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

[Will McLaren]

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.

Cheers

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).
>
> ॐ
>
> 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
>
> This message is intended only for the use of the addressee and may contain
> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY
> WORK PRODUCT. If you are not the intended recipient, you are hereby notified
> that any dissemination of this communication is strictly prohibited. If you
> have received this communication in error, please erase all copies of the
> message and its attachments and notify us immediately. Thank you.
>
>
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>