Chemical Entity Normalization Protocol

While recognizing chemical mentions is valuable, many tasks ultimately require the mention to be identified or normalized. We have thus paired our named entity recognition system with a straightforward lexical approach for normalization. Our lexicon of chemical entities and their names was collected from MeSH [32 (link)] and ChEBI [33 (link)]. The system converts both mentions from the literature and entity names in the lexicon to lowercase and removes all whitespace and punctuation. For example, "flavone-C-glycoside" becomes "flavonecglycoside." The system then assigns a MeSH identifier to those mentions which can be found in the lexicon, or a ChEBI identifier if a matching MeSH identifier cannot be found. Mentions that correspond to a short form recognized by Ab3P are assigned the same identifier as the long form found by Ab3P [29 (link)]. Mentions which do not map to a specific identifier are ignored and mentions which can be assigned to both a MeSH and ChEBI identifier are only assigned the MeSH identifier.