Hi Arek and Francesca
Apologies for the delayed response. I have asked someone from our
regulation team about this and we currently do not provide a
Nucleotide Universal Identifier and it is unlikely that we will in the
near future. We do hash our sequences before importing, so we already
group identical probes into the same record for a given vendor e.g.
Affy. We do not do this across vendors.
For example:
mysql> select * from probe p, array_chip ac where p.probe_id=22404456
and p.array_chip_id=ac.array_chip_id;
+----------+--------------+----------+--------+---------------
+--------------+-------------+---------------+----------------
+----------+----------------+
| probe_id | probe_set_id | name | length | array_chip_id |
class | description | array_chip_id | design_id | array_id
| name |
+----------+--------------+----------+--------+---------------
+--------------+-------------+---------------+----------------
+----------+----------------+
| 22404456 | 304739 | 305:71; | 25 | 72 |
EXPERIMENTAL | NULL | 72 | HG-Focus | 32
| HG-Focus |
| 22404456 | 304739 | 442:101; | 25 | 74 |
EXPERIMENTAL | NULL | 74 | HG-U133A | 34
| HG-U133A |
| 22404456 | 304739 | 442:185; | 25 | 76 |
EXPERIMENTAL | NULL | 76 | HG-U133_Plus_2 | 36
| HG-U133_Plus_2 |
| 22404456 | 304739 | 501:105; | 25 | 73 |
EXPERIMENTAL | NULL | 73 | HG-U133A_2 | 33
| HG-U133A_2 |
+----------+--------------+----------+--------+---------------
+--------------+-------------+---------------+----------------
+----------+----------------+
4 rows in set (0.03 sec)
I hope this helps
Regards
Rhoda
On 7 Feb 2012, at 14:38, Arek Kasprzyk wrote:
Hi Francesca,
I forwarding this email to the users mailing list because this
question would be best answered by someone from the BioMart data
provider community. Perhaps Ensembl? Rhoda: would you like to
comment on that?
a.
On Tue, Feb 7, 2012 at 7:31 AM, Francesca Buffa <[email protected]
> wrote:
Dear Arek
I just wanted to ask if Biomart provides Nucleotide Universal
Identifier or will it provide this information in the future?
thank you
kind regards
Francesca
--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
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