Phenotype Curation

The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes.

• Terms from the Dicty Phenotype Ontology must be used for phenotype annotations.
• If you require a phenotype term not present in the phenotype ontology, make a request in the Issue Tracker, marking the section 'Phenotype Ontology.'
• After all curators approve the changes, follow the instructions for editing the Dicty Phenotype and Mutant Type Ontologies.

The Mutant Types Ontology is a hierarchical controlled vocabulary used for defining the strains from which phenotypes are derived.

• Terms from the Mutant Types Ontology must be used for phenotype annotations.
• Currently the Mutant Types Ontology consists of the following terms:
  • deletion
  • endogenous gene mutation
  • exogenous expression
  • insertion
  • multiple deletion
  • multiple insertion
  • multiple substitution
  • other
  • overexpression
  • reduced expression
  • substitution
  • systematic deletion

The following workflow should be used to edit the ontologies to ensure proper versioning and integration into the database:

• In CVS on your own machine, 'Update' your ontology to the most current version.
• Edit the ontology on your own machine using OBO-Edit (when loading, make sure you use the file path to the obo file on your own machine). Add dbxref DDB:yourinitials when editing. Commit changes in OBO-Edit.
• 'Save As' on your own machine (make sure file path is correct).
• In CVS on your own machine, commit the edited file.
• 'Update' the ontology on cgm-1 with CVS.
• Click on 'Update Dicty Phenotype and Mutant Types Ontology' on testdb. Wait a few moments and the ontologies will be loaded.
• Check testdb to see that your changes have been made.
• 'Update' the ontology on cgm-2 with CVS.
• Click on 'Update Dicty Phenotype and Mutant Types Ontology' on production. Wait a few moments and the ontologies will be loaded.
• Check production to see that your changes have been made.

When both 'no known phenotype' and a mutant phenotype annotations exist for a gene:

• If the annotations are derived from the same publication, omit 'no known phenotype' and annotate only the mutant phenotype.
• If the annotations come from different publications, keep 'no known phenotype' and qualify it with conditional information. See, for example canA.

Dicty Stock Center

PATO

Phenotypes for Dictyostelium mutants