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Migrate Effect Lexicon to Sequence Ontology #1

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awenocur opened this issue Jul 25, 2014 · 0 comments
Open

Migrate Effect Lexicon to Sequence Ontology #1

awenocur opened this issue Jul 25, 2014 · 0 comments

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@awenocur
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Recent versions of SnpEff default to using strings from the Sequence Ontology to identify types of effects, rather than using the SnpEff-specific EffectType enum names.

Eventually, the importer should be able to identify effects based on the Sequence Ontology strings. Ideally, there should be a way of recognizing effects based on either nomenclature, as they are mutually exclusive when evaluated in a case-sensitive manner, and unambiguous even when ignoring case.

It won't be as simple a matter as adding duplicate entries in the effect table, as the Sequence Ontology strings should map to the same entities as the corresponding classic strings.

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