Difference between revisions of "User:Dilvan"
| (9 intermediate revisions by the same user not shown) | |||
| Line 22: | Line 22: | ||
3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page). | 3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page). | ||
| − | 4- In the | + | 4- In the Protege menu, choose Project->Configure...->Annotation Tab. |
| − | + | 5- 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]] | + | The NCBI taxonomy (used in the GO annotation) 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:BioAnnotation.zip|Download BioAnnotation plugin]] | ||
| + | [[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. | 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 | + | 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]] | ||
| + | |||
| + | 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 | + | 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). |
Latest revision as of 16:20, 3 April 2007
Test page:
OWL Export/Import plugin for OboEdit
That is the development version of the OWL Export/Import plugin for OboEdit . 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...
Download plugin (for OBOEdit 1.002).
If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.
BioAnnotation Tab for Protege
That is the development version of the BioAnnotation Tab for Protege. To install:
1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.
2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).
3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).
4- In the Protege menu, choose Project->Configure...->Annotation Tab.
5- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".
The NCBI taxonomy (used in the GO annotation) 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.
Download OBO Converter plugin Download BioAnnotation plugin 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.
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:
Download Yeast GO Annotations in OWL Download Human GO Annotations in OWL
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).