-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi there.
I created these tables exactly as you describe below in my local Oracle Express instance, then downloaded martj-0.4 as described on biomart.org and ran MartEditor from that download, and it worked fine. I also tried MartEditor from my development copy of martj-0.5, and that worked fine too. All I can think of is that you may have permissions problems (you could double-check the connection settings you gave MartEditor to check this - database should be SID, schema should be the actual owner of the tables, e.g. scott, username/password are obvious), or these tables are actually synonyms to tables in another schema in which case the mechanism we use to search for tables would not find them. I'm not sure where to go from here. Maybe you could describe what you are doing in a bit more detail and something might jump out. cheers, Richard Arek Kasprzyk wrote: > > On 4 Oct 2006, at 05:33, Twigger Simon wrote: > >> hi Arek, >> >> Took me a little while to get all the details. We have one main table: >> >> RGD_GENES__GENES__MAIN >> -------------------------------------------- >> RGD_ID_KEY NUMBER >> GENE_SYMBOL VARCHAR2 >> GENE_NAME VARCHAR2 >> GENE_DESC VARCHAR2 >> >> It has data in it (23k rows), the RGD_ID_KEY is set as the primary key >> for the table. We have a number of other dimension tables, all named >> RGD_GENES__xxxxx__DM, here's a representative example: >> >> RGD_GENES__GENOME_V3_1_MAP__DM >> ------------------------------------------------------------- >> RGD_ID_KEY NUMBER >> MAP_NAME VARCHAR2 >> CHROMOSOME VARCHAR2 >> STRAND VARCHAR2 >> START_POS NUMBER >> STOP_POS NUMBER >> >> These also all have data in them, dumped directly from the RGD schema >> via SQL. We havent defined foreign key constraints between the >> RGD_ID_KEY values in the __DM tables back to the RGD_ID_KEY in the >> __MAIN table but we could certainly add those in. >> >> From what I can see, assuming that the case doesnt matter, the tables >> are named correctly, the keys are named correctly (presumably NUMBER >> is the correct datatype?), there is data in the tables, the biomart >> user Im connecting with has appropriate privileges and it should work >> - at least based on my experience with MySQL versions. >> >> When I connect to the database using marteditor (v4) I get this message: >> >> "No datasets available, is this a biomart compatible schema" >> >> The tables on my MySQL version are essentially the same but all lower >> case and they worked fine. >> >> Let me know if anyone can see anything obvious that could be causing >> the problems >> >> Thanks in advance! >> > > Hi Simon, > your tables look perfectly fine to me. > Let us investigate more and we'll come back to you > > a. > > > > >> Simon. >> >> -- >> >> Simon N. Twigger, Ph.D. >> Assistant Professor, Department of Physiology >> Medical College of Wisconsin >> 8701 Watertown Plank Road, >> Milwaukee, WI, USA >> tel: 414-456-8802 >> fax: 414-456-6595 >> AIM/iChat: simontatmcw >> >> >> On Sep 29, 2006, at 1:51 PM, Arek Kasprzyk wrote: >> >>> >>> On 29 Sep 2006, at 18:16, Twigger Simon wrote: >>> >>>> Hi there, >>>> >>>> We're moving a mart over to oracle and we've got a main table called: >>>> >>>> RGD_GENES__GENES__MAIN >>>> >>>> When I try and do the naive setup it cant find a dataset and asks if >>>> this is a biomart compatible schema... The schema used to work fine >>>> on MySQL, I wondering if the case change from rgd_genes__genes__main >>>> is causing the problem? Do Biomart table and attribute names have to >>>> be lowercase, or at least the parts that biomart is relying on >>>> (__main, __dm for tables, _key, etc for attributes) >>>> >>>> Thanks in advance for any thoughts on this. >>>> >>> >>> Simon, >>> could you describe your table for us? >>> Also for MEditor to work you need to have at least one entry in this >>> table. >>> Could you check that? >>> >>> a. >>> >>> >>> >>>> Simon. >>>> >>>> -- >>>> >>>> Simon N. Twigger, Ph.D. >>>> Assistant Professor, Department of Physiology >>>> Medical College of Wisconsin >>>> 8701 Watertown Plank Road, >>>> Milwaukee, WI, USA >>>> tel: 414-456-8802 >>>> fax: 414-456-6595 >>>> AIM/iChat: simontatmcw >>>> >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------- >>> >>> Arek Kasprzyk >>> EMBL-European Bioinformatics Institute. >>> Wellcome Trust Genome Campus, Hinxton, >>> Cambridge CB10 1SD, UK. >>> Tel: +44-(0)1223-494606 >>> Fax: +44-(0)1223-494468 >>> ------------------------------------------------------------------------------- >>> >>> >>> >>> >> >> > > > ------------------------------------------------------------------------------- > > Arek Kasprzyk > EMBL-European Bioinformatics Institute. > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > Tel: +44-(0)1223-494606 > Fax: +44-(0)1223-494468 > ------------------------------------------------------------------------------- > > > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFI3u44C5LeMEKA/QRAmOvAKCAfY1fb8znfcUMzaQ521kuGv/DpgCfXbm2 TXG9+VGGaHNRIi96WI+P3ZQ= =LT+U -----END PGP SIGNATURE-----
