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A realistic assessment of methods for extracting gene/protein interactions from free text

Renata Kabiljo, Andrew B Clegg, Adrian J Shepherd
2009 BMC Bioinformatics  
In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users.  ...  tools most widely used to extract gene/protein interactions.  ...  The research of R.K. was supported by the European Commission under FP6-2004-IST-4 contract no. 028069 (the ImmunoGrid project) and the UK ORSAS scheme.  ... 
doi:10.1186/1471-2105-10-233 pmid:19635172 pmcid:PMC2723093 fatcat:tegsxx5mhzbhhjrp3ixgns3iri

Evolution of DNA repair genes, proteins and processes

Jonathan Eisen
2012 Figshare  
PhD Thesis of Jonathan A. Eisen.  ...  help of many people.  ...  ACKNOWLEDGEMENTS Although I never made enormous progress on solving the mechanisms of DNA turnover, thymineless death and/or stationary phase mutagenesis, I never would have gotten anywhere without the  ... 
doi:10.6084/m9.figshare.91470.v1 fatcat:g7ndwanyfbchhcf2you23rsfri

Overview of the BioCreative III Workshop

Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu
2011 BMC Bioinformatics  
Eight teams participated in the PPI interaction method task (IMT) where systems were given full text documents and were required to extract the experimental methods used to establish PPIs and a text segment  ...  The goal was to develop an interactive system to facilitate a user's annotation of the unique database identifiers for all the genes appearing in an article.  ...  This article has been published as part of BMC Bioinformatics Volume 12 Supplement 8, 2011: The Third BioCreative -Critical Assessment of Information Extraction in Biology Challenge.  ... 
doi:10.1186/1471-2105-12-s8-s1 pmid:22151647 pmcid:PMC3269932 fatcat:lp7c4vnknraqrkganmnqt4hfse

A text-mining system for extracting metabolic reactions from full-text articles

Jan Czarnecki, Irene Nobeli, Adrian M Smith, Adrian J Shepherd
2012 BMC Bioinformatics  
Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given  ...  This method extends an approach that has proved effective in the context of the extraction of protein-protein interactions.  ...  Conclusions In this paper we have presented a simple method for extracting metabolic reactions from free text.  ... 
doi:10.1186/1471-2105-13-172 pmid:22823282 pmcid:PMC3475109 fatcat:leqjw2phkbe6veikxy5pcjbhkq

Overview of BioCreAtIvE: critical assessment of information extraction for biology

Lynette Hirschman, Alexander Yeh, Christian Blaschke, Alfonso Valencia
2005 BMC Bioinformatics  
The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied  ...  The results for the advanced task (functional annotation from free text) were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation  ...  Acknowledgements The work of AV and CB was funded by the European Commission as part of the E-BioSci and ORIEL projects, contract numbers QLRI-CT  ... 
doi:10.1186/1471-2105-6-s1-s1 pmid:15960821 pmcid:PMC1869002 fatcat:kktugbhkrzgwvnnwuo7jxszkaq

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

T. C. Wiegers, A. P. Davis, C. J. Mattingly
2014 Database: The Journal of Biological Databases and Curation  
The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort for evaluating a wide variety of text mining  ...  calls from CTD's asynchronous, batch-oriented text-mining pipeline to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of simple XML formats) for inter-process  ...  The reasons for failure of the remaining Web services were unclear. Gene/Protein NER Results Among the 12 submissions for gene/protein NER, nine were successfully tested.  ... 
doi:10.1093/database/bau050 pmid:24919658 pmcid:PMC4207221 fatcat:pmqid43cabdyrabpo7lpuoqndi

BioCreative III interactive task: an overview

Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Giglio, Ian Harrow, Eva Huala, Martin Krallinger (+15 others)
2011 BMC Bioinformatics  
The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain.  ...  Members of the UAG curated three articles for training and assessment purposes, and each member was assigned a system to review.  ...  and Qinghua Wang from University of Delaware for assisting with manual curation.  ... 
doi:10.1186/1471-2105-12-s8-s4 pmid:22151968 pmcid:PMC3269939 fatcat:p4k5g76ccbaczmatbogvotww4q

Proceedings of the second biocreative challenge evaluation workshop

Lynette Hirschman, Martin Krallinger, Alfonso Valencia
2007 Zenodo  
Proceedings of the Second BioCreative Challenge Evaluation Workshop  ...  We thank DaeHyun Kim and Balaji Ramesh for developing the figure text extraction system.  ...  funding from "Fundação Para a Ciência e a Tecnologia" (FCT) under the project number PTDC/EIA-CCO/100541/2008 (FCOMP-01-0124-FEDER-010029).  ... 
doi:10.5281/zenodo.6519852 fatcat:k6q4vrkd65hbthlvwnhy2ufiey

