[ensembl-dev] Inconsistencies in Variation/Utils/Constants.pm

Will McLaren wm2 at ebi.ac.uk
Tue Jul 17 20:01:27 BST 2012

Hi Michael,

The current live version of Ensembl is out of sync with the current
version of the SO.

This will be rectified in the next release of Ensembl, due in a couple of weeks.

The IDs with "X" in are temporary and artificial, for use in beta
development software. They will also be removed for Ensembl 68.


Will McLaren
Ensembl Variation

On 17 July 2012 19:53, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> There are a few instances in the Constants.pm OVERLAP_CONSEQUENCES hash
> where the SO_accession is an SO alt_id rather than the primary ID of the
> current Sequence Ontology so.obo file dated 02:05:2012 11:08.
> name Constants.pm SequenceOntology
> synonymous_variant SO:0001588 SO:0001819
> inframe_codon_gain SO:0001651 SO:0001821
> inframe_codon_loss SO:0001652 SO:0001822
> Also, I can’t find SO:X000101, SO:X000102, and SO:X000103 in the SO document
> (partial_overlap, entirely_within_feature, and complete_overlap_feature).
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
> Los Angeles CA 90095-8348 USA
> myourshaw at ucla.edu
> 970.691.8299
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