> > 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. > > > Junjun: these features are really easy to implement. Is there a chance you could add it to the rc6 (or whatever the bmc is currently running on) for Peter please?
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. | >> ______________________________**_________________ >> Users mailing list >> [email protected]<mailto:Users**@biomart.org <[email protected]>> >> >> https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users> >> >> >> > -- > 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. | > ______________________________**_________________ > Users mailing list > [email protected] > https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users> >
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