Difference between revisions of "Ontology workflow"

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(Created page with "ZigVersion is the SVN client we use for keeping local copies of ontologies on your computer synchronized with those in the SVN (SubVersion server) * Note: we will start using Sma...")
 
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ZigVersion is the SVN client we use for keeping local copies of ontologies on your computer synchronized with those in the SVN (SubVersion server)
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====Using Version Control ====
* Note: we will start using SmartSVN because ZigVersion is no longer being developed or maintained.
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SmartSVN is the SVN client we use for keeping local copies of ontologies on your computer synchronized with those in the SVN (SubVersion server)
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To get SmartSVN, go to their site [http://www.smartsvn.com/SmartSVN]].
  
 
General workflow; begin each day by:
 
General workflow; begin each day by:
Starting up Zigversion and connect to repository
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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.
 
For ontology editing, use the “Vocab” URL in Zigversion. “Vocab” folder contains ontology files for OBO-Edit.
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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.
 
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 updates using ZigVersion and OboEdit====
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====Making ontology edits using Protege 4====
1. Start OboEdit. Go to File>Load ontologies.
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1. Start P4. Go to File>Load ontologies.
Select the correct “stored adapter settings” for the ontology you want to update
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Navigate to Phenoscape-ext on your versioned directory on your hardrive.
Nizar will have VAO-edit and Amniote-draft settings saved
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Browse Path or URL will connect to the local copies of these ontologies
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Make sure “allow dangling references” is checked
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4.  ID profile mismatch message: hit yes
 
 
5.  Make edits...
 
  
 
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.
 
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 local file
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7. Saving to same file location regularly
File>Save as. Ignore non-fatal warnings.Create new “stored adapter settings” for your ontology.  In Tag filtering, uncheck “modification date”, “modified by”, “creation_date”, and “created_by”.
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Make sure “filter tags” and “allow dangling parents” are checked.
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8. Commit to SVN repository
ID rules: select “Write originally loaded ID rules”
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Hit OK, overwrite is OK.
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8. Save to SVN repository
 
Open Zigversion
 
 
Navigate to ontology file and hit “View changes” to verify your updates
 
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.
 
Hit “check in” and add a comment (e.g., “added new terms: scapula, coracoid) and hit check in.
 
Opening ontology files in OBO-Edit  --
 
1. Create new “Stored adaptor settings” for each ontology (e.g., VTO, VAO, AMAO)
 
2. Hit “+” button next to stored adapter settings field, and type in ontology name
 
3. Hit “add” button to specify the ontology file location; hit “browse” to find the file
 
 
OORT for reasoning
 
 
Anatomy ontology call minutes, development plans
 
http://phenoscape.org/wiki/Anatomy_Ontology_Conf_calls
 
 
http://phenoscape.org/wiki/Ontologies
 
 
https://phenoscape.org/wiki/Project_Plan
 
 
Recent phenoscape-curators discussions:
 
http://sourceforge.net/mailarchive/forum.php?forum_name=phenoscape-curators
 
 
Open issues
 
- provenance documentation in ontologies
 
- terminology vs. ontology; use of synonyms (related; incorrect); produce ‘slim’ version of VAO/AMAO for archosaur group
 
- tracker items: see CARO tracker, VAO tracker, Uberon tracker
 

Revision as of 14:53, 25 September 2012

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.