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BC4GO: a full-text corpus for the BioCreative IV GO task

K. Van Auken, M. L. Schaeffer, P. McQuilton, S. J. F. Laulederkind, D. Li, S.-J. Wang, G. T. Hayman, S. Tweedie, C. N. Arighi, J. Done, H.-M. Muller, P. W. Sternberg (+3 others)
2014 Database: The Journal of Biological Databases and Curation  
Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community.  ...  This result demonstrates the need of using full-text articles for text mining GO annotations.  ...  Matis, Fiona McCarthy, Sandra Orchard and Phoebe Roberts from the BioCreative IV User Advisory Group for their helpful discussions.  ... 
doi:10.1093/database/bau074 pmid:25070993 pmcid:PMC4112614 fatcat:cvogyfaztrenzongyrja6xwcnu

tmBioC: improving interoperability of text-mining tools with BioC

Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu
2014 Database: The Journal of Biological Databases and Curation  
The resulting BioC wrapped toolkit, which we have named tmBioC, consists of our tools in BioC, an annotated full-text corpus in BioC, and a format detection and conversion tool.  ...  Furthermore, through participation in the 2013 BioCreative IV Interoperability Track, we empirically demonstrate that the tools in tmBioC can be more efficiently integrated with each other as well as with  ...  in BioC XML format for the BioCreative IV GO task.  ... 
doi:10.1093/database/bau073 pmid:25062914 pmcid:PMC4110697 fatcat:2wg4mnf4jjgmpnpaonlxt7xqky

Overview of the gene ontology task at BioCreative IV

Y. Mao, K. Van Auken, D. Li, C. N. Arighi, P. McQuilton, G. T. Hayman, S. Tweedie, M. L. Schaeffer, S. J. F. Laulederkind, S.-J. Wang, J. Gobeill, P. Ruch (+14 others)
2014 Database: The Journal of Biological Databases and Curation  
To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV.  ...  Database URL: http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/.  ...  Acknowledgements The authors would like to thank Lynette Hirschman, John Wilbur, Cathy Wu  ... 
doi:10.1093/database/bau086 pmid:25157073 pmcid:PMC4142793 fatcat:e72af2fpcnczbbj3hdtidnyy2u

BioC interoperability track overview

D. C. Comeau, R. T. Batista-Navarro, H.-J. Dai, R. Islamaj Do an, A. Jimeno Yepes, R. Khare, Z. Lu, H. Marques, C. J. Mattingly, M. Neves, Y. Peng, R. Rak (+6 others)
2014 Database: The Journal of Biological Databases and Curation  
The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format.  ...  BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format.  ...  BC4GO is the official data set for the BioCreative IV Track-4 GO Task (34) , which tackles the challenge of automatic GO annotation through literature analysis.  ... 
doi:10.1093/database/bau053 pmid:24980129 pmcid:PMC4074764 fatcat:tez7f6bevzbmrlqj4cxub2yf7a

Automatic Consistency Assurance for Literature-based Gene Ontology Annotation [article]

Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor
2021 bioRxiv   pre-print
We evaluate this method using a synthetic dataset generated by directed manipulation of instances in an existing corpus, BC4GO.  ...  We propose a novel and efficient method using state-of-the-art text mining models to automatically distinguish between consistent GO annotation and the different types of inconsistent GO annotation.  ...  Acknowledgements Not applicable Consent for publication Not applicable  ... 
doi:10.1101/2021.05.26.445910 fatcat:arpvv5ustnbh3dkk6y4ovdtrru

Automatic consistency assurance for literature-based gene ontology annotation

Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor
2021 BMC Bioinformatics  
We evaluate this method using a synthetic dataset generated by directed manipulation of instances in an existing corpus, BC4GO.  ...  We propose a novel and efficient method using state-of-the-art text mining models to automatically distinguish between consistent GO annotation and the different types of inconsistent GO annotation.  ...  The BC4GO corpus was created by eight expert curators from five different model organism databases for the GO annotation task in BioCreative IV [23] .  ... 
doi:10.1186/s12859-021-04479-9 pmid:34823464 pmcid:PMC8620237 fatcat:u4z4maa2ajbltcalwp3vyy2m4q

A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C. Tsoi
2017 International Journal of Genomics  
The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been  ...  Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles.  ...  Acknowledgments The authors acknowledge the support from the Undergraduate Research Opportunity Program (UROP) from the University of Michigan, the Dermatology Foundation, the Arthritis National Research  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Semantic annotation in biomedicine: the current landscape

Jelena Jovanović, Ebrahim Bagheri
2017 Journal of Biomedical Semantics  
As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing.  ...  The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such  ...  Funding The second author graciously acknowledges funding from The Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1186/s13326-017-0153-x pmid:28938912 pmcid:PMC5610427 fatcat:jby2gq576vfdfmf4lsusahjrrm

Exploring automatic inconsistency detection for literature-based gene ontology annotation

Jiyu Chen, Benjamin Goudey, Justin Zobel, Nicholas Geard, Karin Verspoor
2022
Assurance of the quality of GOA is crucial for supporting biological research.  ...  However, a range of different kinds of inconsistencies in between literature as evidence and annotated GO terms can be identified; these have not been systematically studied at record level.  ...  The BC4GO corpus was created by eight expert curators from five different model organism databases for the GO annotation task in BioCreative IV (Van Auken et al., 2014) .  ... 
doi:10.1093/bioinformatics/btac230 pmid:35758780 pmcid:PMC9235499 fatcat:5qfrd363rfdtzex4djagqvogky

Recognition and normalization of terminology from large biomedical ontologies and their application for pharmacogene and protein function prediction [article]

Christopher Stanley Funk
2021
BioCreative IV -Gene Ontology task BC IV also had a task focused on manual curation of gene function and consists of two different tasks (Mao et al., 2014) : A) retrieving GO evidence for relevant genes  ...  There have also been sub-tasks within the BioCreative I and IV Mao et al., 2014) community challenges that involve a task similar, but more difficult, to GO term recognition -relating relevant GO concepts  ...  Because the CRAFT corpus contains only a small portion of the whole GO (1,108) and these rules only account for reordering of tokens and enumeration of common phrases within GO, we did not expect to see  ... 
doi:10.25677/fxns-0x58 fatcat:zg4wsyne4nferiphlz2qvfq4v4