Species not in Ensembl

Question

[Ruben]

I am working on a species that is not found on Ensembl, Folsomia candida (Metazoa / Arthropoda). However, it is in the NCBI database, UniProt and KEGG. How are new species admitted to the Ensembl database?

I have not been able to find the answer, sorry if their is something fundamental that I do not understand of the database.

[GenoMax]

Tagging: Emily_Ensembl

She may have some insight into which species are chosen for inclusion in Ensembl database. But a reasonably complete genome sequence is likely to be a major requirement.

[Ruben]

Thank you so much @ Astrid_Ensembl @ Ben_Ensembl for your answers I will take this up with my supervisors and we'll send you an email shortly!

Best wishes,

Ruben

[Astrid_Ensembl]

We are happy to help and have received your email!

[Michael]

Your species would possibly fit into ensembl metazoa. Do you have a species for which you have a new good genome assembly and annotation? Then you should contact Ensembl to negotiate the terms on which it is possible to include. For NCBI, UniProt, etc. each species that has at least a single sequence assigned will appear in their taxonomy, but that doesn't mean there is a genome sequence.

Answer 1

[Ben_Ensembl]

Hi Ruben,

For an organism to be included in Ensembl Metazoa (https://metazoa.ensembl.org), the genome needs to be in INDSC, with annotation.

Having spoken to my colleagues, it looks like this organism has both a reasonable quality assembly and annotation at the NCBI - so it’s a candidate we'd be interested in import into Ensembl Metazoa.

If you could send a direct e-mail to [e-mail] with a request to include this species, we can start the ball rolling.

Best wishes

Ben Ensembl Helpdesk

Answer 2

[Astrid_Ensembl]

Ensembl Genomes imports genome assemblies with sufficient quality and their annotation from ENA. Please contact us at helpdesk[at]ensemblgenomes.org to discuss specific requirements and the possibility of including this species.