Hi Peter, i did not make myself clear. I was not talking about bringing user defined linking back in. I was more thinking along the lines that there are typically certain datasets and that your users should like to link in order to do their favourite multi-dataset queries. If you tell us what they are we'll be able to preconfigure the interface such that these queries become possible again without users being forced to do the GUI gymnastics as they used to do in 0.7.
We just need concrete examples of multi-datasets queries that your users typically do and we could preconfigure them for you if it makes sense. As i mentioned in my previoius email, in the future you will be able to do such things on the central portal yourself but this is ... in the future. For now we need an email from you with concrete examples so we can see if we can help you and keep your users happy :) a On Tue, Sep 27, 2011 at 9:01 AM, Peter Stevenson < [email protected]> wrote: > 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<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.**emous**eatlas.org/emagewebapp/**<http://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.**oi**cr.on.ca <http://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 <http://mrc.ac.uk>< >>>> [email protected].**uk <[email protected]>>> >>>> >>>> EMAP Computer Support | >>>> http://www.emouseatlas.org/****emage<http://www.emouseatlas.org/**emage> >>>> <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<Users@biomart.**org<[email protected]> >>>> >> >>>> >>>> https://lists.biomart.org/****mailman/listinfo/users<https://lists.biomart.org/**mailman/listinfo/users> >>>> <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> >>> <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> >>> <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
