Text mining and its potential applications in systems biology.

By Sophia Ananiadou, Douglas B. Kell, Junichi Tsujii. Trends in Biotechnology, 2006

350 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/42a921cd9d0c2f87860077689180cbcd7bd42878

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In Molecular Biology

Citations in the corpus

Biomedical text mining and its applications in cancer research (2013, neutral): “Several review articles for biomedical text mining have been published in past years [2–8], in this review, we pay much attention to the application of text mining in cancer research.”
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts (2011, background): “For relevant reviews on methods in text mining see e.g. ([37,63,64,65]).”
Construction of an annotated corpus to support biomedical information extraction (2009, background): “Without automated means, it is difficult for researchers to keep abreast of developments within biomedicine [2-6].”
Corpus annotation for mining biomedical events from literature (2008, positive): “Recently, advanced NLP software which uses grammatical knowledge and/or machine learning techniques has been increasingly applied to TM for the bio-medical domain [9-21].”
Controlled vocabularies and semantics in systems biology (2011, background): “Where this critical information is communicated through free-text descriptions or non-standard annotations, it can only—if at all—be computationally interpreted with complex text-mining procedures (and hardly even with those; Ananiadou et al , 2006).”
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature (2018, background): “However, identification of biological entities within the literature has proven difficult due to term variation and term ambiguity [105], because a biological entity can be expressed by various realisations.”
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008, background): “Several commentators have recognized the difficulties caused by synonyms 4,33,38 .”
Frontiers of biomedical text mining: current progress (2007, methodology): “We also issued bibliographic queries for: ‘text mining’ in Bioinformatics (MEDLINE), ‘biology’ or ‘medicine’ in ACM journals and PubMed ‘related articles,’ starting from the review papers [5–7].”