Difference between revisions of "Ontology workflow"

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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)
 
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 [http://www.smartsvn.com/SmartSVN]].
 
To get SmartSVN, go to their site [http://www.smartsvn.com/SmartSVN]].
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Do an SVN checkout of [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/]
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Contact Hilmar or Jim if you need help with passwords.
  
 
General workflow; begin each day by:
 
General workflow; begin each day by:
Starting up SmartSVN and update the phenoscape-ext repository.
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Starting up SmartSVN and update the edit (phenoscape-ext) directory.
  
For ontology editing, use the “Vocab” URL in Zigversion. “Vocab” folder contains ontology files for OBO-Edit.
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===Read Me File===
Select the top-level folder named with a forward slash (/)
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NOTE that there is a "Read Me" file in the phenoscape-ext directory here:
Click "update" to download recent versions of files to your local, working folder
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[http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/edit/README.txt?view=log]
  
Within OBO-edit, open the local copy of your file and proceed with your curation work.
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The content here is to get you started, but you should always be working in such a way as to be consistent with the Read Me file. Look for updates to this file when you update your SVN.
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.
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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.
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===Setting up your ID range===
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Ensure that you have Protege configured to generate new IRIs in your own range. The ranges are indicated in this file:
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[http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/edit/phenoscape-idranges.owl?view=log]
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Note that if you edit multiple files, you need to check this every time to ensure that the proper settings are in place.
  
 
====Making ontology edits using Protege 4====
 
====Making ontology edits using Protege 4====
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Navigate to Phenoscape-ext on your versioned directory on your hardrive.
 
Navigate to Phenoscape-ext on your versioned directory on your hardrive.
  
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2. Switch on the Elk reasoner. If you are making changes, be sure to
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synchronize the reasoner. If you do not have the ELK reasoner, you can get it here:
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[http://code.google.com/p/elk-reasoner/downloads/list]
  
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.
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You have access rights to any classes that are highlighted in bold font. Do not make changes to classes that are NOT in bold - changes here go through the uberon tracker, or be brought up on the mailing
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list. Note that it is fine for any request to go on the uberon tracker.  
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The tracker is here: [https://github.com/cmungall/uberon/issues?direction=desc&sort=created&state=open]
  
7. Saving to same file location regularly
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3. Saving to same file location regularly.
  
8. Commit to SVN repository
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4. Commit regularly. Always describe the changes you have made at a high level in the svn commit messages. These are searchable in the logs and very helpful for troubleshooting. It is ok to be verbose, it is not ok to be too terse. Always do a "svn diff" before committing to look at your changes. It is easier to look at a few changes, as there are often serialization changes from Protege, usually you can see that things have moved around but not really changed. You should be able to identify the intended changes.
  
Navigate to ontology file and hit “View changes” to verify your updates
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8. Commit to SVN repository
Hit “check in” and add a comment (e.g., “added new terms: scapula, coracoid) and hit check in.
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Revision as of 21:29, 4 October 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]].

Do an SVN checkout of [2] Contact Hilmar or Jim if you need help with passwords.

General workflow; begin each day by: Starting up SmartSVN and update the edit (phenoscape-ext) directory.

Read Me File

NOTE that there is a "Read Me" file in the phenoscape-ext directory here: [3]

The content here is to get you started, but you should always be working in such a way as to be consistent with the Read Me file. Look for updates to this file when you update your SVN.

Setting up your ID range

Ensure that you have Protege configured to generate new IRIs in your own range. The ranges are indicated in this file: [4]

Note that if you edit multiple files, you need to check this every time to ensure that the proper settings are in place.

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.

2. Switch on the Elk reasoner. If you are making changes, be sure to synchronize the reasoner. If you do not have the ELK reasoner, you can get it here: [5]

You have access rights to any classes that are highlighted in bold font. Do not make changes to classes that are NOT in bold - changes here go through the uberon tracker, or be brought up on the mailing list. Note that it is fine for any request to go on the uberon tracker. The tracker is here: [6]

3. Saving to same file location regularly.

4. Commit regularly. Always describe the changes you have made at a high level in the svn commit messages. These are searchable in the logs and very helpful for troubleshooting. It is ok to be verbose, it is not ok to be too terse. Always do a "svn diff" before committing to look at your changes. It is easier to look at a few changes, as there are often serialization changes from Protege, usually you can see that things have moved around but not really changed. You should be able to identify the intended changes.

8. Commit to SVN repository