Thanks Joachim, that was a very useful blogpost! I successfully built my local ensembl mart by following your instructions. As you predicted I did see some error messages like:
Compiler warnings: line 170: Attribute 'graph' outside of element. line 183: Attribute 'autoCompletion' outside of element. "Problem finding a placeholder dataset for chromosome_name push actions. Have you set the correct databases in the schema database connection box?" which I ignored for now. One problem I have right now is that in MartView, I don't see the Microarray section in the Feature Attributes page under the External attributes group. I do see the microarray attributes in MartEditor when I import from my local mart. During the 'Upload All' step, I uploaded the following xml files: gene_ensembl_template.template.xml probe_set_template.template.xml probe_template.template.xml hsapiens_gene_ensembl.xml (as I was not interested in the other species) But when I import (either from martdb or localmart) I only see 'gene_ensembl' as the template, I don't see the probe or probe_set templates. I am not sure if this is related to the missing Microarray attributes problem. I'd appreciate any pointers to fixing this problem. Thanks, -Kiran On Thu, 2009-12-17 at 22:28 +0000, Joachim Baran wrote: > 2009/12/17 Kiran Mukhyala <[email protected]>: > > In that case, I think I will need the MartBuilder XML files to create > > Ensembl-56 marts from scratch. I just asked for these files on > > ensembl-dev but please let me know in case you know where to find them. > Have a look at: http://bergman-lab.blogspot.com/search/label/biomart > > I described there how to add custom data to the existing marts and I > also provided XML-files for the Ensembl Mart 55. Unless you do > something fancy, you can probably use the 55 XMLs and then run 'Update > All Schemas' from the MartBuilder menu to let it pick up any changes. > You have to do that step anyway to incorporate your custom data. > > If I remember correctly, either MartBuilder or MartEditor will come up > with some error messages. Those are fine though. I can find out the > exact messages and their cause once I am back from my holidays in two > weeks. > > Best Wishes, > Joachim >
