Hi Ellen yes it does. You can definitely do the 2 & 3 (I just checked with the XML I sent you previously by changing properties of the config to multi-select). For the (1) as I said before v 08 requires that each datasets lives in a different database so i am not sure if there is way round it
Happy New Year to you too! :) a On Thu, Jan 3, 2013 at 2:25 PM, Ellen Schofield < [email protected]> wrote: > Happy New Year! Sorry, only back to work today after teh Xmas period. > > OK, in an ideal, this is what I would like..... > > 1 database with data split into different datasets depending on version > (dbSNP130, dbSNP135 etc.) so it's easy to replace/update datasets. > 2. All datasets have same db structure and same mart (xml) configuration > 3. You can multiselect across the datasets, thus doing the same query > multiple times, once on each dataset and then combined results being > returned. > > Does that make sense? > > > Thanks, > Ellen. > > -- [email protected] > JDRF/WT Diabetes and Inflammation Laboratory (DIL) > Cambridge Institute for Medical Research (CIMR) > Wellcome Trust/MRC Building > Addenbrooke's Hospital Hills Road Cambridge CB2 0XY > Tel: 01223 763215 > > On 21/12/12 17:35, Arek Kasprzyk wrote: > > Hi Ellen, > > Are you concerned about the backend or the GUI? > > You can configure GUI to look identical to the Ensembl interface if you > split datasets to different dbs. They do not have to reside physically in > one db (One dataset per database is just a v 08 convention). > Another example is 'cancer types' in the Cancer Portal (ICGC). > > > a > > > > On Fri, Dec 21, 2012 at 2:35 PM, Ellen Schofield < > [email protected]> wrote: > >> I'm not sure this is what I want. I wanted a single db with multiple >> datasets (of the same db structure) residing in that db. >> >> An example is the ensembl snp_mart - one database, lots of datasets.... >> >> | hsapiens_snp__variation__main | >> | mmusculus_snp__variation__main | >> | rnorvegicus_snp__variation__main | >> >> etc. >> >> But instead of different species, I want different databases. Does that >> make more sense? >> >> Sorry to be a pain :-( >> >> Thanks for all your help. >> >> Ellen >> >> -- [email protected] >> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >> Cambridge Institute for Medical Research (CIMR) >> Wellcome Trust/MRC Building >> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >> Tel: 01223 763215 >> >> On 21/12/12 11:40, Arek Kasprzyk wrote: >> >> XML attached >> >> >> On Fri, Dec 21, 2012 at 11:38 AM, Arek Kasprzyk >> <[email protected]>wrote: >> >>> Hi Ellen, >>> I understand now. >>> >>> Here is what you have to do: >>> >>> >>> 1. Create separate database for each dataset (e.g hs_130, hs_137, etc) >>> 2. Make sure the table names are identical in each database (eg ... >>> marker__main). >>> 3. Open MConfigurator 'add source' (eg 'hs_130) >>> 4. Right panel, 'data source management'. 'add' (eg hs_137) >>> 5. Update data source >>> 6. Add access point >>> 7. Start the server. >>> >>> I checked it properly this time (inserting different values to >>> different databases) and everything seemed to be querying ok >>> >>> Below are examples that I used (please do not get confused with the >>> use of 'marker_130' table names in both databases, I was just too lazy to >>> edit it properly but principle remains the same: identical names) >>> >>> >>> +-------------------------------+ >>> | Tables_in_ellen_130 | >>> +-------------------------------+ >>> | hs_dbsnp130__markers__main | >>> | hs_dbsnp130__markers_func__dm | >>> +-------------------------------+ >>> >>> +-------------------------------+ >>> | Tables_in_ellen_137 | >>> +-------------------------------+ >>> | hs_dbsnp130__markers__main | >>> | hs_dbsnp130__markers_func__dm | >>> +-------------------------------+ >>> 2 rows in set (0.00 sec) >>> >>> >>> >>> (I am sending an example XML working with these tables in a separate >>> email) >>> >>> Please let me know if this solves the problem >>> >>> Merry Xmas :) >>> >>> a >>> >>> >>> >>> >>> >>> >>> On Thu, Dec 20, 2012 at 11:10 AM, Ellen Schofield < >>> [email protected]> wrote: >>> >>>> Hi Arek, >>>> >>>> Many thanks for your help, sorry I've not got back to you before now, >>>> other work took over :-) >>>> >>>> I have loaded up your xml, tweaked to point at my db to see how it >>>> works. All starts ok etc, but when I select the dbSNP137 dataset, it is >>>> still searching against the dbSNP130 data. >>>> >>>> An example from the BioMart Portal could be the ensembl one. There is >>>> a single starting point (ensembl) and then multiple datasets (humna, mouse >>>> etc) that you can choose, all, I guess witht he same structure behind the >>>> scenes and the same queries etc. >>>> >>>> Thanks, >>>> >>>> Ellen. >>>> >>>> -- [email