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
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