biostudies-literatureWang KNHLBI NIH HHSNIMH NIH HHSBiotechnology and Biological Sciences Research CouncilEngineering and Physical Sciences Research Council38https://www.ebi.ac.uk/biostudies/studies/S-EPMC8528865biostudies-literatureUnknown7(1)Machine reading (MR) is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades^1,2, 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 scientifiNPJ systems biology and applicationsNERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding.PMC8528865EP/S014128/1EP/R022925/2EP/R022925/1GR/S47656/01EP/K030469/1BB/F008228/1EP/R022941/1U01 HL108634BEP17028BB/G000662/1EP/K030582/1BB/D006503/1R01 HL122712BB/E018025/1EP/M015688/1P50 MH094267EP/W004801/11441239K12 HL143959BB/D00425X/1EP/M015661/1Alachram HChristopoulou FMatthew JStevens RChambers BSchoene AMWang KSheng EAnaniadou SHermjakob UGalstyan AGarg SRzhetsky AEvans JAKing RPan WSoldatova LLi MBeißbarth TMarcu DLi YWingender EGao XAmbite JLKhomtchouk BBfalseNERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding.Machine reading (MR) is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades^1,2, 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 scientifi2021-01-01T00:00:00Z2021 Oct2026-05-07T22:20:39.799Z2025-02-19T03:53:08.14ZS-EPMC85288653467103910.1038/s41540-021-00200-x