Ontology workflow

Using Version Control

SmartSVN is the SVN client we use for keeping local copies of ontologies on your computer synchronized with those in the SVN (SubVersion server) To get SmartSVN, go to their site [1]].

General workflow; begin each day by: Starting up SmartSVN and update the phenoscape-ext repository.

For ontology editing, use the “Vocab” URL in Zigversion. “Vocab” folder contains ontology files for OBO-Edit. Select the top-level folder named with a forward slash (/) Click "update" to download recent versions of files to your local, working folder

Within OBO-edit, open the local copy of your file and proceed with your curation work. After saving your file, go back to ZigVersion and “check in” your modified file(s) to the repository. Remember to add a comment to the bottom of the check in window describing the changes you made to the file.

Wasila uses SmartCVS as the CVS client for obtaining local copies of ontologies on the OBO CVS server. Question: do all curators need this? Could also download ontologies directly from OBOFoundry and Phenoscape ontologies are kept in SVN.

Making ontology edits using Protege 4

1. Start P4. Go to File>Load ontologies. Navigate to Phenoscape-ext on your versioned directory on your hardrive.

6. When adding a new term, make sure a high ID number is assigned. If assigned number is XX:0000000, then fix the ID in the ID Manager panel under Metadata. Click “+” to add new ID profile; Then hit gears button. Give Profile name (e.g., TAO) and Default rule (e.g., TAO:$sequence(7,0,9999999)$). Hit commit.

7. Saving to same file location regularly

8. Commit to SVN repository

Navigate to ontology file and hit “View changes” to verify your updates Hit “check in” and add a comment (e.g., “added new terms: scapula, coracoid) and hit check in.