How to cite a community gene


Gene models are manually annotated by the community using Apollo from VectorBase. This allows all other members of the community to visualize changes instantly. Once a sufficient number of gene annotations has been accumulated for an organism, these new gene models are included in the next revision of the official gene set.

Cite a community gene or a manually annotated gene
Apollo has a gene annotation track in genome browsers to allow public display of ongoing Apollo edits. Apollo identifiers shown on the track are not stable identifiers and must not be used in publications referencing data as they may be deprecated without warning. If you require stable annotation IDs for Apollo gene model edits, please contact VectorBase directly and in your paper give the location of the gene (chromosome or scaffold, start, end).

Example of sentence: "The gene 'x' in the organisms 'y', was submitted to VectorBase as community annotation and is now available in the Apollo with the gene coordinates 'z', ... "

Gene metadata
The gene metadata, such as symbol (name), e.g., rpl2 and, a short functional description, e.g., ribosomal protein L2 should also be mentioned in your paper. If you are not sure on how to name a gene please follow these links for mosquitoes and other arthropods and for molluscans.

e.g.: Cornman et al. (2008). 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.

Why submit your genes to VectorBase?
VectorBase looks after the GenBank records of the genomic assemblies (and their gene annotation) for all VectorBase organisms. 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 Gene 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 instantly in Apollo, and ensures that we are consistent in the use of gene symbols.

For information about how to cite VectorBase; how to cite a gene assembly and gene set and; how to cite an external data resource, please follow this link.