We propose a framework for identifying, disambiguating and storing protein-related abbreviations as found in the full texts of scientific papers, in order to build and maintain a publicly available abbreviation repository via a semi-automatic process. This process involves information extraction methods and techniques for acronym identification and resolution, based on lexical clues and syntactical, largely domain-independent criteria. A dictionary and an ontology for proteins provide the means for matching and disambiguating the biological entities. User feedback is gathered at the end of the process and the confirmed entries are then stored and made available to the scientific community for further reviewing.
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