0
0
Entering edit mode
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

I encounter following 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
0
Entering edit mode

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]

1
Entering edit mode

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.

0
Entering edit mode

Thanks Emily_Ensembl

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.

0
Entering edit mode

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.

0
Entering edit mode

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

0
Entering edit mode

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

0
Entering edit mode

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