Dear Junjun, This is indeed what I am looking for, however I have installed and created mart for Biomart 0.8 candidate 6 instead of Biomart 0.7. Is it possible to do the same with this latest Biomart release?
Could you please provide further details and configuration on creating hidden helper mart? Also with regards to GUI; biomart 0.8 offers MartForm, MartWizard, MartAnalysis and MartExplorer, is it possible to use MartView GUI used by Biomart 0.7? If yes could you please provide the details. Thanks and I do appreciate all the guidance provided by the Biomart team. Thanks and regards, Parul Kudtarkar > Dear Parul, > > If I understand your question correctly, then yes, this is support in > BioMart 0.7. Your use case is similar to the ontology filters in Ensembl > gene data mart. See the query below (please copy and paste the whole URL > into your web browser): > > http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.anatomical_system&FILTERS=hsapiens_gene_ensembl.default.filters.anatomical_system_term."endocrine"|hsapiens_gene_ensembl.default.filters.ensembl_gene_id."ENSG00000198712"&VISIBLEPANEL=resultspanel > > In this example, user specify a anatomical term: endocrine, the system > returns sub-terms that are under it, such as: thyroid, adrenal gland etc. > > Briefly, here is how it works: in addition to a usual data mart, we need > to create a hidden helper mart which does the conversion of user-specified > term into sub-terms. More specifically, the helper mart has a filter that > takes the term as input, it also has an exportable that gives output of > sub-terms. The sub-terms will be fed to the main mart to retrieve > corresponding records. > > Below is how the table in the helper mart looks like for the example I > gave: > > mysql> select * from hsap_evoc_AnatomicalSystem__Vocabulary__main where > term_108 = "endocrine"; > +----------------------+-----------------+-----------+-------------+ > | unrolled_name | Node_id_108_key | Term_108 | unrolled_id | > +----------------------+-----------------+-----------+-------------+ > | endocrine | 144 | endocrine | 144 | > | endocrine pancreas | 144 | endocrine | 145 | > | pineal gland | 144 | endocrine | 147 | > | pituitary gland | 144 | endocrine | 148 | > | thyroid | 144 | endocrine | 149 | > | parathyroid | 144 | endocrine | 150 | > | adrenal gland | 144 | endocrine | 151 | > | thymus | 144 | endocrine | 154 | > | islets of Langerhans | 144 | endocrine | 146 | > | adrenal cortex | 144 | endocrine | 152 | > | adrenal medulla | 144 | endocrine | 153 | > +----------------------+-----------------+-----------+-------------+ > 11 rows in set (0.00 sec) > > If you confirm this is what you are looking for, we will provide more > details on how to create and configure necessary marts. > > Cheers, > Junjun > > > On 11-08-22 1:02 PM, "Parul Kudtarkar" > <[email protected]<mailto:[email protected]>> wrote: > > Dear Biomart users, > > I want to filter my results based on functional category which has class > and corresponding sub class. If I select a particular class, I want the > system to auto pull corresponding sub classes related to that class. For > example if I select class: Adhesion , I want the system to pull only the > corresponding sub classes present in the database such as > Adhesion_Cadherin, Adhesion_Collagen, Adhesion_ECM, Adhesion_GPCR, > Adhesion_IgFN3Receptor, Adhesion_Integrin,Adhesion_LRRReceptor etc. > > Is this possible in biomart, if yes how? > > Thanks, > Parul Kudtarkar > > > -- > Parul Kudtarkar > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > > > > > > > > -- > Parul Kudtarkar > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > > > > > _______________________________________________ > Users mailing list > [email protected]<mailto:[email protected]> > https://lists.biomart.org/mailman/listinfo/users > > -- Parul Kudtarkar Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
