[mart-dev] datasets species and types
I'm a little confused by the behavior of martivew on http://www.biomart.org/biomart/martview/ You know (please correct me if it's wrong) that each database is linked to a series of datasets by the mart file that you can download using url like: http://www.biomart.org/biomart/martservice?type=datasetsmart=ensembl http://www.biomart.org/biomart/martservice?type=datasetsmart=ensembl On martview, for the first database listed (ENSEBL 45 GENES - SANGER) you can choose on a list of simple datasets. However If you choose ENSEMBL 45 HOMOLOGY - SANGER, datasets are divided into species and type. If we look the mart file, you can find CSV lines, like: TableSetcompara_agam_agam_paralogsAnopheles gambiae (AgamP3)|Anopheles gambiae (AgamP3)|Paralogues TableSetcompara_agam_btau_orthologs Anopheles gambiae (AgamP3)|Bos taurus (Btau_3.1)|Orthologues1 TableSetcompara_agam_btau_paralogsAnopheles gambiae (AgamP3)|Bos taurus (Btau_3.1)|Paralogues1 A dataset is indicated by the unique internal name (after Tableset). The third CSV element is the Display name for selections, and (I suppose) species and type are separated by a | char. The question is: Is normal that after I select Anopheles gambiae as first specie in the website, I can choose for example XENOPUS TROPICALIS as second, instead only Anopheles gambiae or bos taurus, how I may expect looking the mart file? Is there a problem with html and javascript or I miss something? thank you Gianfranco -- Gianfranco Frau CRS4 - Bioinformatics Phone +39 070 9250 438 Loc. Pixina Manna Edificio 1 Pula 09010 (CA), Italy http://www.bioinformatica.crs4.org msn contact: [EMAIL PROTECTED]
Re: [mart-dev] datasets species and types
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello again. For any given combination of species A and B with type C, you will find only one entry in the downloaded CSV file. MartView then allows the user to select any combination of A and B for type C and will translate it to the appropriate single entry. So, for A.Gam and X.Tro with Orthologues, there is only one entry in the CSV file - compara_agam_xtro_ortholog. This is the entry that will get selected regardless of the order in which the user selects the two species involved. cheers, Richard Gianfranco Frau wrote: Richard Holland ha scritto: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry but I'm not sure I understand your question fully. Are you asking us how to restrict the list of species available, or how to add to it? What is the problem in HTML/JavaScript that you refer to? The list of second species and types is restricted to only those combinations that have corresponding datasets in the homology mart tables. If you can't find a particular combination, then it is because there is no dataset for that combination. May be I give you the worst example. My problem is that I don't understand the logic of restrictions. In some case I don't see any restriction! for example I can select: database: ENSEMBLE 45 HOMOLOGY (SANGER) first specie: Xenopus tropicalis (JGI4.1) second specie: Anopheles gambiae (AgamP3) type: Paralogues for this selection I expect to find in the mart file a line like: Tableset internalname Xenopus tropicalis (JGI4.1)|Anopheles gambiae (AgamP3)|Paralogues with Xonopus before Anopheles, but I can find only these (truncated): TableSetcompara_aaeg_xtro_orthologsAedes aegypti (AaegL1)|Xenopus tropicalis (JGI4.1)|Orthologues1 TableSet compara_aaeg_xtro_paralogsAedes aegypti (AaegL1)|Xenopus tropicalis (JGI4.1)|Paralogues1 so, I change my question: first and second species are hierarchically connected or not? In other terms Is the order of first and second species important? (The vertical bar separation is unique to Compara mart and is not intended for use in other marts - it's a temporary solution whilst we think of a better way of doing things.) cheers, Richard -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuC/y4C5LeMEKA/QRAvX7AJ0Wycx1AS6Y3Yt46gLjtgcjlEohcACePMP5 BExCNiKRybu2va2gHiVvYDE= =/DwB -END PGP SIGNATURE-
