Help:How to cite a community gene

From VectorBase Help System

Gene models that are submitted by the community or that are manually annotated are, after approval, temporarily displayed on the genome browser, in a separate track (DAS track), until they are included in the next revision of the official gene set.

These genes models won't have definitive identifiers until they are included in the gene set, so you can't cite formal identifiers until after inclusion (we do not recommend using their temporary internal identifiers: these are for internal use only, can't be searched for, and won't be tracked).

[edit] Cite a community gene or a manually annotated gene

If you want to refer to a gene from the Community & Manual Annotation DAS track:

• If the gene has an approved gene symbol, you could use it to refer to the gene, as this symbol will continue to be used after the gene is incorporated
• The best solution, however, would be to give the location of the gene (chromosome or scaffold, start, end).

Example of sentence: "The gene ABC, available in the VectorBase Community Annotation Database' (http://www.vectorbase.org), ... "

[edit] Submit a gene model and cite it in a publication

If you want to submit a gene model to the VectorBase Community Annotation Database, then cite it in an article:

• If you give a name (gene symbol) to your gene, it will be easier to cite it in your article. You can discuss with our community representative if you are not sure on how to name a gene.
• We recommend that you also give the location of the gene (chromosome or scaffold, start, end).

e.g.: Cornman et al. deposited in VectorBase a large set of Anopheles CPR genes and published an article citing the genes and their structures in Vectorbase. They named their genes but also provide in the Supplementary Material a list of the genes with their location on the Anopheles genome. Because many of their genes were already incorporated into the official gene set, they could also provide VB stable identifiers.

[edit] Why submit your genes to VectorBase?

VectorBase looks after the GenBank records of the genomic assemblies (and their gene annotation) for Anopheles gambiae (PEST), Aedes aegypti, Culex quinquefasciatus and Ixodes scapularis. This means that when we update the official VectorBase gene set, we will also update the GenBank records so gene models will appear in GenBank. Although the GenBank record will not directly cite the submitter of a gene, it will link to the VectorBase GeneView page, which will show that submitter.

When people have transcript sequences that are based on new sequencing, we anticipate that they will certainly want to submit that data directly to GenBank/EMBL/DDBJ; but we encourage them also to submit it to VB. Submission to VectorBase means that it will appear very quickly in the Community & Manual Annotation DAS track, and ensures that we are consistent in the use of gene symbols.