Automatic Protein Abbreviations Discovery and Resolution from Full-Text Scientific Papers: The PRAISED Framework

Daniele Toti 1 , Paolo Atzeni 1  and Fabio Polticelli 2 , 3
  • 1 Department of Computer Science and Automation, University of Roma Tre, 00146 Rome, Italy
  • 2 Department of Biology, University of Roma Tre, 00146 Rome, Italy
  • 3 National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy

Abstract

This paper describes a methodology for discovering and resolving protein names abbreviations from the full-text versions of scientific articles, implemented in the PRAISED framework with the ultimate purpose of building up a publicly available abbreviation repository. Three processing steps lie at the core of the framework: i) an abbreviation identification phase, carried out via domain-independent metrics, whose purpose is to identify all possible abbreviations within a scientific text; ii) an abbreviation resolution phase, which takes into account a number of syntactical and semantic criteria in order to match an abbreviation with its potential explanation; and iii) a dictionary-based protein name identification, which is meant to select only those abbreviations belonging to the protein science domain. A local copy of the UniProt database is used as a source repository for all the known proteins. The PRAISED implementation has been tested against several known annotated corpora, such as the Medstract Gold Standard Corpus, the AB3P Corpus, the BioText Corpus and the Ao and Takagi Corpus, obtaining significantly high levels of recall and extremely fast performance, while also keeping promising levels of precision and overall f-measure, in comparison to the most relevant similar methods. This comparison has been carried out up to Phase 2, since those methods stop at expanding abbreviations, without performing any entity recognition. Instead, the entity recognition performed in the last phase provides PRAISED with an effective strategy for protein discovery, thus moving further from existing context-free techniques. Furthermore, this implementation also addresses the complexity of full-text papers, instead of the simpler abstracts more generally used. As such, the whole PRAISED process (Phase 1, 2 and 3) has been also tested against a manually annotated subset of full-text papers retrieved from the PubMed repository, with significant results as well.

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The journal Bio-Algorithms and Med-Systems provides a forum for the exchange of information in the interdisciplinary fields of computational methods applied in medicine presenting new algorithms and databases that allow the progress in collaboration between medicine, informatics, physics, and biochemistry.

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