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

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers
2017 Database: The Journal of Biological Databases and Curation  
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.  ...  This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two  ...  Acknowledgements The authors would like to thank the BioCreative V organizers and the BioCreative V BioC task participants.  ... 
doi:10.1093/database/baw147 pmid:28077563 pmcid:PMC5225395 fatcat:s7dpik24cfct3ihiz3sbghbbdq

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos (+23 others)
2016 Database: The Journal of Biological Databases and Curation  
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.  ...  Acknowledgements The authors would like to thank Cecilia Arighi for providing resources for the user questionnaire.  ...  molecular interaction names and passages useful for curating the 120 full text articles.  ... 
doi:10.1093/database/baw121 pmid:27589962 pmcid:PMC5009341 fatcat:bqe4o77fizadhf5e3xese3i23y

BioC-compatible full-text passage detection for protein–protein interactions using extended dependency graph

Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker
2016 Database: The Journal of Biological Databases and Curation  
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.  ...  In BioCreative V, we participated in the BioC task and developed a PPI system to detect text passages with PPIs in the full-text articles.  ...  Qinghua Wang (CBCB, University of Delaware) for assisting in the annotation of the corpus. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw072 pmid:27170286 pmcid:PMC4915133 fatcat:svjmoaztzjbjfbuaez4ewt5hfq

MeSHup: A Corpus for Full Text Biomedical Document Indexing [article]

Xindi Wang, Robert E. Mercer, Frank Rudzicz
2022 arXiv   pre-print
We release a large scale annotated MeSH indexing corpus, MeSHup, which contains 1,342,667 full text articles in English, together with the associated MeSH labels and metadata, authors, and publication  ...  Currently, the vast number of biomedical articles in the PubMed database are manually annotated by human curators, which is time consuming and costly; therefore, a computational system that can assist  ...  Acknowledgements We thank all reviewers for their constructive comments and feedback. Resources used in preparing this research were provided, in part, by Compute Ontario  ... 
arXiv:2204.13604v1 fatcat:srvmuhrgjbb4nnysru2xhkzouy

The Treasury Chest of Text Mining: Piling Available Resources for Powerful Biomedical Text Mining

Nícia Rosário-Ferreira, Catarina Marques-Pereira, Manuel Pires, Daniel Ramalhão, Nádia Pereira, Victor Guimarães, Vítor Santos Costa, Irina S. Moreira
2021 BioChem  
When applied to biomedical literature, text mining is named biomedical text mining and its specificity lies in both the type of analyzed documents and the language and concepts retrieved.  ...  The array of documents that can be used ranges from scientific literature to patents or clinical data, and the biomedical concepts often include, despite not being limited to genes, proteins, drugs, and  ...  The funding agencies had no role in the design of the study, in the collection, analyzes, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/biochem1020007 fatcat:qve6xgoxuvbwzpqz6q45s7wlly

BioCreative-IV virtual issue

C. N. Arighi, C. H. Wu, K. B. Cohen, L. Hirschman, M. Krallinger, A. Valencia, Z. Lu, J. W. Wilbur, T. C. Wiegers
2014 Database: The Journal of Biological Databases and Curation  
Acknowledgments This issue is dedicated to the memory of our friend and colleague Phoebe Roberts who contributed significantly to the BioCreative effort in the past years.  ...  We would like to thank the the BioCreative User Advisory Group and the task co-organizers Donald Comeau, Rezarta Islamaj Dogan, Obdulia Rabal, Julen Oyarzabal, Allan Davis, Carolyn Mattingly, Kimberly  ...  full-text papers; the establishment of such a textual evidence corpus has long been recognized as critical for TM algorithm development, but was never made available because of the high cost of curation  ... 
doi:10.1093/database/bau039 pmid:24852177 pmcid:PMC4030502 fatcat:ov6v6jhv3vdinasqvot5zrm5cu

