Hi Syed,
The URLs are internal (relative) to www.wormbase.org, or
dev.wormbase.org, or one of the wormbase mirrors depending on the
httpd. I set this on a per-server basis using exturl setting in
settings.conf. I cannot really hard-code the path due to mirroring
issues.
Will
On 28 Mar 2008, at 16:08, Syed Haider wrote:
Will, who runs Wormbase, is cc'ed would be able to comment.
Will, you need to edit your XMLs and prepend servername for attributes
with external URL links as this is expected to have www.wormbase.org
instead of www.ensembl.org.
On Fri, 2008-03-28 at 17:02 +0100, Isabelle Phan wrote:
wow that's real service!
now the results look good:
Anatomy Term ID Anatomy Term
WBbt:0003679 neuron
however when I click on the link
http://www.ensembl.org/db/ontology/anatomy?name=WBbt:0003679;class=Anatomy_term
the page returns:
404 not found.
?
Isabelle
Syed Haider wrote:
Hi Isabelle,
www.biomart.org has the patch now. thanks for your patience.
cheers
syed
On Fri, 2008-03-28 at 11:32 -0400, Arek Kasprzyk wrote:
On 28-Mar-08, at 11:09 AM, Isabelle Phan wrote:
I have now found some queries that work great!
However I will have a hard time explaining why some data seem to
be
missing from the results table....
MartView query:
Dataset: MSD
Filters: R < 2A, single crystal X-ray diffraction
Attributes: Molecule name, Organism Name, PDB ID(s)
combined with
Dataset: Uniprot proteomes
Filters: none
Attributes: UniProt AC
Filter for unique rows: selected
View: 200 rows
I am getting entries with no organism data, e.g.:
CYCLOPHILIN 3 1e3b P52011
both the PDB and UniProt data seem to contain the correct organism
(C.elegans) with the correct taxID.
Hi Isabelle,
Why is the query not returning the organism data? Is this a
synchronization issue?
most likely, MSD as well as UNIPROT are just prototype data
sources so
not really kept up to date.
You would be probably better off using something which is regularly
updated e.g. Ensembl
a.
PS. We are investigating the Wormbase issue that you reported.
we'll
get back to you on this shortly
thanks for spotting it
thanks for any hints you may provide!
I.
--
Isabelle Phan, D.Phil.
Swiss Institute of Bioinformatics Tel: (+41 22) 379 51 89
CMU - 1, rue Michel Servet Fax: (+41 22) 379 58 58
CH - 1211 Geneva 4 Switzerland email: [EMAIL PROTECTED]
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
---
William Spooner
Visiting Scientist
[EMAIL PROTECTED]
