Overview of the BioCreative VI text-mining services for Kinome Curation Track.
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ABSTRACT:
SUBMITTER: Gobeill J
PROVIDER: S-EPMC6191643 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
Overview of the BioCreative VI text-mining services for Kinome Curation Track.
Gobeill Julien J Gaudet Pascale P Dopp Daniel D Morrone Adam A Kahanda Indika I Hsu Yi-Yu YY Wei Chih-Hsuan CH Lu Zhiyong Z Ruch Patrick P
Database : the journal of biological databases and curation 20180101
The text-mining services for kinome curation track, part of BioCreative VI, proposed a competition to assess the effectiveness of text mining to perform literature triage. The track has exploited an unpublished curated data set from the neXtProt database. This data set contained comprehensive annotations for 300 human protein kinases. For a given protein and a given curation axis [diseases or gene ontology (GO) biological processes], participants' systems had to identify and rank relevant articl ...[more]
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Project description:The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system's ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users. Database URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-4/.
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