Automated extraction of information on protein-protein interactions from the biological literature

By Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi. Bioinform., 2001

462 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0c3411e652dc036239ec3103ed9ace2b4165783f

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Citations in the corpus

Implementing the iHOP concept for navigation of biomedical literature (2005, background): “…in the text. knowledge can thus be seen as networks of concurrent genes and proteins that include relationships ranging from direct physical interaction (Ono et al., 2001) to less direct associations with phenotypic observations and pathologies (Jenssen et al., 2001; Perez-Iratxeta et al., 2002).”
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].”
MeInfoText: associated gene methylation and cancer information from text mining (2008, background): “Over the past few years, a considerable number of studies have been made on the mining and extraction of information from bio-medical literature, such as disease candidate genes [13,14], protein-protein interactions [15,16], protein functions [17] and modifications [18].”
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature (2018, background): “For BioCreative II, Smith et al. [46] mention three tasks: gene mention (GM), gene normalisation (GN), and protein-protein interaction (PPI); the first two are within the scope of NER, whilst the third is a relation extraction task that has NER as a subtask [47].”
Text mining and its potential applications in systems biology. (2006, methodology): “Some approaches have been based on using dictionaries [ 1 ,43] to locate terms in the text; however, many terms cannot be recognized if we use straightforward dictionary or database look-up owing to term variation and homonyms (see Glossary).”
Construction of an annotated corpus to support biomedical information extraction (2009, background): “There now exists a number of corpora (e.g., [13,15,16]) and systems (e.g., [17-19]) tailored to this task.”
Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature (2004, background): “Another approach has involved semantic and/or syntactic text-pattern recognition methods with a keyword representing an interaction (Sekimizu et al. 1998; Thomas et al. 2000; Friedman et al. 2001; Ono et al. 2001).”
Extracting interactions between proteins from the literature (2008, unknown): “coli’’, ‘‘protein’’, and ‘‘interaction’’ [72]”