How to cite a gene

Answer: 


Gene annotations

Providing in your publication VectorBase gene IDs allows for the easiest, most convenient and unequivocal strategy to identify the genes of interest, allowing other users to find your genes with text searches. More information about the gene IDs can be found in this FAQ.

The (automatic) gene models are manually annotated by the community using Apollo from VectorBase, as seen above in the 'user-created annotations' track. 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 the 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 will be deprecated without warning.

VectorBase generates gene IDs not only for new genes but also to genes with corrected intron/exon boundaries. Once you are done with your manual annotations in Apollo, contact us at info@vectorbase.org and let us know when would you be submitting your paper with these new or corrected models. Please plan accordingly and contact us with as many months in advance of publication submission as possible. If we are not able to provide you with the new gene IDs in time for your publication, we strongly encourage you to provide the location of the gene, with chromosome or supercontig/scaffold and, base pair start and end.


Gene metadata

The gene metadata, such as symbol (name), e.g., rpl2 or gprop5 and, a description (function), e.g., ribosomal protein L2 or long wavelength sensitive opsin, 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. Follow this link for metadata submission instructions.

For example, Giraldo-Calderón et al. (2017), deposited in VectorBase the manual annotations and metadata of 13 Culex quinquefasciatus, 12 Anopheles gambiae and 10 Aedes aegypti opsin genes. In one of the paper's tables (Table 1), the genes were referenced with their metadata, INSDC accession, VectorBase gene ID and genome location, among other information details.


Links from your paper to VectorBase

We also strongly encourage you to work with the journal to provide the genome browser gene page link for each gene ID as shown in these two papers, Giraldo-Calderón et al. 2017 (Table 1) and Rund et al. 2011 (embed within the text).


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 in turn submit this update to NCBI. 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, as shown above in the Genome Browser 'Literature' link (click here to learn how to submit your publication citation).

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 later in the corresponding gene page in the Genome Browser.


How to cite VectorBase?

Follow this link to the FAQ that describes how to cite VectorBase, a gene and genome assembly and gene set.