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature

Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadic, Julie Klein, John Keane, Robert Stevens
2018 Journal of Biomedical Semantics  
Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task.  ...  This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve  ...  Acknowledgements Thanks to Tim Furmston for help with software and e-infrastructure, and to the anonymous reviewers for their useful comments. Funding  ... 
doi:10.1186/s13326-018-0181-1 pmid:29650041 pmcid:PMC5896136 fatcat:rnyqpxihlralfcs7c5wxa5aaci

Text mining for biology - the way forward: opinions from leading scientists

Russ B Altman, Casey M Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Jensen, Martin Krallinger (+6 others)
2008 Genome Biology  
The responses identify several broad themes, including the possibility of fusing literature and biological databases through text mining; the need for user interfaces tailored to different classes of users  ...  and supporting community-based annotation; the importance of scaling text mining technology and inserting it into larger workflows; and suggestions for additional challenge evaluations, new applications  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
doi:10.1186/gb-2008-9-s2-s7 pmid:18834498 pmcid:PMC2559991 fatcat:6cerr44envaqrfatnatmiy5nbq

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

J. F. Moxley, M. C. Jewett, M. R. Antoniewicz, S. G. Villas-Boas, H. Alper, R. T. Wheeler, L. Tong, A. G. Hinnebusch, T. Ideker, J. Nielsen, G. Stephanopoulos
2009 Proceedings of the National Academy of Sciences of the United States of America  
Fluxes are the modelindependent rates of metabolite interconversion that emerge through the interplay of genes, proteins, and metabolites at multiple regulatory levels.  ...  Although mRNA expression alone did not directly predict metabolic response, this correlation improved through incorporating a network-based model of amino acid biosynthesis (from r ‫؍‬ 0.07 to 0.80 for  ...  Alliance, and National Center for Research Resources award 018627.  ... 
doi:10.1073/pnas.0811091106 pmid:19346491 pmcid:PMC2672541 fatcat:ynqb5ouarva3rdqpebvlowjm3m

Discovering semantic features in the literature: a foundation for building functional associations

Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo, Alberto Pascual-Montano
2006 BMC Bioinformatics  
We present a method to create literature profiles for large sets of genes or proteins based on common semantic features extracted from a corpus of relevant documents.  ...  The presented method can create literature profiles from documents relevant to sets of genes.  ...  genes/proteins from a corpus of documents known to be relevant to each gene/protein.  ... 
doi:10.1186/1471-2105-7-41 pmid:16438716 pmcid:PMC1386711 fatcat:md2l4p6f5vgehnhz752xqwz5ny

Extraction of semantic biomedical relations from text using conditional random fields

Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp, Hans-Peter Kriegel
2008 BMC Bioinformatics  
The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining.  ...  Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that  ...  We thank Sonja Hopf from the Evolutionary and Functional Genomics group (LMU Munich) for valuable biological feedback.  ... 
doi:10.1186/1471-2105-9-207 pmid:18433469 pmcid:PMC2386138 fatcat:xw2ccis23nh3lls2762inr3e5u

BioPPISVMExtractor: A protein–protein interaction extractor for biomedical literature using SVM and rich feature sets

Zhihao Yang, Hongfei Lin, Yanpeng Li
2010 Journal of Biomedical Informatics  
Protein-protein interactions play a key role in various aspects of the structural and functional organization of the cell.  ...  However, the amount of biomedical literature regarding protein interactions is increasing rapidly and it is difficult for interaction database curators to detect and curate protein interaction information  ...  Acknowledgments This work is supported by grant from the Natural Science Foundation of China (No. 60373095 and 60673039) and the National High Tech Research and Development Plan of China (2006AA01Z151)  ... 
doi:10.1016/j.jbi.2009.08.013 pmid:19706337 fatcat:rwb6ukl535dozaxtp3asbfrjna

Status of text-mining techniques applied to biomedical text

Ramón A-A. Erhardt, Reinhard Schneider, Christian Blaschke
2006 Drug Discovery Today  
In the context of text analysis, two entities are said to co-occur if they appear together in the same piece of text, such as a sentence or a paragraph. Disambiguation.  ...  Abbreviations formed from the initial letter or letters of words, such as NATO (North Atlantic Treaty Organization) and HTML (Hyper Text Markup Language) with notable exceptions, such as XML, which stands  ...  The BioCreative (critical assessment of information extraction in biology) assessment [49] [50] [51] provided a systematic evaluation for a set of biological text mining tasks.  ... 
doi:10.1016/j.drudis.2006.02.011 pmid:16580973 fatcat:3r46esfy7rcjjd4cpwxeu3k5ke
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