Hi Chad,
I think the following is what you were referring to:
<AttributeCollection description="Ensembl Annotated Attributes and Features"
displayName="Ensembl" internalName="ensembl_attributes">
<AttributeDescription internalName="snp_ensembl_gene_id"
pointerAttribute="ensembl_gene_id" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_ensembl_transcript_id"
pointerAttribute="ensembl_transcript_id"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_ensembl_peptide_id"
pointerAttribute="ensembl_peptide_id" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="sequence_canonical_transcript_id"
pointerAttribute="canonical_transcript_id"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_chromosome_name"
pointerAttribute="chromosome_name" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_start_position"
pointerAttribute="start_position" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_end_position"
pointerAttribute="end_position" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_strand" pointerAttribute="strand"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_band" pointerAttribute="band"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_external_gene_id"
pointerAttribute="external_gene_id" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_external_gene_db"
pointerAttribute="external_gene_db" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_ensembl_CDS_length"
pointerAttribute="ensembl_CDS_length" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_ensembl_cDNA_length"
pointerAttribute="ensembl_cDNA_length" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_ensembl_peptide_length"
pointerAttribute="ensembl_peptide_length"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_transcript_count"
pointerAttribute="transcript_count" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
<AttributeDescription internalName="snp_percentage_gc_content"
pointerAttribute="percentage_gc_content"
pointerDataset="oanatinus_gene_ensembl" pointerInterface="default" />
<AttributeDescription internalName="snp_description"
pointerAttribute="description" pointerDataset="oanatinus_gene_ensembl"
pointerInterface="default" />
</AttributeCollection>
For the above 17 attributes (they are all pointer attributes), 13 of them
appear on MartView. The four missing ones are:
sequence_canonical_transcript_id
snp_ensembl_CDS_length
snp_ensembl_cDNA_length
snp_ensembl_peptide_length
The reason they are missing is that the Attributes they are referring to do not
exist (of course, this is a configuration mistake). For example,
'sequence_canonical_transcript_id' refers to 'canonical_transcript_id', which
does not exist in the pointerDataset (ie, oanatinus_gene_ensembl).
For other pointerAttributes, such as 'snp_ensembl_gene_id', it refers to
'ensembl_gene_id', which does exist in pointerDataset (oanatinus_gene_ensembl)
defined as the following:
<AttributeDescription default="true" description="Ensembl Stable ID of the
Gene" displayName="Ensembl Gene ID" field="stable_id_1023"
internalName="ensembl_gene_id" key="gene_id_1020_key"
linkoutURL="exturl|/Ornithorhynchus_anatinus/Gene/Summary?db=core;g=%s"
maxLength="15" tableConstraint="main" />
Hope this makes it clearer. Let us know if there are any further questions.
Best regards,
Junjun
________________________________
From: [email protected] [mailto:[email protected]] On Behalf Of
Chad Clites
Sent: Monday, January 25, 2010 9:51 PM
To: [email protected]
Subject: [mart-dev] remote datasets
Hello,
I hate to revisit this, but I am apparently too thick to understand what is
happening. I have a dataset (oanatinus_gene_ensembl) for which I am essentially
duplicating the Biomart interface. When I use Martview, under Attributes,
Variations, Gene, Ensembl, I see 13 attributes. When parsing the dataset
myself, I find 17 attributes, none of which exactly correspond to the
attributes displayed under the Martview.
When I asked this before, it was explained to me that the 'pointerDataset'
attribute points to an external data set that provides the display information
that MartView uses. I am not understanding how the 17 attributes that I find
correlate to the 13 attributes displayed in the MartView. I can do a query for
the remote data, but what I am failing to see is how that remote data set
correlates with the original data set.
