PMC text mining subset in BioC: about three million full-text articles and growing

Autor: Donald C. Comeau, Zhiyong Lu, Chih-Hsuan Wei, Rezarta Islamaj Dogan

Motivation Interest in text mining full-text biomedical research articles is growing. To facilitate automated processing of nearly 3 million full-text articles (in PubMed Central® Open Access and Author Manuscript subsets) and to improve interoperab

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3efcce7c6b99879b70ca3f958110ff3
https://europepmc.org/articles/PMC6748740/

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

Autor: Chih-Hsuan Wei, Donald C. Comeau, Andrew Chatr-aryamontri, Rezarta Islamaj Dogan, Yifan Peng, Zhiyong Lu, Sun Kim

Publikováno v: BioNLP

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 tr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::3298cc2cdbbfa65acd8e736046cfa225
https://doi.org/10.18653/v1/w17-2321

Author name disambiguation forPubMed

Autor: Zhiyong Lu, Won Kim, Sun Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Wanli Liu, Rezarta Islamaj Dogan

Publikováno v: Journal of the Association for Information Science and Technology

Log analysis shows that PubMed users frequently use author names in queries for retrieving scientific literature. However, author name ambiguity may lead to irrelevant retrieval results. To improve the PubMed user experience with author name queries,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::56195d6362fb0cf6e9c8dc697ddf564a
https://doi.org/10.1002/asi.23063

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions

Autor: Donald C. Comeau, W. John Wilbur, Andrew Chatr-aryamontri, Sun Kim, Kara Dolinski, Jennifer M. Rust, Rose Oughtred, Mike Tyers, Rezarta Islamaj Dogan, Christie S. Chang

Publikováno v: Database: The Journal of Biological Databases and Curation

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyse

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3caf1b5feb91e3d38d4aa890a76075c0
https://pubmed.ncbi.nlm.nih.gov/28077563

Crowdsourcing and curation: perspectives from biology and natural language processing

Autor: Stéphanie Boué, Rezarta Islamaj Dogan, Lynette Hirschman, Nikos C. Kyrpides, Kevin Bretonnel Cohen, Karën Fort

Publikováno v: Database-The journal of Biological Databases and Curation
Database-The journal of Biological Databases and Curation, Oxford University Press, 2016, 2016, ⟨10.1093/database/baw115⟩
Database: The Journal of Biological Databases and Curation
Hirschman, L; Fort, K; Boue, S; Kyrpides, N; Dogan, RI; & Cohen, KB. (2016). Crowdsourcing and curation: perspectives from biology and natural language processing. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. doi: 10.1093/database/baw115. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/3cz3q48m

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodol

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9d9ca1a5ae5f362413bbb18bc933345
https://hal.inria.fr/hal-01373210