[BioC] Question about "structure_exon_chrom_end" attributes in biomaRt

[steffen at stat.Berkeley.EDU]

Hi Ligang,

A week ago or so there was a new release of Ensembl (This usually happens
every two months).  Normally there are few changes in attribute names,
however there were some attribute name changes in this release.

Use the command below to get all attributes related to structures.
You'll see that you now have to use ensembl_exon_id, rank, exon_chrom_end
and exon_chrom_start do get what you want.

Cheers,
Steffen


> listAttributes(mart,category="Structures")
                                name
1                    ensembl_exon_id
2                     exon_chrom_end
3                   exon_chrom_start
4                              phase
5                               rank
6            struct_transcript_count
7                  structure_biotype
8  structure_canonical_transcript_id
9              structure_cdna_length
10              structure_cds_length
11              structure_chrom_name
12             structure_description
13        structure_external_db_name
14        structure_external_gene_id
15          structure_gene_chrom_end
16        structure_gene_chrom_start
17          structure_gene_stable_id
18          structure_peptide_length
19    structure_transcript_chrom_end
20  structure_transcript_chrom_start
21 structure_transcript_chrom_strand
22    structure_transcript_stable_id
23   structure_translation_stable_id
               description
1          Ensembl Exon ID
2        Exon Chr End (bp)
3      Exon Chr Start (bp)
4                    phase
5  Exon Rank in Transcript


> hello, there,
>
>
> I run into some problems in using biomaRt to mine the transcript
> structures:
>
> ==============
> library(biomaRt)
> mart<-useMart("ensembl", dataset="hsapiens_gene_ensembl")
> listAttributes(mart)$name->attrs
> attrs[grep("exon",attrs)]
> ==============
>
>
>
> why "structure_exon_stable_id", "structure_exon_chrom_start",
> "structure_exon_chrom_end" and "structure_exon_rank" are not avaliable?
>
>
>
> ================
> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] GenomeGraphs_1.0.0 biomaRt_1.14.0     RCurl_0.9-4
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.1 XML_1.96-0
> =================
>
>
> Thanks,
>
> ---
> Ligang
>
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>
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