NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding

Research output: Contribution to journalArticlepeer-review

  • External authors:
  • Annika Schoene
  • Maolin Li
  • Fenia Christopoulou
  • et al.

Abstract

Machine reading is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades, the most dramatic advances in machine-reading have followed in the wake of critical corpus development1 Large, well-annotated corpora have been associated with punctuated advances in machine reading methodology and automated knowledge extraction systems in the same way that ImageNet 2 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 automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.

Bibliographical metadata

Original languageEnglish
Journalnpj Systems Biology and Applications
Publication statusAccepted/In press - 17 Sep 2021