There have been changes to existing attributes and filters in Biomart release 50.
The complete list is below.
If your Biomart query uses any of the changes below please update your workflow accordingly.
Key
- 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
- 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
+ ensembl_transcript_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
- exon_stable_id
+ ensembl_exon_id
- external_db_name
- transcript_stable_id
- translation_stable_id
