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Ontology learning from text

Wilson Wong, Wei Liu, Mohammed Bennamoun
2012 ACM Computing Surveys  
The explosion of textual information on the Read/Write Web coupled with the increasing demand for ontologies to power the Semantic Web have made (semi-)automatic ontology learning from text a very promising  ...  Ontologies are often viewed as the answer to the need for interoperable semantics in modern information systems.  ...  Over the years, that realization gave rise to a research area now known as ontology learning from text which aims to turn facts and patterns from an ever growing body of information into shareable high-level  ... 
doi:10.1145/2333112.2333115 fatcat:4uo5bazvivh3fpbxj7yf4yoe2u

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) cellular component curation

Kimberly Van Auken, Joshua Jaffery, Juancarlos N Chan, Hans-Michael Muller, Paul W Sternberg
2009 BMC Bioinformatics  
Text mining software that can semi-or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts.  ...  which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology.  ...  Acknowledgements We gratefully acknowledge helpful comments on the manuscript from Tanya Berardini, Kara Dolinski, Ranjana Kishore, Mike Livstone, and Tracy Teal, and Seth Carbon for assistance with GO  ... 
doi:10.1186/1471-2105-10-228 pmid:19622167 pmcid:PMC2719631 fatcat:cs2gir5npnaidhhdiuazhgtb6e

Text mining for the biocuration workflow

L. Hirschman, G. A. P. C. Burns, M. Krallinger, C. Arighi, K. B. Cohen, A. Valencia, C. H. Wu, A. Chatr-Aryamontri, K. G. Dowell, E. Huala, A. Lourenco, R. Nash (+3 others)
2012 Database: The Journal of Biological Databases and Curation  
the survey for biocuration workflow and text mining.  ...  Acknowledgements We gratefully acknowledge the participation of Carl Schmidt and Peter D'Eustachio who contributed to the pre-workshop study of the biocuration workflow and Pascale Gaudet who helped on  ...  Text mining tools have the potential to speed up the curation process if they perform useful tasks with sufficient accuracy and speed.  ... 
doi:10.1093/database/bas020 pmid:22513129 pmcid:PMC3328793 fatcat:g4foc66eerbq7cvipwolq6pe5y

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

C. N. Arighi, B. Carterette, K. B. Cohen, M. Krallinger, W. J. Wilbur, P. Fey, R. Dodson, L. Cooper, C. E. Van Slyke, W. Dahdul, P. Mabee, D. Li (+29 others)
2013 Database: The Journal of Biological Databases and Curation  
The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly ($1.7-to 2.5-fold) over manual  ...  In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set.  ...  Acknowledgements The authors would like to thank all the teams and the biocurators who participated in this activity. Conflict of interest. None declared.  ... 
doi:10.1093/database/bas056 pmid:23327936 pmcid:PMC3625048 fatcat:hofjvjt55fhcre55nfsa6s2qcm

Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

Hans-Michael Müller, Eimear E Kenny, Paul W Sternberg, Michael Ashburner
2004 PLoS Biology  
Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to  ...  Full text access increases recall of biological data types from 45% to 95%.  ...  We thank Juancarlos Chan for programming help, Andrei Petcherski for his help with evaluating the Textpresso system, Robert Li for developing the PDF-to-text conversion software package, and Daniel Wang  ... 
doi:10.1371/journal.pbio.0020309 pmid:15383839 pmcid:PMC517822 fatcat:dcxfopl5ibf4pbbpmvafoj35ri

Genescene: An ontology-enhanced integration of linguistic and co-occurrence based relations in biomedical texts

Gondy Leroy, Hsinchun Chen
2005 Journal of the American Society for Information Science and Technology  
Currently, they are used to facilitate the integration of the two relation types, and to select the more interesting and high-quality relations for presentation.  ...  The increasing amount of publicly available literature and experimental data in biomedicine makes it hard for biomedical researchers to stay up-to-date.  ...  We want to thank the National Library of Medicine, the Gene Ontology Consortium, and the Hugo Nomenclature committee for making the UMLS, GO, and the HUGO Nomenclature freely available to researchers.  ... 
doi:10.1002/asi.20135 fatcat:3uy3xkpborgk5eijwx6jrtm7u4

Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models

Belén Juanes Cortés, José Antonio Vera-Ramos, Ruth C. Lovering, Pascale Gaudet, Astrid Laegreid, Colin Logie, Stefan Schulz, María del Mar Roldán-García, Martin Kuiper, Jesualdo Tomás Fernández-Breis
2021 Biochimica et Biophysica Acta. Gene Regulatory Mechanisms  
In this work, we study how such knowledge models can be generated from cartoons of gene regulation scenarios.  ...  The proposed method consists of generating descriptions in natural language of the cartoons; extracting the entities from the texts; finding those entities in existing ontologies to reuse as much content  ...  Acknowledgements We thank the support of the Noctua development team, and the scientific exchange with the members of the GO, SO and GREEKC consortia.  ... 
doi:10.1016/j.bbagrm.2021.194766 pmid:34710644 fatcat:4lc2w2otgfhfrjyjxqaxtiv6zm

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  
This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next  ...  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  ...  Acknowledgements The BioCreative II challenge and workshop were sponsored by the Frontiers of Functional Genomics Programme of the European Science Foundation (ESF) and by Genoma Espana  ... 
doi:10.1186/gb-2008-9-s2-s7 pmid:18834498 pmcid:PMC2559991 fatcat:6cerr44envaqrfatnatmiy5nbq

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  
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  ...  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 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

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
Some problems, such as abbreviationhandling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon.  ...  However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  KBC was supported by NIH grants 'Construction of a Full Text Corpus for Biomedical Text Mining' (#1G08LM009639-01) and 'Technology Development for a Molecular Biology Knowledge-base' (#5R01 LM008111-03  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy

Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production

Hong Cui, James A Macklin, Joel Sachs, Anton Reznicek, Julian Starr, Bruce Ford, Lyubomir Penev, Hsin-Liang Chen
2018 Biodiversity Data Journal  
With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality.  ...  It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses.  ...  Neither of these problems can be adequately addressed by manual curation or text-mining techniques because computers are at their weakest with semantic and pragmatic analyses and cannot be expected to  ... 
doi:10.3897/bdj.6.e29616 pmid:30473620 pmcid:PMC6235995 fatcat:pgutctogyneidpdweh4dngulze

Biomedical text mining and its applications in cancer research

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
We hope that this review can (i) provide a useful overview of the current work of this field; (ii) help researchers to choose text mining tools and datasets; and (iii) highlight how to apply text mining  ...  With the development of systems biology, researchers tend to understand complex biomedical systems from a systems biology viewpoint.  ...  Text mining can help us to mine information and knowledge from a mountain of text and it is now widely applied in biomedical research.  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Supporting the Curation of Biological Databases with Reusable Text Mining

Olivo Miotto, Tin Wee Tan, Vladimir Brusic
2005 Genome Informatics Series  
Curators of biological databases transfer knowledge from scientific publications, a laborious and expensive manual process.  ...  These results show that the method we propose can deliver the level of performance needed to assist database curation.  ...  Database curators search biomedical research literature for facts of interest, and manually transfer knowledge from published papers to the database.  ... 
doi:10.11234/gi1990.16.2_32 fatcat:ptmmatc3bfdbzgcpc47y3i2sze

Automatic consistency assurance for literature-based gene ontology annotation

Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor
2021 BMC Bioinformatics  
Background Literature-based gene ontology (GO) annotation is a process where expert curators use uniform expressions to describe gene functions reported in research papers, creating computable representations  ...  Manual assurance of consistency between GO annotations and the associated evidence texts identified by expert curators is reliable but time-consuming, and is infeasible in the context of rapidly growing  ...  There are many challenges to assess the quality of GOA [18] . Some researchers have estimated a relatively high error rate of GO-curated sequence annotations [19] .  ... 
doi:10.1186/s12859-021-04479-9 pmid:34823464 pmcid:PMC8620237 fatcat:u4z4maa2ajbltcalwp3vyy2m4q

Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
In fact, bio-ontologies are beginning to proliferate in step with accruing biological data.  ...  The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspectiveçdescribing how bio-ontologies can and are being used.  ...  Acknowledgements This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1093/bib/bbm059 pmid:18077472 fatcat:z3orlk75yzherjf37i3nehqlmm
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