Question: Species not in Ensembl
0
gravatar for Ruben
9 months ago by
Ruben20
the Netherlands, Amsterdam, Vrije Universiteit
Ruben20 wrote:

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.

ensembl • 364 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by Ruben20
2

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.

ADD REPLYlink written 9 months ago by genomax68k
2

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

ADD REPLYlink written 9 months ago by Ruben20
1

We are happy to help and have received your email!

ADD REPLYlink written 9 months ago by Astrid_Ensembl220
1

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.

ADD REPLYlink written 9 months ago by Michael Dondrup46k
6
gravatar for Ben_Ensembl
9 months ago by
Ben_Ensembl1.0k
EMBL-EBI
Ben_Ensembl1.0k wrote:

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 helpdesk@ensemblgenomes.org with a request to include this species, we can start the ball rolling.

Best wishes

Ben Ensembl Helpdesk

ADD COMMENTlink written 9 months ago by Ben_Ensembl1.0k
6
gravatar for Astrid_Ensembl
9 months ago by
EMBL-EBI
Astrid_Ensembl220 wrote:

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.

ADD COMMENTlink written 9 months ago by Astrid_Ensembl220
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