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

Michael Yourshaw myourshaw at ucla.edu
Tue Jul 17 19:53:31 BST 2012

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

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