Entering edit mode
9.3 years ago
Assa Yeroslaviz
★
1.8k
Hi,
Is there a way to take a list of Ensembl IDs and convert them to Entrez IDs using the eutilities from NCBI?
I know I can do it with biomaRt, but I would like to compare the results also to the NCBI site itself, as I have a lot of Ensembl IDs, for which I didn't get any hits in biomaRt.
I just want to make sure, that they are really not there. I guess some of the Ensembl IDs are retired, obsolete etc.
Thanks in advance
Assa
Generally, it would be a good idea to post some examples..
an example of what? some ensembl IDs?
I don't have an example, as I didn't find out, whether or not this is possible. I don't want to post a biomart example, because this is done so many times.
sorry
Input and expected output..
For example, with Entrez Direct you could:
Here the output is protein GI. Is that the ID you're after?
Or maybe it is the Gene ID you're after?
As far as I know, there is no such thing as "Entrez ID"..
Sorry for the misunderstanding about the examples.
Yes, this is what I am looking for, but for over 10K of ensembl IDs. Is it possible to run it in a loop or to let esearch read it from a file?
Well, you could
`
for next in $(cat list) do GENEID=$(esearch -db gene -query "$next" | efetch -format uid) echo "$next<literal tab>$GENEID" done ```But I don't think that they would appreciate at the NCBI you bombing their servers like that (they might ban your IP). You could add
sleep 5
or something like that after the echo if you can wait longer for the output. Overall, perhaps it would be a better idea to make use of the gene2ensembl mapping fileIt is interesting to see, that this list of gene IDs does not correspond to the results of the biomaRt search I have run.
But still thanks for everything.