tab:

Nigam: /* OboEdit OWL plugin */

2007-08-13T20:27:03Z

OboEdit OWL plugin

Nigam: /* OBO Converter Protege tab: */

2007-08-13T20:26:41Z

OBO Converter Protege tab:

Easr: /* obo2owl and owl2obo using PERL */

2007-06-25T12:39:46Z

obo2owl and owl2obo using PERL

Easr: /* Tools for the mapping */

2007-05-29T23:32:36Z

Tools for the mapping

Phismith: /* Overview of Other Mapping efforts */

2007-05-21T12:26:11Z

Overview of Other Mapping efforts

Phismith: /* Overview of Other Mapping efforts */

2007-05-21T12:25:30Z

Overview of Other Mapping efforts

@@ Line 70: / Line 70: @@
    [http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
-   [http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
+   [http://bioontology.org/tools/oboinowl/OBOConverter.zip Binaries for OBO Converter Tab]
    [http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

@@ Line 70: / Line 70: @@
    [http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
-   [http://stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
+   [http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
    [http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

@@ Line 70: / Line 70: @@
    [http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
-   [http://smi-protege.stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
+   [http://stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
    [http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

@@ Line 70: / Line 70: @@
    [http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
-   [http://smi-protege.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
+   [http://smi-protege.stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
    [http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

@@ Line 85: / Line 85: @@
 We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...
-  [http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].
+  [http://smi-protege.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].
 If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

@@ Line 99: / Line 99: @@
 Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]
-== obo2owl using PERL ==
+== obo2owl and owl2obo using PERL ==
-The '''onto-perl''' package implements the '''OboInOwl''' mapping. In order to run the PERL conversion script, first install the latest [http://search.cpan.org/~easr/ onto-perl] distribution like any other CPAN module (those modules deal with the '''OBO''' parsing task among other things). Then, execute the '''obo2owl.pl''' script by providing the '''input OBO''' file and, alternatively, specifying the '''output''' file location (by default the standard output) like in the following line:
+The '''onto-perl''' package implements the '''OboInOwl''' mapping. In order to run the PERL conversion scripts, first install the latest [http://search.cpan.org/~easr/ onto-perl] distribution like any other CPAN module (those modules deal with the '''OBO''' and '''OWL''' ontology parsing tasks among other things). Then, in order to convert from '''OBO to OWL''', execute the '''obo2owl.pl''' script by providing the '''input OBO''' file and, alternatively, specifying the '''output''' file location (by default the standard output) like in the following line:
 <code>$./obo2owl.pl my_ontology.obo > my_ontology.owl</code>
-The conversion script has been tested with some ontologies such as [http://www.cellcycleontology.org CCO] and [http://www.geneontology.org/ GO]. Moreover, the produced '''OWL''' files were successfully loaded into '''Protege'''. Besides, these OWL files were checked with [http://projects.semwebcentral.org/projects/vowlidator/ vowlidator] and [http://owl-eclipse.projects.semwebcentral.org/ SWeDE].
+This conversion script has been tested with some ontologies such as [http://www.cellcycleontology.org CCO] and [http://www.geneontology.org/ GO]. Moreover, the produced '''OWL''' files were successfully loaded into '''Protege'''. Besides, these OWL files were checked with [http://projects.semwebcentral.org/projects/vowlidator/ vowlidator] and [http://owl-eclipse.projects.semwebcentral.org/ SWeDE].
-The '''owl2obo.pl''' conversion script is still under development. This script will be released in the near future and it will complete this conversion circuit.
+Finally, to convert back from '''OWL to OBO''', use the '''owl2obo.pl''' conversion script by providing the '''input OWL''' file. This script completes the conversion circuit ('''obo2owl <=> owl2obo'''):
 [[Image:obo2owl.png|center]]

← Older revision		Revision as of 23:32, 29 May 2007
Line 98:		Line 98:

	Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]		Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]
		+
		+	== obo2owl using PERL ==
		+
		+	The '''onto-perl''' package implements the '''OboInOwl''' mapping. In order to run the PERL conversion script, first install the latest [http://search.cpan.org/~easr/ onto-perl] distribution like any other CPAN module (those modules deal with the '''OBO''' parsing task among other things). Then, execute the '''obo2owl.pl''' script by providing the '''input OBO''' file and, alternatively, specifying the '''output''' file location (by default the standard output) like in the following line:
		+
		+	<code>$./obo2owl.pl my_ontology.obo > my_ontology.owl</code>
		+
		+	The conversion script has been tested with some ontologies such as [http://www.cellcycleontology.org CCO] and [http://www.geneontology.org/ GO]. Moreover, the produced '''OWL''' files were successfully loaded into '''Protege'''. Besides, these OWL files were checked with [http://projects.semwebcentral.org/projects/vowlidator/ vowlidator] and [http://owl-eclipse.projects.semwebcentral.org/ SWeDE].
		+
		+	The '''owl2obo.pl''' conversion script is still under development. This script will be released in the near future and it will complete this conversion circuit.
		+
		+	[[Image:obo2owl.png\|center]]

	=URIs=		=URIs=

@@ Line 112: / Line 112: @@
    [http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]
-See also: Christine Golbreich and Ian Horrocks, "The OBO to OWL mapping, GO to OWL 1.1!", OWLED 2007, [www.med.univ-rennes1.fr/lim/doc_175.pdf]
+See also: Christine Golbreich and Ian Horrocks, "The OBO to OWL mapping, GO to OWL 1.1!", OWLED 2007 [http://www.med.univ-rennes1.fr/lim/doc_175.pdf]
 =Progress Notes=

@@ Line 107: / Line 107: @@
 =Overview of Other Mapping efforts=
 We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.
    [http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]
 =Progress Notes=