Hi Junjun: Is there an alternative dataset including exportable HGNC symbol to which I can link? I can see a lot biomart implementations have such a link. If anyone else has a clue, please let me know. Thanks in advance for help!
Suo --- On Tue, 5/24/11, Junjun Zhang <[email protected]> wrote: > From: Junjun Zhang <[email protected]> > Subject: Re: [BioMart Users] Problem with Configure links between datasets > To: "suo" <[email protected]>, "[email protected]" <[email protected]> > Date: Tuesday, May 24, 2011, 7:40 AM > Hi Suo, > > I looked into it, it seems there is no exportable defined > for HGNC symbol > in Ensembl mart 55. The way to check it is to look for > exportable that > specifies hgnc symbol as the attribute. Unfortunately no > such exportable > was found. > > Junjun > > > On 11-05-19 11:32 PM, "suo" <[email protected]> > wrote: > > >Hi Junjun: > > > >Got it to work. Thanks for guiding me through. > >which one is the exportable defined for HGNC Symbol in > Ensembl_55 mart? > >I want to link gene names. > > > >Suo > > > >--- On Thu, 5/19/11, Junjun Zhang <[email protected]> > wrote: > > > >From: Junjun Zhang <[email protected]> > >Subject: Re: [BioMart Users] Problem with Configure > links between datasets > >To: "suo" <[email protected]>, > "[email protected]" > ><[email protected]> > >Date: Thursday, May 19, 2011, 7:09 PM > > > >Hi Suo, > >In order to federate two datasets, a link needs to be > built through an > >exportable/importable pair. If you link your dataset > with Ensembl, you > >can create an importable on your config that can later > be paired with an > >existing exportable at the Ensembl side. As the > tutorial shows, Ensembl > >has an exportable called "ensembl_gene_id", you just > need to create an > >importable in your side. To create it do this: > > > > > >The importable's internalName and linkName on your side > must be exactly > >the same as shown above. Also, please make sure you do > have a filter > >called stable_id_1023 exist, otherwise the importable > is not valid. > >Furthermore, the corresponding database column of the > filter: > >stable_id_1023 has to contain real Ensembl Gene IDs, > otherwise the query > >will not return anything. > >Follow the tutorial carefully. Once you have your side > configured > >correctly, you need to prepare a registry file (name it > something like > >my_mart.xml) look like the follow: > > > >It includes both your dataset and ensembl dataset. Use > this registry to > >start biomart server (as follow). > > > > > >If everything configured correctly, from martview after > you choose your > >own dataset, you should be able to see and click on the > second "Dataset" > >(as below), from there you can choose ensembl human > dataset and pick up > >its attributes. > > > >If I can not see the second "Dataset", it means no link > was built to your > >dataset. Go back check carefully which part was not > done properly. > >Hope this helps, > >Junjun > > > > > >On 11-05-19 7:50 PM, "suo" <[email protected]> > wrote: > >Hi, > >The one I asked is about the biomart 0.7 I installed > not the > >biomart.org.Any clue? > >--- On Thu, 5/19/11, Joachim Baran <[email protected]> > wrote: > > From: Joachim Baran <[email protected]> > Subject: Re: [BioMart > >Users] Problem with Configure links between datasets > To: > >"[email protected]" > <[email protected]> > Date: Thursday, May 19, 2011, > >4:43 PM Hi! On 11-05-19 7:36 PM, "suo" <[email protected]> > wrote: > >>How to add the second > dataset? From > >>http://www.biomart.org/biomart/martview > take the following steps: 1. > >>Choose Database: ENSEMBL GENES 2. > Choose Dataset: Homo sapiens genes > >>3. On the left-hand side, click on the lower > 'Dataset' (black text, gray > >>background) 4. Choose Additional > Dataset: REACTOME pathway 5. Click > >>on 'Results' Hope that solves the > problem. Best Wishes, Joachim > >>_______________________________________________ > Users mailing list > >>[email protected] > https://lists.biomart.org/mailman/listinfo/users > >>_______________________________________________Users > mailing > >>[email protected]https://lists.biomart.org/mailman/listinfo/users > > > > > > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
