General (faqs)

FAQ category.

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Can I use pictures posted in the Images section of VectorBase?

Answer: 

VectorBase has curated all available images and has included both the license and photographer into the image viewer on the site.

Nearly all of these images are in the public domain and freely available for non-commercial use. As an example, most images are from the CDC's Public Health Image Library and were taken by James Gathany, professional photographer for the US Centers for Disease Control and Prevention. The specimens were provided by Frank Collins (University of Notre Dame). Because these are US Government photographs, there are no copyright restrictions. However, if you use these photos, you should credit James Gathany as the photographer and directly contact him (jdg1@cdc.gov) if you wanted to use any photographs for a commercial use, e.g., a DVD or a documentary. For the few images that are not from CDC/Gathany details are included with the image via the viewer.

When using images from this image gallery we kindly ask you to please acknowledge the source as 'VectorBase, www.vectorbase.org/'.

Do you have VectorBase introductory documentation or a tour?

Answer: 

Yes, we do. First, we suggest you go to VectorBase 'About' page, which gives you a quick and complete overview of data types and resources, with a Tour video and screen shots with sample queries and analyses, among other important information. If you want want to learn more, you may want to go to the tutorials page (in the Help navigation tab) and take a to look at the available tutorials in the 'General' category. If what you are looking for is more specific, we also have detailed tutorials for all our tools and resources, most with practice exercises and their corresponding answer keys.

Please, do not hesitate to email us to info@vectorbase.org, if you have any questions or would like to provide us with feedback.

Do you have workshops on using VectorBase?

Answer: 


Host a workshop

We invite labs and institutes to host VectorBase hands-on workshops. You are free to select the topics you would like us to cover, follow this link for details. If you are interested, please contact us at info@vectorbase.org for more details.

Attend a workshop

Follow this link to the VectorBase calendar of outreach events and find a date and location that works for you.

Webinars and other online help and documentation

The webinar series (March to July and August to November) are another opportunity to learn how to use our data, tools and resources, follow this link for the material shared on previous sessions or to sign up for an upcoming event. Our FAQs, tutorials and about page will give you an overview of how to use VectorBase.

Ensembl

Because in VectorBase we use the Ensembl Genome Browser and BioMart data mining tool, another option is to use Ensembl online material, or attend their webinars and workshops.

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

INSERT Apollo track-genome browser IMAGE HERE SHOWING THE SAME GENE SEEN ABOVE IN APOLLO

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 will also update the GenBank records. 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 ensures that we are consistent in the use of gene metadata.

How to cite VectorBase?

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

How to cite VectorBase

Answer: 


Cite VectorBase most recent paper

If you use VectorBase data, tools or resources, we invite you to please cite our most recent paper:

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D. 2015. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Research 43(Database issue):D707-13.


Reference a species geneset

VectorBase, www.vectorbase.org (VectorBase most recent paper), <Species_name><isolate/strain> <Assembly, Gene set>.

Worked example

For example if you want to reference your usage of the Anopheles gambiae AgamP4.9 set of predictions you would use:

VectorBase, www.vectorbase.org (Giraldo-Calderón et al 2015), Anopheles gambiae PEST, AgamP4.9.


How to cite a gene?

Follow this link to the FAQ that describes how to cite a gene.

How to subscribe to a mailing list

Answer: 

An overview of the mailing lists hosted a VectorBase is available here

Not all are open for subscription.

Most of the VectorBase users are more likely to be interested in:
- news at vectorbase . org: receive information about VectorBase releases.
- info at vectorbase . org: contact VectorBase to ask for information or provide feedback.

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