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LocText: relation extraction of protein localizations to assist database curation

Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen, Burkhard Rost
2018 BMC Bioinformatics  
Funding Alexander von Humboldt Foundation through German Federal Ministry for Education and Research, Ernst Ludwig Ehrlich Studienwerk, and the Novo Nordisk Foundation Center for Protein Research (NNF14CC0001  ...  Conclusions Here, we presented LocText, a new text mining method optimized to assist database curators for the annotation of protein subcellular localizations.  ...  Extrinsic evaluation: high accuracy enables database curation Encouraged by the high precision of LocText, it was applied to extract protein localization GO annotations Repetitions of relationships were  ... 
doi:10.1186/s12859-018-2021-9 pmid:29343218 pmcid:PMC5773052 fatcat:ioraubiqkfhgpdkxtv237w5s6y

UPCLASS: a deep learning-based classifier for UniProtKB entry publications

2020 Database: The Journal of Biological Databases and Curation  
to decide whether a publication is relevant for further curation for a protein accession.  ...  according to the evidence provided for the protein.  ...  Text mining has also supported more specific curation tasks, such as protein localization.  ... 
doi:10.1093/database/baaa026 pmid:32367111 pmcid:PMC7198315 fatcat:mkgx4v36w5dyjp7w5xtzuuaetu