GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

By Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky. Intelligent Systems in Molecular Biology, 2001

581 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ee3e2a5608033acda22bcc7abc9f767e3e8fc912

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Citations in the corpus

Classifying Semantic Relations in Bioscience Texts (2004, methodology): “The GENIES system (Friedman et al., 2001) uses a hand-built semantic grammar along with hand-derived syntactic and semantic constraints, and recognizes a wide range of relationships between biological molecules.”
Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts (2013, background): “Sekine and Nobata give definitions and rule-based taggers for 200 categories of entities, as well as a standard taxonomy of general entities [23].”
Mining knowledge from text using information extraction (2005, background): “Consequently, a growing number of recent projects have focused on developing IE systems for biomedical literature [33; 23; 7; 55; 32].”
Literature mining for the biologist: from information retrieval to biological discovery (2006, background): “However, many biomedical NLP systems have combined the syntactic parser and the semantic extraction rules into a customized partial parser that specifically targets only the relevant parts of sentences and directly extracts the fact”
PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine (2003, methodology): “Full-text searching has been attempted by few text-mining systems [10] due mainly to the difficulties involved in obtaining access to full-text articles.”
Extracting Semantic Predications from Medline Citations for Pharmacogenomics (2006, methodology): “[17] use extensive linguistic processing for relations on molecular pathways, while Lussier et al.”
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): “In GENIES [58] , a parser and a semantic grammar consisting of a large set of nested semantic patterns (incorporating some syntactic knowledge) are used.”
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text (2009, methodology): “Some systems can support semantic concept-based search or relationship extraction, including Relemed [3], iHOP [4], Ingenuity Pathways [5], GENIES [6], CBioC [7], and GeneWays [8], but these systems do not generally provide search within full text and visual mark-up of the search results within the…”