Ah - sorry - Didn't know the distinction between ENSEMBLE Biomart database and Biomart portal. Understandably any database of this scale is likely maintained by multiple groups. unfortunately, a lot of us traditional biologists did not and still do not know it. Thank you for cc'ing my report to Arek, or whoever is involved in Biomart portal maintenance. And I apologize again for troubling you with an inappropriate issue.
On Wed, Apr 10, 2013 at 5:00 AM, Rhoda Kinsella <[email protected]> wrote: > Hi Brenden > As I mentioned in previous emails, I don't work for the BioMart project so > I cannot comment on whether anything has changed with the ID converter on > the BioMart Central portal. I have cc'd Arek who might be able to help you. > Regards > Rhoda > > On 9 Apr 2013, at 20:12, Brenden Chen <[email protected]> wrote: > > Hi, Rhonda > > Today (Apr 9th, 2013), the same phenomenon (as described in our prior > correspondence, see below) occurred again. Please see attachments for the > details. > As you could see in the screenshot.docx, several UCSC IDs have no matching > HGNC symbols. > However, in the downloaded file - result040913.txt - all unmatched UCSC > IDs were removed. > I am not clear if you meant a new version of ID converter will remove the > unmatched IDs (or not remove?). > But as of today, it looks like the program chooses to remove them, even > though the unmatched UCSC IDs are true transcripts of respective genes. > I do hope the program would keep all unmatched IDs, as long as they are > legitimate transcripts. > > Could you confirm if a new version of ID converter has been implemented ? > > Best, > Brenden > > > On Fri, Apr 5, 2013 at 4:42 AM, Rhoda Kinsella <[email protected]> wrote: > >> Hi Brenden >> Here are my responses to Q1 and Q2: >> >> Q1: I tried to replicate your issue using the Ensembl biomart databases >> at www.ensembl.org, for which my team are responsible for creating and >> maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters >> selected) and downloaded the results in TSV format. Here is a sample of >> what I got: >> >> HGNC ID(s) UCSC ID >> uc022acc.1 >> 32652 uc003eoi.2 >> 38207 >> uc021rcb.1 >> 41892 uc003imv.3 >> 33192 >> uc021vrp.1 >> 32622 uc009ywe.3 >> 43036 >> 38305 >> 32982 uc021sci.1 >> uc021zag.1 >> uc021tlh.1 >> uc021xuv.1 >> >> You will see that for some lines there is a UCSC ID but no HGNC ID and >> vice versa. For these instances there is a blank space for the missing ID. >> This is the expected BioMart behaviour. If I understand you correctly, you >> have input UCSC IDs and in the interface you see that input ID with a >> corresponding blank space if there is no HGNC ID. I think that if the >> database does not contain the UCSC ID that you have input, it should not >> report back anything on the interface or on the output file. This may be a >> new feature of the BioMart 0.8 interface, so I would be grateful if you >> could provide some example IDs for which this is occurring so that I can >> investigate further. >> >> Q2: As I mentioned in my previous emails to you, I work for the Ensembl >> project and we create the Ensembl BioMart databases that are added to the >> BioMart central portal along with many other databases from different >> projects. If you have a query about the data in the Ensembl BioMart >> databases, please do email [email protected]. For any BioMart central >> portal issues, please email this [email protected] mailing list. >> >> I hope that helps, >> Regards >> Rhoda >> >> >> >> >> On 26 Mar 2013, at 20:48, Brenden Chen <[email protected]> wrote: >> >> To whom it may concern, >> >> My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York >> (US). >> I have a few questions regarding Biomart and hope that someone could help >> clarify them. >> >> Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few >> days ago. The return at the time included several blank HGNC IDs, which is >> fine as, I was told later, >> UCSC updates their database daily whereas HGNC/Ensemble database does >> not. However, earlier today (Mar. 26, 2013) when I was trying with the same >> ID converter, while the >> result in the pop-up window still included blank HGNC IDs, the download >> file actually removed those that did not have a matching HGNC IDs. Is this >> "removal" functionality a revised version of Biomart ID converter or a >> glitch? From a user's standpoint, it's still useful to have unmatched blank >> IDs listed, at least we could manually fill in the blank. Now we need to >> manually add those UCSC IDs that do not have a matching HGNC IDs. >> >> Q2. The website seems to be maintained by several groups around the >> globe. One of my prior communication with Biomart mentioned that I could >> have further inquiries emailed to >> [email protected]. What is the "correct" corresponding emails for >> any similar question like the one above. >> >> Please advise. Thank you >> >> Brenden >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> >> Rhoda Kinsella Ph.D. >> Ensembl Production Project Leader, >> European Bioinformatics Institute (EMBL-EBI), >> Wellcome Trust Genome Campus, >> Hinxton, >> Cambridge, >> CB10 1SD >> >> >> >> > <results040913.txt><screenshot.docx> > > > Rhoda Kinsella Ph.D. > Ensembl Production Project Leader, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton, > Cambridge, > CB10 1SD > > > >
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