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. 2024 Apr 4;52(W1):W540–W546. doi: 10.1093/nar/gkae235

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Published by Oxford University Press on behalf of Nucleic Acids Research 2024.

This work is written by (a) US Government employee(s) and is in the public domain in the US.

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Figure 2. — (A) The PubTator 3.0 processing pipeline: AIONER (8) identifies six types of entities in PubMed abstracts and PMC-OA full-text articles. Entity annotations are associated with database identifiers by specialized mappers and BioREx (9) identifies relations between entities. Extracted data is stored in MongoDB and made searchable using Solr. (B) Entity recognition performance for each entity type compared with PubTator2 (also known as PubTatorCentral) (13) on the BioRED corpus (15). (C) Relation extraction performance compared with SemRep (11) and notable previous best systems (12,13) on the BioCreative V Chemical-Disease Relation (14) corpus. (D) Comparison of information retrieval for PubTator 3.0, PubMed, and Google Scholar for entity pair queries, with respect to total article count and top-20 article precision.