<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Dear all,</div><div class=""><br class=""></div><div class="">Please note that we have moved to a new system this release to generate and populate the ensembl marts filters/attributes. As a result, we have improved the consistency of our mart across the vertebrate and other ensembl divisions. The following filters and attributes names have changed and will affect script using the BiomaRt package or BioMart Perl/RESTful APIS</div><div class="">Please find the full list below or on our FTP site: <a href="ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt" class="">ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">1) External references</div><div class=""><br class=""></div><div class="">entrezgene_transcript_name -> entrezgene_trans_name</div><div class="">hgnc_transcript_name -> hgnc_trans_name</div><div class="">rfam_transcript_name -> rfam_trans_name</div><div class="">mirbase_transcript_name -> mirbase_trans_name</div><div class="">uniprot_genename -> uniprot_gn</div><div class="">uniprot_sptrembl -> uniprotsptrembl</div><div class="">uniprot_swissprot -> uniprotswissprot</div><div class="">go_id -> go</div><div class="">goslim_goa_accession -> goslim_goa</div><div class="">zfin_transcript_name -> zfin_id_trans_name</div><div class="">wormbase_gene_seq_name -> wormbase_gseqname</div><div class="">genome_rnai -> genomernai</div><div class="">go_to_gene_id -> go_to_gene</div><div class="">mgi_transcript_name -> mgi_trans_name</div><div class="">clone_based_ensembl_gene_name -> clone_based_ensembl_gene</div><div class="">clone_based_ensembl_transcript_name -> clone_based_ensembl_transcript</div><div class="">clone_based_vega_gene_name -> clone_based_vega_gene</div><div class="">clone_based_vega_transcript_name -> clone_based_vega_transcript</div><div class="">vgnc_genename -> vgnc</div><div class="">rgd_transcript_name -> rgd_trans_name</div><div class="">xenbase_transcript_name -> xenbase_trans_name</div><div class="">zfin_id -> zfin_id_id</div><div class=""><br class=""></div><div class="">2) Microarray probes/probesets</div><div class=""><br class=""></div><div class="">efg_agilent_* -> agilent_* (e.g: efg_agilent_012795 -> agilent_012795)</div><div class="">efg_nimblegen_gpl8673 -> nimblegen_gpl8673</div><div class="">efg_slri_gpl3518 -> slri_gpl3518</div><div class="">efg_ucsf_gpl9450 -> ucsf_gpl9450</div><div class="">efg_wustl_wustl_c_elegans -> wustl_wustl_c_elegans</div><div class="">leiden_leiden2 -> spaink_lab_leiden_leiden2</div><div class="">leiden_leiden3 -> spaink_lab_leiden_leiden3</div><div class="">codelink -> codelink_codelink</div><div class="">illumina_human_methylation_27 -> illumina_humanmethylation27</div><div class="">illumina_human_methylation_450 -> illumina_humanmethylation450</div><div class="">affy_xtropicalis -> affy_x_tropicalis</div><div class=""><br class=""></div><div class="">3) Protein domains and protein features</div><div class=""><br class=""></div><div class="">low_complexity -> seg</div><div class="">low_complexity_end -> seg_end </div><div class="">low_complexity_start -> seg_start</div><div class="">profile -> pfscan</div><div class="">profile_end -> pfscan_end</div><div class="">profile_start -> pfscan_start</div><div class="">signal_domain -> signalp</div><div class="">signal_domain_end -> signalp_end</div><div class="">signal_domain_start -> signalp_start</div><div class="">transmembrane_domain -> tmhmm </div><div class="">transmembrane_domain_end -> tmhmm_end</div><div class="">transmembrane_domain_start -> tmhmm_start</div><div class="">prosite -> scanprosite</div><div class="">prosite_end -> scanprosite_end</div><div class="">prosite_start -> scanprosite_start</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">4) Other</div><div class=""><br class=""></div><div class="">percentage_gc_content -> percentage_gene_gc_content</div><div class="">so_parent_name -> so_mini_parent_name</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Please make sure to update your scripts and commands.</div><div class="">Kind Regards,</div><div class="">Thomas</div><div class="">
<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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