Adding Terms and Regenerating the Import Files: Difference between revisions
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See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions. | |||
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: | |||
# Navigate to the imports folder on GitHub, located at https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports. | |||
# Look in the list of ontologies for the ontology that contains the term you wish to import. | |||
# 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. | |||
# Click on the icon of a pencil in the upper right corner of the window to edit the file. | |||
# Add the new term on the next available line at the bottom of the file. | |||
# Click preview changes. | |||
# You can now either commit the file directly to master or create a branch and a pull request as described in the [[Ontology_Editors_Daily_Workflow]]. | |||
See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions. | |||
== Review Status == | |||
Last reviewed: June 7, 2018 | |||
[http://wiki.geneontology.org/index.php/Ontology_Editing_Guide Back to: Ontology Editing Guide] | |||
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] | [[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] |
Revision as of 20:33, 7 June 2018
See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.
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:
- Navigate to the imports folder on GitHub, located at https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports.
- Look in the list of ontologies for the ontology that contains the term you wish to import.
- 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.
- Click on the icon of a pencil in the upper right corner of the window to edit the file.
- Add the new term on the next available line at the bottom of the file.
- Click preview changes.
- You can now either commit the file directly to master or create a branch and a pull request as described in the Ontology_Editors_Daily_Workflow.
See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.
Review Status
Last reviewed: June 7, 2018