We (mostly Nicole) have been quietly working with Pablo Cingolani and Uma Devi Paila on mapping the SnpEff variant effect terms to SO and adding new terms where we were missing concepts. SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). The latest release, 3.6 is fully compatible with SO. These mappings are also available in SO as synonyms.
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