dictyBase SOPs: General Curation Guidelines
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General Curation Guidelines

Last updated April 3, 2006
General Guidelines Gene Name/Synonym
Gene Product
Name Description
Notes Annotation issues in need of further discussion
Useful Links for Curation

Gene Name/Synonym [TOP]
Published Sequencing Center names:
If a paper refers to a gene by its Sequencing Center name (e.g., JC3V2_0_01611, BC5V2_0_01947), add the Sequencing Center name as a synonym, but ONLY if that is the only identifier. If the dictyBaseID is also provided, do not include the Sequencing Center name as a synonym. This is not ideal, however, it occurs infrequently.

Gene Product [TOP]
When the function/process of a gene product is unknown, and it does not contain any functional protein domains, use the gene product 'unknown.' Gene products such as 'hypothetical' and 'protein of unknown function' are unacceptable in our GenBank submission.

Conserved protein of unknown function:
In cases where a protein is a clear ortholog/highly similar to proteins from other species but its function/process is undetermined, use the gene product 'unknown.' Use the description field to explain the sequence similarity, e.g., 'conserved hypothetical protein' or 'conserved hypothetical Dictyostelium protein.'

Description [TOP]

Name Description [TOP]
Use of the Name Description field:
Inclusion of the name description is mandatory, even if it is redundant with the gene product. The rationale behind this is that name descriptions are often difficult to find, and we would like to provide this information whenever possible.

Letters and numbers in the Name Description:
When the last letter/number of a gene name is important, include it in the name description. When the last letter/number is arbitrary, do not include it. Examples:
        sad = <b>S</b>ubstrate <b>AD</b>hesion
        vasP = <b>VA</b>sodilator <b>S</b>timulated <b>P</b>hosphoprotein

Annotation issues in need of further discussion [TOP]
  • Curation of papers using inhibitors (issue #0041).
  • Descriptions containing "similar to" (issue #0042).
  • Abbreviations in the gene product and description (issue #0043).
  • "Disease gene-related" literature topic (issue #0044).
  • Psuedogene annotation (issue #0056).
  • "Homolog" in gene product (issue #0059).
  • "Unpublished" sequences for Curated Model annotation (issue #0060).

Useful Links for Curation [TOP]


Dictyostelium Anatomy Ontology (DDANAT)

Gene Ontology (GO) Consortium

Generic Model Organism Database (GMOD)


HUGO Gene Nomenclature Committee (HGNC)


National Center for Biomedical Ontology

Open Biomedical Ontologies


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