Peter,
On 26/09/2011 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.
^^^ v0.8 is supposed to avoid this as much as possible in the favour of implicit (under the hood) linking. Basically, the explicitly Linked Dataset concept of v0.7 can now be perceived as attributes and filters of all linked datasets appearing in different sections (folders) within the first (point of entry) dataset. This also lifts the 2 dataset linking limit of v0.7. This (n>20) type of linking is already implemented and functional. However, the central.biomart.org has old (v0.7) style configurations whereby there is no such example to demonstrate it.
Best, Syed
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. | _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users
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