Journal article Open Access

DrugProt Large-Scale Text Mining corpus: Biocreative VII Track 1 - Text mining drug and chemical-protein interactions

Miranda-Escalada, Antonio; Jouni Luoma; Farrokh Mehryary; Sampo Pyysalo; Krallinger, Martin

This Zenodo contains the BioCreative VII Large scale DrugProt Additional Subtrack abstracts and entity annotations.



  • large_scale_abstracts.tsv This file contains plain-­text, UTF8-­encoded, NFC normalized DrugProt PubMed records in a tab­ ‐ separated format. In total 2366081 records are provided, where each line in the fails contains a single PMID, title and abstract separated by tabulators. Due to PubMed inconsistencies, there is a minor percentage of duplicated records. Indeed, we have identified 222 records with different PMID but the same abstract title and body.


Entity mention annotations

  • large_scale_entities.tsv. This file contains the automatically labeled mention annotations of chemical compounds and genes/proteins (so-­called gene and protein-related objects as defined during BioCreative V) generated for the Large Scale records. There are 53993602 entity annotations.


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