Hi Arek,
I just meant linking in the v0.7 sense of using importables/exportables in order for the user to get
attributes from separate datasets. I can give details of the importables/exportables I used if
that's useful. However it sounds from the replies from Jonathan and Syed that its possibly not that
straightforward to bring that type of configuration into a v0.8 model?
Regards,
Peter.
On 09/26/11 19:14, Arek Kasprzyk wrote:
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.
Hi Peter,
it would be helpful if could suggest what type of linking you are after.
This can be pre-configured for you on BMC so your users would not be
affected. In the future we'll be able to do add your source yourself and
configure it in the Central Registry through our configuration tool
MConfigurator but for now you need to do via email :)
a
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<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<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:
Peter.Stevenson@hgu.**mrc.ac.uk<[email protected]>>
EMAP Computer Support |
http://www.emouseatlas.org/**emage<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<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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