User:Dilvan - Revision history

Dilvan: /* BioAnnotation Tab for Protege */

2007-04-04T00:20:26Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-04-04T00:19:59Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T21:15:51Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T18:23:50Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T18:06:44Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T17:37:05Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T17:35:05Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T17:27:24Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T17:26:38Z

BioAnnotation Tab for Protege

Dilvan: /* BioAnnotation Tab for Protege */

2007-03-27T17:26:11Z

BioAnnotation Tab for Protege

@@ Line 42: / Line 42: @@
 TIP: When using Protege to display any of the OWL files above, you have the option of showing the classes more meaningful labels in place of their rdf:ID names, just:
 - In menu OWL->Preferences... in the Visibility Tab choose owl:Class
 - In the Forms Tab select owl:Class and in the Form Editor choose Display Slot: rdfs:label
 NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

← Older revision		Revision as of 00:19, 4 April 2007
Line 40:		Line 40:

	If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".		If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".
		+
		+	TIP: When using Protege to display any of the OWL files above, you have the option of showing the classes more meaningful labels in place of their rdf:ID names, just:
		+	1- In menu OWL->Preferences... in the Visibility Tab choose owl:Class
		+	2- In the Forms Tab select owl:Class and in the Form Editor choose Display Slot: rdfs:label

	NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).		NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

← Older revision		Revision as of 21:15, 27 March 2007
Line 41:		Line 41:
	If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".		If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

−	NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.	+	NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

@@ Line 22: / Line 22: @@
 - Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).
-- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.
+- In the Protege menu, choose Project->Configure...->Annotation Tab.
-The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only  see a reference to the species you are working with.
+- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".
   [[Media:Oboconverter.zip|Download OBO Converter plugin]]

@@ Line 36: / Line 36: @@
   [[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
   [[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]
 NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

← Older revision		Revision as of 17:37, 27 March 2007
Line 37:		Line 37:
	[[Media:Human_annotations.zip\|Download Human GO Annotations in OWL]]		[[Media:Human_annotations.zip\|Download Human GO Annotations in OWL]]

−	NOTE: In the ~~Amia~~ paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.	+	NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

@@ Line 32: / Line 32: @@
 Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.
-If you just want to see the  GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:
+If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:
   [[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
   [[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]
-NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.
+NOTE: In the Amia paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

@@ Line 26: / Line 26: @@
 The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only  see a reference to the species you are working with.
-  [[Media:Oboconverter.zip | Download OBO Converter plugin]].
+  [[Media:Oboconverter.zip|Download OBO Converter plugin]]
-  [[Media:BioAnnotation.zip | Download BioAnnotation plugin]].
+  [[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
-  [[Media:Go_ontology.zip | Download GO Ontology in OWL]].
+  [[Media:Go_ontology.zip|Download GO Ontology in OWL]]
 Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.
@@ Line 34: / Line 34: @@
 If you just want to see the  GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:
-  [[Media:Yeast_annotations.zip | Download Yeast GO Annotations in OWL]].
+  [[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
-  [[Media:Human_annotations.zip | Download Human GO Annotations in OWL]].
+  [[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]
 NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

@@ Line 27: / Line 27: @@
   [[Media:Oboconverter.zip | Download OBO Converter plugin]].
-  [http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
+  [[Media:BioAnnotation.zip | Download BioAnnotation plugin].
-  [http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].
+  [[Media:Go_ontology.zip | Download GO Ontology in OWL].
 Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.
@@ Line 34: / Line 34: @@
 If you just want to see the  GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:
-  [http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
+  [[Media:Yeast_annotations.zip | Download Yeast GO Annotations in OWL].
-  [http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].
+  [[Media:Human_annotations.zip | Download Human GO Annotations in OWL].
 NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.