Help downloading gene descriptions using Ensembl biomart fungi portal
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3.0 years ago

I am trying to extract gene descriptions using Ensembl gene ids for candida glabrata using Ensembl BioMart website, however , when I select the species from the drop down

select

I encounter following error

error

Error link can be accessed here

What I have with me are the Ensembl ids like these

CAGL0L12386g
CAGL0M04477g
CAGL0M04851g
CAGL0M06193g
CAGL0M12452g
CAGL0M13299r
ENSRNAG049947011
ENSRNAG049947025
ENSRNAG049947039
ENSRNAG049947051
ENSRNAG049947068
ENSRNAG049947077

And I am interested in the corresponding gene descriptions. Any help will be appreciated.

Also tagging, Emily_Ensembl

ensembl biomart fungi • 793 views
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Are those real Ensembl ID's? I tried 2-3 and can't seem to pull up any results via search.

Note 1: If you search at https://fungi.ensembl.org then you get hits.
Note 2: BioMart at https://fungi.ensembl.org does not have the species you need.

@Emily: REST API is not enabled for Fungi?

NCBI unix Utils gets the CAG* ids but not the ENS* since they are Ensembl specific.

$ esearch -db protein -query "CAGL0L12386g" | efetch -format fasta | grep ">"
>XP_449307.1 uncharacterized protein CAGL0L12386g [[Candida] glabrata]
>CAG62281.1 unnamed protein product [[Candida] glabrata]
$ esearch -db protein -query "CAGL0M12452g" | efetch -format fasta | grep ">"
>XP_449884.1 uncharacterized protein CAGL0M12452g [[Candida] glabrata]
>CAG62864.1 unnamed protein product [[Candida] glabrata]
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You can get fungi through the Ensembl Genomes REST API.

Certain species and strains in Ensembl Fungi are not available in BioMart – this occurs when we imported the data directly from INSDC.

I tried a few of those IDs and the search worked for me.

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Thanks Emily_Ensembl

Could you please correct the API link which appears broken/incorrect?

Apart from the REST API, there is no other way you mean? I am not familiar with this. Also, generally the description is there in the GTF file, I have seen it seen it several times; I don't know why it's not there in this case in the GTF file.

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Because the genome comes from the INSDC import, the description is only there if it was there in the original data in INSDC. We just might not have it – it wouldn't be available by REST either.

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@Vijay: That link is just http://rest.ensemblgenomes.org

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My source of GTF file was this and indeed these ids are there

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That search looks like you're searching your genome for the name of your species. That's not going to work.

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