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

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

Please cite if you use any DrugProt resource:

Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gasco, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger, Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations, Database, Volume 2023, 2023, baad080

@article{miranda2023overview,  title={Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical--protein relations},  author={Miranda-Escalada, Antonio and Mehryary, Farrokh and Luoma, Jouni and Estrada-Zavala, Darryl and Gasco, Luis and Pyysalo, Sampo and Valencia, Alfonso and Krallinger, Martin},  journal={Database},  volume={2023},  pages={baad080},  year={2023},  publisher={Oxford University Press UK} }

Miranda, Antonio, et al. "Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations." Proceedings of the seventh BioCreative challenge evaluation workshop. 2021.

@inproceedings{miranda2021overview,  title={Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations},  author={Miranda, Antonio and Mehryary, Farrokh and Luoma, Jouni and Pyysalo, Sampo and Valencia, Alfonso and Krallinger, Martin},  booktitle={Proceedings of the seventh BioCreative challenge evaluation workshop},  year={2021} }

Abstracts

• 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.

Related resources:

•  
• Web
• DrugProt corpus
• Evaluation library
• Online evaluation (CodaLab)
• Relation annotation guidelines
• Gene and protein annotation guidelines
• Chemicals and drugs annotation guidelines
• DrugProt Silver Standard Knowledge Graph
• FAQ
• DrugProt Large Scale Additional SubTrack
• DrugProt Large Scale document collection protocol
• DrugProt Complete PubMed Knowledge Graph