User:Dilvan

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 BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

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.

 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.

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: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.