OntoGene web services for biomedical text mining

Fabio Rinaldi, Simon Clematide, Hernani Marques, Tilia Ellendorff, Martin Romacker, Raul Rodriguez-Esteban
2014 BMC Bioinformatics  
Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical  ...  The web services leverage a state-of-the-art platform for text mining (OntoGene) which has been tested in several community-organized evaluation challenges, with top ranked results in several of them.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the  ... 
doi:10.1186/1471-2105-15-s14-s6 pmid:25472638 pmcid:PMC4255746 fatcat:oufaw2qdcfhjraterrruhy7l4q

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu (+15 others)
2019 Database: The Journal of Biological Databases and Curation  
In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine.  ...  containing experimentally verified protein-protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs).  ...  Acknowledgements We thank the BioGRID database curators Rose Oughtred, Jennifer Rust, Christie S. Chang and Lorrie Boucher for annotating the evaluation data set. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay147 pmid:30689846 pmcid:PMC6348314 fatcat:jvsf4xwr7jbbnb75d3oqczrjrq

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork, Lars J Jensen, Christian von Mering
2018 Nucleic Acids Research  
Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels  ...  Proteins and their functional interactions form the backbone of the cellular machinery.  ...  We thank Tudor Oprea and the Illuminating the Druggable Genome project for help in improving the text mining, and Daniel Mende and Sofia Forslund for their help in selecting a non-redundant set of high-quality  ... 
doi:10.1093/nar/gky1131 pmid:30476243 fatcat:l6c2fugi3re7pk7agroo52cqqq

Overview of the interactive task in BioCreative V

Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai (+44 others)
2016 Database: The Journal of Biological Databases and Curation  
The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey.  ...  The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration  ...  Acknowledgements We would like to acknowledge all the users and team members who have participated in this activity throughout BioCreative. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw119 pmid:27589961 pmcid:PMC5009325 fatcat:ldpn6gjxircjlibqtysi57cztq

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature

H.-M. Müller, K. M. Van Auken, Y. Li, P. W. Sternberg
2018 BMC Bioinformatics  
To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to  ...  and category searches with viewing search results in the context of the full text.  ...  Acknowledgments We would like to thank Daniela Raciti, Christian Grove, and Valerio Arnaboldi for testing the system and helpful discussion, and Seth Carbon and Chris Mungall for assistance with the Noctua-Textpresso  ... 
doi:10.1186/s12859-018-2103-8 pmid:29523070 pmcid:PMC5845379 fatcat:2iba2i67ufer7btystzo3bnzfm

PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

Yung-Chun Chang, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, Wen-Lian Hsu
2016 Database: The Journal of Biological Databases and Curation  
Abstract Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field.  ...  PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/baw101 pmid:27524807 pmcid:PMC4983456 fatcat:t54qwjehhzbafhdnixnpp72k5a

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
National Research Council of Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica  ...  Acknowledgements The Onco-i2b2 project is funded by the "Regione Lombardia" in Italy. We gratefully acknowledge Prof. Carlo Bernasconi and the Collegio Ghislieri in Pavia for their active support.  ...  We manually pre-filled the wiki with a corpus of 30 documents composed of PubMed abstracts and their corresponding full-text papers, selected by two expert biocurators.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Overview of the Interactive Task in BioCreative V

Qinghua Wang, Fabio Rinaldi, Et Al
2015
The full level participation involved training on the system, curation of a set of documents with and without text mining assistance, tracking of time-on-task, and completion of a user survey.  ...  The full level participation involved training on the system, curation of a set of documents with and without text mining assistance, tracking of time-on-task, and completion of a user survey.  ...  Acknowledgment We would like to acknowledge all the users and team members who have participated in this activity.  ... 
doi:10.5167/uzh-116471 fatcat:elfvz7vs3zcx3obt33nak26rii

Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014)

S.N.
2014
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ...  Acknowledgment The authors would like to thank Hideyuki Tanushi for preparing the data and Maria Skeppstedt for good advice on using NegEx.  ...  Since the mentions of the proteins involved in an interaction are not annotated in BioGrid, all we know is the fact that in article A, protein c 1 interacts with protein c 2 .  ... 
doi:10.5167/uzh-98982 fatcat:avtlvr27hrdyfjfto47x2lfulu
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