Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature

Abdullatif Köksal, Hilal Dönmez, Rıza Özçelik, Elif Ozkirimli, Arzucan Özgür

Abstract
Coronavirus Disease of 2019 (COVID-19) created dire consequences globally and triggered an intense scientific effort from different domains. The resulting publications created a huge text collection in which finding the studies related to a biomolecule of interest is challenging for general purpose search engines because the publications are rich in domain specific terminology. Here, we present Vapur: an online COVID-19 search engine specifically designed to find related protein - chemical pairs. Vapur is empowered with a relation-oriented inverted index that is able to retrieve and group studies for a query biomolecule with respect to its related entities. The inverted index of Vapur is automatically created with a BioNLP pipeline and integrated with an online user interface. The online interface is designed for the smooth traversal of the current literature by domain researchers and is publicly available at https://tabilab.cmpe.boun.edu.tr/vapur/.
Anthology ID:
2020.nlpcovid19-2.21
Volume:
Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020
Month:
December
Year:
2020
Address:
Online
Editors:
Karin Verspoor, Kevin Bretonnel Cohen, Michael Conway, Berry de Bruijn, Mark Dredze, Rada Mihalcea, Byron Wallace
Venue:
NLP-COVID19
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
Language:
URL:
https://aclanthology.org/2020.nlpcovid19-2.21
DOI:
10.18653/v1/2020.nlpcovid19-2.21
Bibkey:
Cite (ACL):
Abdullatif Köksal, Hilal Dönmez, Rıza Özçelik, Elif Ozkirimli, and Arzucan Özgür. 2020. Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. In Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020, Online. Association for Computational Linguistics.
Cite (Informal):
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature (Köksal et al., NLP-COVID19 2020)
Copy Citation:
PDF:
https://preview.aclanthology.org/add_acl24_videos/2020.nlpcovid19-2.21.pdf
Code
 boun-tabi/vapur
Data
CORD-19, GENIA
PDF Search Code