Accomplishments and challenges in literature data mining for biology

By Lynette Hirschman, Jong C. Park, Junichi Tsujii, Limsoon Wong, Cathy H. Wu. Bioinform., 2002

349 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e875652115fcd5dc9ec57bfcdffb99baf42773fb

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In Molecular Biology

Citations in the corpus

CoPub Mapper: mining MEDLINE based on search term co-publication (2005, background): “Therefore, mining the MEDLINE database for all information on a set of genes of interest to extract and evaluate their cooccurrences with biological keywords and other genes, could reveal biologically relevant pathways [3-6].”
Extracting interactions between proteins from the literature (2008, positive): “In general , the methods proposed so far rely on the techniques from one or more areas [29] [30] [31] [32] including Information Retrieval (IR) [27] [33], Machine Learning (ML) [34] [35], Natural Language Processing (NLP) [36] [37] [38], Information Extraction (IE) [39] [40] [41] [42] and Text…”
BioInfer: a corpus for information extraction in the biomedical domain (2007, background): “As a result, there has been an increased interest in applying Natural Language Processing (NLP) methods to the domain of biomedical publications accessible in literature databases such as PubMed [1-4].”
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning (2008, background): “Information extraction from biomedical research publications has been a topic of intense research during recent years [1-3].”
Corpus annotation for mining biomedical events from literature (2008, background): “Background Due to the ever-increasing amount of scientific articles in the bio-medical domain, Text Mining (TM) has been recognized as one of the key technologies for future bio-medical research [1-8].”
Overview of BioCreAtIvE: critical assessment of information extraction for biology (2005, background): “However, each group has tackled a different problem and reported on a different data set [23].”
From distributional to semantic similarity (2004, background): “Already NLP is considered crucial for exploiting textual information in expanding scientific domains such as bioinformatics (Hirschman et al., 2002).”
Extracting Semantic Predications from Medline Citations for Pharmacogenomics (2006, methodology): “Automatic methods, including NLP, are increasingly used as important aspects of the research process in biomedicine [3,4,5,6].”