Arek,
If people want to contact Ensembl helpdesk, then the eMail address is
[EMAIL PROTECTED]
Xose
Arek Kasprzyk wrote:
Hi,
Ensembl mart has moved to automatic mart builds from release 50 and as a
result there have been some changes to the existing attributes and filters.
The complete list is below. Please adjust your scripts and workflows
accordingly. The test server is provided for your convenience at
test.biomart.org.
I am sending this email on behalf of Ensembl team for the last time as
biomart team is no longer directly involved in the Ensembl mart production
and Ensembl team has now taken over. Please contact Ensembl team directly at
[EMAIL PROTECTED] if you require any help or info.
The ETA for Central Portal update to Ensembl 50 is mid next week.
A.
< means GONE
means REPLACEMENT
--------
Attributes
--------
< 3utr_end
< 3utr_start
< 5utr_end
< 5utr_start
< cdna_length
< cds_length
< constitutive
< gene_chrom_end
> end_position
< gene_chrom_start
> start_position
< gene_stable_id
> ensembl_gene_id
< ensembl_cdna_length
< ensembl_cds_length
< ensembl_peptide_length
< exon_cdna_end
< exon_cdna_start
< exon_cds_end
< exon_cds_start
< exon_chrom_strand
> strand
< exon_coding_end
< exon_coding_start
< exon_stable_id
> ensembl_exon_id
< external_db_name
< family
< family_description
< feat_chr_end
< feat_chr_name
< feat_chr_start
< feature_set
< feature_type
< feature_value
< str_chrom_name
> chromosome_name
< struct_biotype
> biotype
< struct_description
> description
< struct_external_gene_id
< struct_family
< struct_transcript_count
> transcript_count
< transcript_chrom_end
< transcript_chrom_start
< transcript_chrom_strand
< transcript_display_id
< transcript_stable_id
> ensembl_transcript_id
< translation_stable_id
> ensembl_peptide_id
< type
< unified_uniprot
< unified_uniprot_accession
< uniprot_varsplic_id
< evidence_code
< go
> go_biological_process_id
> go_cellular_component_id
> go_molecular_function_id
< go_description
> go_bilogical_process_linkage_type
> go_cellular_component_linkage_type
> go_molecular_functions_linkage_type
< *species*_external_db
< *species*_external_id
< *species*_dn_ds
-------------
FILTERS
-------------
< with_3utr
< with_5utr
< biol_process
> go_biol_process_filters
< cell_component
> go_cell_location_filters (fix this name in 51)
< evidence_code
> go_mol_function_filters
< evidence_code_biol_process
> go_biol_process_evidence_code
< evidence_code_cell_component
> go_cell_location_evidence_code (fix this name in 51)
< constitutive
--
Xose M. Fernandez
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
Great Britain
