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News: Ensembl 88 is out!
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gravatar for Thomas Maurel
5 months ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

Dear all

The new Ensembl marts for release 88 are now live on www.ensembl.org.

If you are using biomaRt, you can change your host to access our most recent data:

ensembl_mart_88 <- useEnsembl(biomart=“ensembl")

Change affecting all marts: Species dropdown now displays species common name instead of species latin name

Ensembl Genes 88
    Region filter performance improvement
    Renamed some filter/attributes internal and display names
    Renamed attribute "% GC content" to "Gene % GC content" 
Mouse Genes 88
    Region filter performance improvement
Ensembl Variation 88
    Region filter performance improvement
Ensembl Regulation 88
    Region filter performance improvement
Vega 68

You can find the complete list of the changes at http://www.ensembl.org/info/website/news.html

Important: 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.
Please find the full list below or on our FTP site: ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt

1) External references

entrezgene_transcript_name -> entrezgene_trans_name
hgnc_transcript_name -> hgnc_trans_name
rfam_transcript_name -> rfam_trans_name
mirbase_transcript_name -> mirbase_trans_name
uniprot_genename -> uniprot_gn
uniprot_sptrembl -> uniprotsptrembl
uniprot_swissprot -> uniprotswissprot
go_id -> go
goslim_goa_accession -> goslim_goa
zfin_transcript_name -> zfin_id_trans_name
wormbase_gene_seq_name -> wormbase_gseqname
genome_rnai -> genomernai
go_to_gene_id -> go_to_gene
mgi_transcript_name -> mgi_trans_name
clone_based_ensembl_gene_name -> clone_based_ensembl_gene
clone_based_ensembl_transcript_name -> clone_based_ensembl_transcript
clone_based_vega_gene_name -> clone_based_vega_gene
clone_based_vega_transcript_name -> clone_based_vega_transcript
vgnc_genename -> vgnc
rgd_transcript_name -> rgd_trans_name
xenbase_transcript_name -> xenbase_trans_name
zfin_id -> zfin_id_id

2) Microarray probes/probesets

efg_agilent_* -> agilent_* (e.g: efg_agilent_012795 -> agilent_012795)
efg_nimblegen_gpl8673 -> nimblegen_gpl8673
efg_slri_gpl3518 -> slri_gpl3518
efg_ucsf_gpl9450 -> ucsf_gpl9450
efg_wustl_wustl_c_elegans -> wustl_wustl_c_elegans
leiden_leiden2 -> spaink_lab_leiden_leiden2
leiden_leiden3 -> spaink_lab_leiden_leiden3
codelink -> codelink_codelink
illumina_human_methylation_27 -> illumina_humanmethylation27
illumina_human_methylation_450 -> illumina_humanmethylation450
affy_xtropicalis -> affy_x_tropicalis

3) Protein domains and protein features

low_complexity -> seg
low_complexity_end -> seg_end 
low_complexity_start -> seg_start
profile -> pfscan
profile_end -> pfscan_end
profile_start -> pfscan_start
signal_domain -> signalp
signal_domain_end -> signalp_end
signal_domain_start -> signalp_start
transmembrane_domain ->  tmhmm 
transmembrane_domain_end -> tmhmm_end
transmembrane_domain_start ->  tmhmm_start
prosite -> scanprosite
prosite_end -> scanprosite_end
prosite_start -> scanprosite_start

4) Other

percentage_gc_content -> percentage_gene_gc_content
so_parent_name -> so_mini_parent_name


Please make sure to update your scripts and commands.

 

Kind Regards,

Thomas

ADD COMMENTlink modified 5 months ago • written 5 months ago by Thomas Maurel700

Dear Thomas,

I was checking the new release and I noticed that the EntrezGene ID is no more provided as an option in the FILTERS -> GENE section: there is only EntrezGene transcript name ID(s).

Looking at the xml code I found that NCBI gene ID(s) has the same filter name than the old EntrezGene ID (i.e. entrezgene). I tried then to convert some entrez ids that were working until yesterday with the previous version, but I don't get any results back.

In particular, I am selecting:

DATABASE: Ensembl Genes 88

DATASET: Human genes (GRCh38.p10)

FILTERS: NCBI gene ID(s) - VALUES: 10418, 10669, 10777

ATTRIBUTES: HGNC symbol, AFFY HG U133 Plus 2 probe

Am I doing anything wrong? Or is there any problem with the new release?

Kind Regards,

Alex

ADD REPLYlink modified 5 months ago • written 5 months ago by Alex0

Dear Thomas,

I just made few tests and I think I found the problem. The filter is not using the NCBI ID(s) but the HGNC symbol instead.

The provided example for the NCBI ID(s) filter in the mart page in fact is a HGNC symbol, A1BG. The Gene ID for this symbol should be 1. I tried other HGNC symbols and this way is working.

Any chance this will be corrected?

Kind regards,

Alex

ADD REPLYlink written 5 months ago by Alex0
1
gravatar for Thomas Maurel
5 months ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

Dear Alex,

Thanks a lot for reporting this to us. We're aware of problems with the biomart service and are working on a fix at the moment. We will make it available as soon as possible.

Apologies for any inconvenience caused
Kind Regards,
Thomas

ADD COMMENTlink written 5 months ago by Thomas Maurel700
1
gravatar for Thomas Maurel
5 months ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

Dear Alex,

The issue has now been fixed on the www.ensembl.org website, our ensembl asia, useast and uswest mirrors will be updated as soon as possible.
You are right, we have renamed the "EntrezGene ID" filters and attribute to "NCBI ID(s)" to match what we display on the ensembl website. The filter/attribute are now displaying the gene id, e.g: 1 instead of the HGNC symbol.

Apologies for any inconvenience caused
Kind Regards,
Thomas
 

 

ADD COMMENTlink written 5 months ago by Thomas Maurel700

Thank you for the prompt fix, I was having the same issue and I could not figure out the reason.

Kind Regards,
Marco

 

ADD REPLYlink written 5 months ago by MT0
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