Difference between revisions of "Adding Terms and Regenerating the Import Files"

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#Create a pull request. If all checks pass, merge.
#Create a pull request. If all checks pass, merge.
==Checking import files From Ontobot==
==Checking automatic import files From Ontobot==
* Taxon constrains get regenerated daily. Other imports weekly.
== Review Status ==
== Review Status ==

Latest revision as of 10:34, 10 February 2020

 See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.

Adding terms to import files

Terms are imported to GO from other ontologies, but not all terms from external ontologies are imported. Occasionally, you will find that a valid identifier exists in an external ontology, but the identifier is not available in Protege because that term is not yet imported. To import a term from an external ontology:

  1. Navigate to the imports folder on GitHub, located at https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports.
  2. Look in the list of ontologies for the ontology that contains the term you wish to import.
  3. Identify the ontology_terms.txt file for the target ontology. For example, for the addition of a new taxon, the file can be found at https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/ncbitaxon_terms.txt.
    1. Note that the different import files have different example lines. Be sure to follow the correct format if you are using the IRIs. There is an underscore between the prefix and the term identifier: https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/chebi_terms.txt
  4. Click on the icon of a pencil in the upper right corner of the window to edit the file.
  5. Add the new term on the next available line at the bottom of the file.
  6. Click preview changes.
  7. Create a new branch and a pull request as described in the Ontology_Editors_Daily_Workflow.
  Note that you can also edit the file in your local machine and commit as part of the same branch as the ontology changes.  
 See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Regenerating import files Manually

  1. Install docker [1] on your local machine
  After installing, in the docker tool, select preferences, then go to 'advanced" and use the sliders to set the memory to 14 gig.  Press 'apply and restart'
  Note: docker must be running in order for the following steps to work
  1. Create a new branch for regenerating the import: git checkout -b chebi-import-2018-09-10
  2. The command for regenerating imports is: ./run.sh make imports/something_import.obo (Generating the obo file will automatically generate the owl file.)
  3. Once the file is regenerated, sanity check it with a git diff
  4. If all looks good, commit the new file and push it to origin.
  5. Create a pull request. If all checks pass, merge.

Checking automatic import files From Ontobot

  • Taxon constrains get regenerated daily. Other imports weekly.

Review Status

Last reviewed: May 24, 2017

Back to: Editing the Ontology