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
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