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NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Stevens, Robert 
Alachram, Halima 

Abstract

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.

Description

Keywords

31 Biological Sciences, 3102 Bioinformatics and Computational Biology

Journal Title

NPJ Syst Biol Appl

Conference Name

Journal ISSN

2056-7189
2056-7189

Volume Title

7

Publisher

Springer Science and Business Media LLC
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/F008228/1)
Biotechnology and Biological Sciences Research Council (BB/G000662/1)
Biotechnology and Biological Sciences Research Council (BB/D00425X/1)
Biotechnology and Biological Sciences Research Council (BB/E018025/1)
Engineering and Physical Sciences Research Council (EP/S014128/1)
Engineering and Physical Sciences Research Council (EP/R022925/1)
Engineering and Physical Sciences Research Council (EP/M015688/1)
Engineering and Physical Sciences Research Council (EP/K030469/1)
EPSRC (EP/R022925/2)
EPSRC (EP/W004801/1)