Automatic discovery and resolution of protein abbreviations from full-text scientific papers: A light-weight approach towards data extraction from unstructured biological sources

Daniele Toti, Paolo Atzeni, Fabio Polticelli

Risultato della ricerca: Contributo in libroContributo a convegno

4 Citazioni (Scopus)

Abstract

We propose a methodology for discovering and resolving a wide range of protein name abbreviations from the full-text versions of scientific articles, as implemented in our PRAISED framework. Three processing steps lie at the core of our approach: an abbreviation identifi- cation phase, carried out via largely domain-independent metrics based on lexical clues and exclusion rules, whose purpose is to identify all pos- sible abbreviations within a scientific text; an abbreviation resolution phase, which takes into account a number of syntactical and semantic criteria and corresponding optimization techniques, in order to match an abbreviation with its potential explanation; and a dictionary-based pro- tein name identification, which is meant to eventually sort out those ab- breviations actually belonging to the biological domain. We have tested our implementation against the well-known Medstract Gold Standard Corpus and a relevant subset of real scientific papers extracted from the PubMed database, obtaining significant results in terms of recall, pre- cision and overall correctness. In comparison to other methods, our ap- proach retains its effectiveness without compromising performance, while addressing the complexity of full-text papers instead of the simpler ab- stracts more generally used. At the same time, computational overhead is kept to a minimum and its light-weight approach further enhances customization and scalability.
Lingua originaleEnglish
Titolo della pubblicazione ospiteSEBD 2011 - Proceedings of the 19th Italian Symposium on Advanced Database Systems
Pagine317-324
Numero di pagine8
Stato di pubblicazionePubblicato - 2011
Evento19th Italian Symposium on Advanced Database Systems, SEBD 2011 - Maratea, ita
Durata: 26 giu 201129 giu 2011

Convegno

Convegno19th Italian Symposium on Advanced Database Systems, SEBD 2011
CittàMaratea, ita
Periodo26/6/1129/6/11

Keywords

  • abbreviations

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