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NERO: a biomedical ...
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding
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- Wang, Kanix (author)
- University of Chicago
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- Stevens, Robert (author)
- University of Manchester
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- Alachram, Halima (author)
- Georg-August-Universität Göttingen,University of Göttingen
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- Li, Yu (author)
- King Abdullah University of Science and Technology (KAUST)
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- Soldatova, Larisa N. (author)
- Goldsmiths, University of London
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- King, Ross, 1962 (author)
- Chalmers tekniska högskola,Chalmers University of Technology,The Alan Turing Institute,University Of Cambridge
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- Ananiadou, Sophia (author)
- University of Manchester
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- Schoene, Annika M. (author)
- University of Manchester
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- Li, Maolin (author)
- University of Manchester
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- Christopoulou, Fenia (author)
- University of Manchester
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Ambite, José Luis (author)
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Matthew, Joel (author)
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Garg, Sahil (author)
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Hermjakob, Ulf (author)
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Marcu, Daniel (author)
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Sheng, Emily (author)
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- Beißbarth, Tim (author)
- Georg-August-Universität Göttingen,University of Göttingen
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- Wingender, Edgar (author)
- geneXplain GmbH
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Galstyan, Aram (author)
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- Gao, Xin (author)
- King Abdullah University of Science and Technology (KAUST)
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- Chambers, Brendan (author)
- University of Chicago
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- Pan, Weidi (author)
- University of Chicago
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- Khomtchouk, Bohdan B. (author)
- University of Chicago
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- Evans, James A. (author)
- University of Chicago
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- Rzhetsky, Andrey (author)
- University of Chicago
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(creator_code:org_t)
- 2021-10-20
- 2021
- English.
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In: npj Systems Biology and Applications. - : Springer Science and Business Media LLC. - 2056-7189. ; 7:1
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Abstract
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- Machine reading (MR) is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades1,2, the most dramatic advances in MR have followed in the wake of critical corpus development3. Large, well-annotated corpora have been associated with punctuated advances in MR methodology and automated knowledge extraction systems in the same way that ImageNet4 was fundamental for developing machine vision techniques. This study contributes six components to an advanced, named entity analysis tool for biomedicine: (a) a new, Named Entity Recognition Ontology (NERO) developed specifically for describing textual entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine; (b) detailed guidelines for human experts annotating hundreds of named entity classes; (c) pictographs for all named entities, to simplify the burden of annotation for curators; (d) an original, annotated corpus comprising 35,865 sentences, which encapsulate 190,679 named entities and 43,438 events connecting two or more entities; (e) validated, off-the-shelf, named entity recognition (NER) automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Språkteknologi (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Language Technology (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Elektroteknik och elektronik -- Inbäddad systemteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Electrical Engineering, Electronic Engineering, Information Engineering -- Embedded Systems (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Elektroteknik och elektronik -- Datorsystem (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Electrical Engineering, Electronic Engineering, Information Engineering -- Computer Systems (hsv//eng)
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- art (subject category)
- ref (subject category)
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To the university's database
- By the author/editor
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Wang, Kanix
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Stevens, Robert
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Alachram, Halima
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Li, Yu
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Soldatova, Laris ...
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King, Ross, 1962
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show more...
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Ananiadou, Sophi ...
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Schoene, Annika ...
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Li, Maolin
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Christopoulou, F ...
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Ambite, José Lui ...
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Matthew, Joel
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Garg, Sahil
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Hermjakob, Ulf
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Marcu, Daniel
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Sheng, Emily
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Beißbarth, Tim
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Wingender, Edgar
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Galstyan, Aram
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Gao, Xin
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Chambers, Brenda ...
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Pan, Weidi
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Khomtchouk, Bohd ...
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Evans, James A.
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Rzhetsky, Andrey
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Language Technol ...
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Electrical Engin ...
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and Embedded Systems
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Electrical Engin ...
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and Computer Systems
- Articles in the publication
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npj Systems Biol ...
- By the university
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Chalmers University of Technology