BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations

Rezarta Islamaj Doğan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald Comeau, Zhiyong Lu


Abstract
The Precision Medicine Track in BioCre-ative VI aims to bring together the Bi-oNLP community for a novel challenge focused on mining the biomedical litera-ture in search of mutations and protein-protein interactions (PPI). In order to support this track with an effective train-ing dataset with limited curator time, the track organizers carefully reviewed Pub-Med articles from two different sources: curated public PPI databases, and the re-sults of state-of-the-art public text mining tools. We detail here the data collection, manual review and annotation process and describe this training corpus charac-teristics. We also describe a corpus per-formance baseline. This analysis will provide useful information to developers and researchers for comparing and devel-oping innovative text mining approaches for the BioCreative VI challenge and other Precision Medicine related applica-tions.
Anthology ID:
W17-2321
Volume:
BioNLP 2017
Month:
August
Year:
2017
Address:
Vancouver, Canada,
Editors:
Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Junichi Tsujii
Venue:
BioNLP
SIG:
SIGBIOMED
Publisher:
Association for Computational Linguistics
Note:
Pages:
171–175
Language:
URL:
https://aclanthology.org/W17-2321
DOI:
10.18653/v1/W17-2321
Bibkey:
Cite (ACL):
Rezarta Islamaj Doğan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald Comeau, and Zhiyong Lu. 2017. BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. In BioNLP 2017, pages 171–175, Vancouver, Canada,. Association for Computational Linguistics.
Cite (Informal):
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations (Islamaj Doğan et al., BioNLP 2017)
Copy Citation:
PDF:
https://aclanthology.org/W17-2321.pdf