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