protected] >>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>> Cambridge Institute for Medical Research (CIMR) >>>> Wellcome Trust/MRC Building >>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>> Tel: 01223 763215 >>>> >>>> On 12/12/12 17:40, Arek Kasprzyk wrote: >>>> >>>> Hi Ellen, >>>> I am sending my XML file. Please let me know if this is what you need >>>> or your problem is different >>>> >>>> a >>>> >>>> >>>> On Wed, Dec 12, 2012 at 2:33 PM, Arek Kasprzyk <[email protected] >>>> > wrote: >>>> >>>>> Hi Ellen, >>>>> perhaps I did not understand what you are after. If you partition >>>>> a table it will create many more smaller tables. I assumed that you were >>>>> looking for the opposite effect to somehow "group" your tables? How do you >>>>> want your datasets to look through GUI? Could you give me an example >>>>> either >>>>> from the BioPortal or from CancerPortal? >>>>> >>>>> cheers, >>>>> a >>>>> >>>>> >>>>> On Wed, Dec 12, 2012 at 12:02 PM, Ellen Schofield < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi Arek, >>>>>> >>>>>> Many thanks for your time. Good to know that the structure is OK. >>>>>> >>>>>> These are the steps that I did... >>>>>> Imported as a relation mart >>>>>> Select a main table and then ticked "Partition Table" at bottom of >>>>>> wizard screen >>>>>> Finish -> Java error & stack trace.... >>>>>> >>>>>> So I didn't get even as far as you :-( >>>>>> >>>>>> Does the above make sense? >>>>>> >>>>>> >>>>>> Ellen. >>>>>> >>>>>> -- [email protected] >>>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>>>> Cambridge Institute for Medical Research (CIMR) >>>>>> Wellcome Trust/MRC Building >>>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>>>> Tel: 01223 763215 >>>>>> >>>>>> On 12/12/12 10:30, Arek Kasprzyk wrote: >>>>>> >>>>>> Hi Ellen, >>>>>> I have now had an opportunity to try your file and it seemed to have >>>>>> produced the correct config structure (if I understood your problem >>>>>> correctly) >>>>>> >>>>>> This is what I did: >>>>>> >>>>>> 1. Imported your schema >>>>>> 2. Added data source with one main table >>>>>> 3. Invoked 'data source management' window >>>>>> 4. Added second dataset >>>>>> 5. Updated both datasets >>>>>> 6. Created a config >>>>>> 7. Started the server >>>>>> >>>>>> I was able to query it through GUI (did not get any results bc the >>>>>> schema was empty but did not get any errors either) >>>>>> >>>>>> >>>>>> a >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Dec 6, 2012 at 2:19 PM, Ellen Schofield < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hi Arek, >>>>>>> >>>>>>> Sent to you directly. >>>>>>> >>>>>>> Many thanks, >>>>>>> >>>>>>> Ellen. >>>>>>> >>>>>>> -- [email protected] >>>>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>>>>> Cambridge Institute for Medical Research (CIMR) >>>>>>> Wellcome Trust/MRC Building >>>>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>>>>> Tel: 01223 763215 >>>>>>> >>>>>>> On 06/12/12 14:10, Arek Kasprzyk wrote: >>>>>>> >>>>>>> Hi Ellen, >>>>>>> would you mind sending me your schema so I can double check here? >>>>>>> >>>>>>> >>>>>>> cheers, >>>>>>> a >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Thu, Dec 6, 2012 at 10:25 AM, Ellen Schofield < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Hi All, >>>>>>>> >>>>>>>> I hope somebody is able to help me as I'm struggling with this. I >>>>>>>> am using BioMart 0.8rc6 and MartConfigurator as part of that. I have >>>>>>>> a db >>>>>>>> with 5 different datasets, all of which have the same structure (one >>>>>>>> main >>>>>>>> table and one dm table). I can use MartConfigurator with one dataset >>>>>>>> to >>>>>>>> create a working mart for the main/dm table in that dataset, suggesting >>>>>>>> that the structure is correct. However, if I try building a mart on >>>>>>>> one of >>>>>>>> the main tables (with it's dimension table) and request building it >>>>>>>> with a >>>>>>>> partition table causes a java null pointer exception >>>>>>>> (MartController.java >>>>>>>> line 1315). Building the same partition-based mart without the dm >>>>>>>> tables >>>>>>>> present works. >>>>>>>> >>>>>>>> Am really hoping somebody can point out what I'm doing wrong? >>>>>>>> >>>>>>>> Many thanks. >>>>>>>> Ellen. >>>>>>>> >>>>>>>> -- >>>>>>>> [email protected] >>>>>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>>>>>> Cambridge Institute for Medical Research (CIMR) >>>>>>>> Wellcome Trust/MRC Building >>>>>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>>>>>> Tel: 01223 763215 <01223%20763215> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Users mailing list >>>>>>>> [email protected] >>>>>>>> https://lists.biomart.org/mailman/listinfo/users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >>>> >>>> >>>> >>> >> >> > >
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