> -----Original Message----- > From: Chad Clites [mailto:[email protected]] > Sent: Monday, January 18, 2010 3:55 PM > To: Junjun Zhang > Subject: RE: Parsing mart Attribute Descriptions > > Thank you. I sent another email to the mart-dev list because > I thought I may have asked the question in the wrong place. > My apologies.
No problem. Mart-dev list is the proper place to ask this type of questions. > > I also didn't explain that I am parsing the data for use in > our own application, so there is no "choose 'File' => > 'Import' from the menu bar" :) Is there a restful call to get > the remote data set? It is possible to get more information about a remote dataset, and there is no difference with what you are doing. For example: hsap_karyotype_start is a remote dataset, you can get configuration using the following martservice request: http://www.biomart.org/biomart/martservice?type=configuration&dataset=hsap_karyotype_start However, there is a small bug in the current biomart version prevents this request for sequence datasets (which are invisible). We are working on the new BioMart release where such requests will be well supported. Please let us know if you need further assistance. Cheers, Junjun > > -----Original Message----- > From: Junjun Zhang [mailto:[email protected]] > Sent: Monday, January 18, 2010 2:39 PM > To: Chad Clites > Cc: Arek Kasprzyk > Subject: RE: Parsing mart Attribute Descriptions > > Dear Chad Clites, > > The short answer to your question is that the displayName is > defined in the remote DataSet. > > The XML states as follows: > <AttributeDescription internalName="transcript_exon_intron" > pointerAttribute="transcript_exon_intron" > pointerDataset="oanatinus_genomic_sequence" > pointerInterface="default"/> > > In the above example you gave, the origin of the attribute is > at oanatinus_genomic_sequence DataSet, which is one of the > DataSets included in ensembl's sequence_mart. Please use > MartEditor to connect to the sequence mart (parameters are > shown in the attached screenshot). Once connected, choose > 'File' => 'Import' from the menu bar, pick > 'oanatinus_genomic_sequence' from the list, then you would > find all of the settings about transcript_exon_intron > Attribute including displayName (Unspliced (Transcript), as > shown in the other screenshot). > > Hope this hopes, > > Junjun > > > > > > -----Original Message----- > > From: Arek Kasprzyk > > Sent: Monday, January 18, 2010 1:39 AM > > To: Junjun Zhang > > Subject: FW: Parsing mart Attribute Descriptions > > > > Hi Junjun, > > Could you help Chad please? > > > > Cheers, > > A. > > > > ------ Forwarded Message > > > From: Chad Clites <[email protected]> > > > Date: Sun, 17 Jan 2010 22:16:04 -0500 > > > To: arek <[email protected]> > > > Subject: Parsing mart Attribute Descriptions > > > > > > Hello, > > > I am using Javascript to parse Biomart configuration data. > > > Specifically, I am parsing the "Ensemble 56 Genes (Sanger > > UK)" mart, > > > "Ornithorhynchus anatinus genes (OANA5)" data set. One of > > the attribute groups is called 'SEQUENCES.' > > > Under Sequences are a dozen attributes, that when selected, > > display an > > > image based upon the selection. For all other Attributes, > > there is an > > > attribute called 'displayName' that I am parsing to get > the data to > > > display. The Sequences Attributes are different though. > > They do not include 'displayName' > > > as an attribute. > > > > > > I am curious as to where the MartView is coming up with the > > display labels? > > > For instance, the XML for one of the attributes looks like: > > > <AttributeDescription internalName="sequence_exon_stable_id" > > > pointerAttribute="ensembl_exon_id" > > pointerDataset="oanatinus_gene_ensembl" > > > pointerInterface="default" /> > > > As displayed in the MartView, the attribute is labeled as > > "Unspliced > > > (Transcript). Where is that labeling information coming from? > > > > > > Thank you, > > > Chad Clites > > > > ------ End of Forwarded Message > > > > > >
