Hi Suo, I do not know any dataset has defined HGNC symbol as an exportable.
You may want to contact Ensembl Helpdesk at [email protected] for help. It might be possible for them to add both exportable and importable for HGNC symbols in a future release. Cheers, Junjun On 11-05-24 5:33 PM, "suo" <[email protected]> wrote: >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
