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Post by DAVID user on Jul 22, 2020 15:29:03 GMT -5
Hi all,
I need to submit a vector of gene symbols to DAVID using RDAVIDWebService but when I call getIdTypes(), I don’t see anything that would indicate that that’s possible. However, the DAVID Web UI has OFFICIAL_GENE_SYMBOL as an option for input list. I’ve tried using Ensembl IDs, which I also have, but those don’t work for some reason, and I’ve also tried manually converting the gene symbols to Entrez IDs, saving that list as a text file, and using that in R, but still, no dice. Am I missing something here? I just have a list of gene symbols, some of which are duplicates, for which I want major functional categories (I’ve chosen GOTERM_BP_ALL).
Thanks,
Arta
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Post by DAVID user on Jul 22, 2020 15:29:33 GMT -5
Hi Arta,
At this time, we do not allow the submission of gene symbols through the web service. Symbols are ambiguous so one symbol can map to genes in multiple species and DAVID currently maps them all. We are currently working on methods for selecting the species of interest during the upload process. Ensembl gene id or Entrez gene id should work however. If you would like to email us your list, we could take a look at the problem.
Regards, Brad
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Post by B on Oct 26, 2020 16:59:04 GMT -5
Hi Arta, At this time, we do not allow the submission of gene symbols through the web service. Symbols are ambiguous so one symbol can map to genes in multiple species and DAVID currently maps them all. We are currently working on methods for selecting the species of interest during the upload process. Ensembl gene id or Entrez gene id should work however. If you would like to email us your list, we could take a look at the problem. Regards, Brad Do you have a prediction for when Gene Symbols will be allowed through the web service? I think both of these features (species selection in upload and gene symbol use) would be extremely useful |
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Post by Tanzira on Mar 2, 2022 13:00:50 GMT -5
Hello Brad!
I was trying to use API and used official gene symbol as idType but not sure what to put inside setCurrentSpecies(). I tried "human" but it did not work. Can you please guide me in the right direction. Thanks!
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Brad
DAVID Bioinformatics Team
Posts: 56
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Post by Brad on Mar 2, 2022 15:06:47 GMT -5
Hi Tanzira,
We have now added the species selection method during the gene symbol upload process for the web interface, but have not yet made it available in the web service and therefore gene symbol upload is still not available. We do understand how important this functionality is to our webservice users and we are working to add it.
The setCurrentSpecies() function takes an integer corresponding to the index of the species in your loaded list. You can use the getSpecies() function to get this list of species in order to determine the index. DAVID orders the species list by the number of genes in your list per species in descending order, so setCurrentSpecies(0) will return the species with the most mapped genes for your list. Follow that by another call to getSpecies() to see the change.
Regards, Brad
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