Hi Jonathan,
Thanks for the quick reply.
> 1. EMAP anatomy ontology database is included: it is under the "Search by organism" tab, under
vertebrates.
OK I missed that - sorry.
> 2. User-definable linking is not currently implemented in 0.8.
This is a pity particularly for us because the EMAGE implementation relies on this feature quite
heavily.
> 3. There is a problem with the 0.7 configuration that prevents these filters and attributes from
being imported into 0.8:
I will have to have a look at why that dataset is different to the others that
have imported OK.
> 4. and 5. BioMart 0.8 does not currently have these capabilities, but they are planned for future
releases.
Again a pity, because I think these are very useful features for users when confronted with long
lists of attributes, and also for developers to set a useful default result set.
Regards,
Peter.
On 09/26/11 15:12, Jonathan Guberman wrote:
Hello Peter,
1. EMAP anatomy ontology database is included: it is under the "Search by
organism" tab, under vertebrates.
2. User-definable linking is not currently implemented in 0.8.
3. There is a problem with the 0.7 configuration that prevents these filters and
attributes from being imported into 0.8: in your configuration XML (available at
http://biomart.emouseatlas.org/biomart/martservice?type=configuration&dataset=EXPRESSION_TEXT_TB)
there is one MainTable/key pair listed at the top of the XML:
<MainTable>EXPRESSION_TEXT_TB__EXPRESSION_TEXT_TB__main</MainTable>
<Key>OID_109_key</Key>
However, certain attributes and filters refer to other keys. E.g.:
<FilterDescription displayName="Experiment ID" displayType="text" field="oid_108"
hideDisplay="true"internalName="oid_108_filter" key="OID_108_key" legal_qualifiers="like" qualifier="like"
tableConstraint="main"/>
And
<AttributeDescription default="true" displayName="Emage ID" field="accession_1037"
internalName="accession_1037"key="OID_1037_key"
linkoutURL="http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s"; maxLength="20"tableConstraint="main"/>
Since these filters and attributes refer to keys about which no information is
provided in the XML, they can not be recreated by 0.8 and are ignored.
4. and 5. BioMart 0.8 does not currently have these capabilities, but they are
planned for future releases.
Sincerely,
Jonathan Guberman, PhD
Application Programmer
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Tel: 647-260-7818
Toll-free: 1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca>
On 2011-09-26, at 9:27 AM, Peter Stevenson wrote:
I was looking at http://central.biomart.org/ after reading the recent paper in
Database.
It's nice work, looks good, and I'm obviously happy to see the EMAGE biomart
included in there.
However I have some quibbles about how the EMAGE interface has been represented
on there...
1. The EMAP anatomy ontology database and its 2 datasets are not included.
2. There is no mechanism to do linked dataset queries.
3. EMAGE text expression annotation dataset has several groups of filters and
attributes missing.
4. There are no default attributes pre-selected.
5. There is no select all/deselect all in groups of attributes.
I don't know if some of these are technical limitations with representing a
v0.7 implementation in
v0.8? I recognise some issues from when I tried to port to a previous v0.8
release candidate. Are
there changes at this end that I could make to help?
Regards,
Peter.
--
Peter Stevenson |
[email protected]<mailto:[email protected]>
EMAP Computer Support | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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--
Peter Stevenson | [email protected]
EMAP Computer Support | http://www.emouseatlas.org/emage
MRC Human Genetics Unit | Phone: +44 (0)131 332 2471
Edinburgh EH4 2XU. U.K. |
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