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

[Michael Yourshaw]

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.





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120717/6d2309fc/attachment.html>