[ensembl-dev] Retirement of Gene and Transcript Status Fields

[Andy Yates]

Hi

As many of you using the Perl API will be aware that we are planning to retire the status field from gene and transcript in release 90. Gene and transcript status is a field that dates back early in Ensembl history when it was seen as important to know the status of a gene. 

Currently status is set to NOVEL unless two conditions are met. The first is when a gene or transcript has a cross reference to a curated resource such as UniProt and RefSeq in the case of KNOWN. The second if if the gene had an ortholog to a well annotated genome as detected by the gene name projection process in the case of KNOWN_BY_PROJECTION.

All gene sets from Ensembl are created using primary evidence such as proteins from UniProt, cDNAs from RefSeq, RNA-seq or by projecting genes from well annotated clade representative genomes. As such we feel the status field no longer conveys what it originally set out to do. In addition we have bought in many other methods of finding well supported transcripts for human and mouse including Transcript Support Levels, GENCODE Basic and Appris principle isoforms.

We feel these methods are better suited than the current status field and the methods used to populate it.

Should you have any queries about this please get back in touch with us either here or on helpdesk.

Thanks,

Andy

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Andrew Yates - Genomics Technology Infrastructure Team Leader
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/