dictyBase SOPs: Phenotype Curation
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Phenotype Curation

Last updated May 12, 2006
Phenotype Annotation Dicty Phenotype Ontology
Mutant Types Ontology
Editing the Dicty Phenotype and Mutant Types Ontology
Annotation Guidelines No known phenotype
Notes Phenotype Resources


Dicty Phenotype Ontology [TOP]
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.
Mutant Types Ontology [TOP]
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
Editing the Dicty Phenotype and Mutant Types Ontology [TOP]
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.
No known phenotype [TOP]
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.
Phenotype Resources [TOP]

Dicty Stock Center

PATO

Phenotypes for Dictyostelium mutants

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