Dear Junjun, Thanks for a very prompt response. I shall try this query first with ICGC as a model and if it is not working we should definitely have a skype session as per your convenience.
Now that I am navigating through ICGC website I like the latest web interface that comes with release 0.8 and the many options it offers to query the mart! Thanks and regards, Parul Kudtarkar > Dear Parul, > > Just to clarify that BioMart 0.8 rc6 does support the query we were > discussing. It does not support creation of the unrolled dataset, this can > be done using MartBuilder in 0.7, Or you can prepare it yourself, you just > need to create a table with two columns, one for parent terms, the other > for child terms under given parent term. See the example below. > > If you are running BioMart 0.8 rc6, you can open one of the registry XML > file under 'registry' folder called icgc6.xml in MartConfigurator. This is > the registry for the ICGC DCC data portal (dcc.icgc.org). In the data > portal, there is a similar filter as well, the 'Pathway name' filter > under: > http://dcc.icgc.org/martanalysis/#!/Quick/gene_ensembl_config_quick?ds=hsapiens_gene_ensembl_QCMGPancreas&_displayname=Acetylation. > Here, user specifies a 'pathway name' for the filter, it converts the > pathway to Ensembl Genes that are involved in the specified pathway. > > The following screenshot shows how this filter is configured in Gene quick > search. > > > [cid:7B21EE9F-0561-49E8-A447-D5B181D7E429] > > > I understand is not possible to provide all the information in this email > for you to set it up yourself. If you need further assistance, maybe we > should set up a Skype session to walk you through all of the steps. > > For your question about MartView, the answer is no, we do not have similar > GUI in 0.8 as it is in 0.7. > > Cheers, > Junjun > > > On 11-08-22 6:31 PM, "Parul Kudtarkar" > <[email protected]<mailto:[email protected]>> wrote: > > 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]><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]><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 > > > -- 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
