Filters








294 Hits in 5.9 sec

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience

M. Krallinger, F. Leitner, M. Vazquez, D. Salgado, C. Marcelle, M. Tyers, A. Valencia, A. Chatr-aryamontri
2012 Database: The Journal of Biological Databases and Curation  
Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information  ...  Special emphasis is given to protein-protein interaction data and PSI-MI terms referring to interaction detection methods.  ...  Acknowledgements We would like to thank Lynette Hirschman and Christian Blaschke for their active feedback in the BioCreative tasks described in this article.  ... 
doi:10.1093/database/bas017 pmid:22438567 pmcid:PMC3309177 fatcat:3q2zwcobxfaebl4rw4hsnddid4

Mining literature for systems biology

P. M. Roberts
2006 Briefings in Bioinformatics  
These uses of literature, specifically manual curation, derived concepts captured in ontologies and databases, and indirect and direct application of text mining, will be discussed as they pertain to systems  ...  ^protein interaction (PPI) databases; both of these are convenient, consistent reductions of more complex concepts expressed as free text in the literature.  ...  In the following section, examples from Table 2 will be used to illustrate how text analytics can be used to efficiently and comprehensively mine relationships from text.  ... 
doi:10.1093/bib/bbl037 pmid:17032698 fatcat:4dhuqwmui5anri6nfqdc7w2uym

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Martin Krallinger, Alfonso Valencia, Lynette Hirschman
2008 Genome Biology  
The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance.  ...  Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the  ...  Thanks to Carlos Rodriguez Penagos and Florian Leitner for useful discussions and feedback. The participation of LH was supported under National Science Foundation Grant II-0640153.  ... 
doi:10.1186/gb-2008-9-s2-s8 pmid:18834499 pmcid:PMC2559992 fatcat:oeqr7ctzgjeo5nnw53fimelwxa

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz, Sophia Ananiadou
2011 BMC Bioinformatics  
ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles.  ...  The contest's Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT).  ...  RB provided data and error analysis. RN constructed the mapping between MeSH and MI IDs. SA supervised all steps of the work. All authors contributed to the preparation of the final manuscript.  ... 
doi:10.1186/1471-2105-12-s8-s11 pmid:22151769 pmcid:PMC3269934 fatcat:qmfgoxabnbd5nctdbokyn7jlfq

Mining physical protein-protein interactions from the literature

Minlie Huang, Shilin Ding, Hongning Wang, Xiaoyan Zhu
2008 Genome Biology  
Conclusion: We present a text-mining framework to extract physical protein-protein interactions from the literature.  ...  Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information.  ...  Acknowledgements 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-s12 pmid:18834490 pmcid:PMC2559983 fatcat:svfuxbehyvcx3ikm25efdxoksm

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011.  ...  to disseminate andinteractwith the typicallyhuge amounts of semiformalknowledge structures extracted by text mining tools.  ...  and normalizing gene/protein mentions, as well as interactions between proteins (PPIs) for abstracts, as well as for full texts (see the surveys of BioCreAtIvE I [24] , BioCreAtIvE II [25] , BioCreAtIvE  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over

Rajinder Gupta, Shrikant S. Mantri
2016 Frontiers in Genetics  
Currently the community efforts like Biocreative 8 to solve the literature mining labyrinth have brought to life many new tools and approaches.  ...  More robust approaches need to be thought of to accommodate the gap between the published literature and manually curated literature.  ...  Copyright © 2016 Gupta and Mantri. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fgene.2016.00046 pmid:27066067 pmcid:PMC4814459 fatcat:w4ulvpfszfemnjt3iqiixwvzla

BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences

K.E. Ravikumar, Majid Rastegar-Mojarad, Hongfang Liu
2017 Database: The Journal of Biological Databases and Curation  
BioCreative V track4 challenge for the first time has organized a comprehensive shared task to test the robustness of the text-mining algorithms in extracting semantically meaningful assertions from the  ...  In this work, we tested the ability of a rule-based semantic parser to extract Biological Expression Language (BEL) statements from evidence sentences culled out of biomedical literature as part of BioCreative  ...  Acknowledgements This work was supported by the grants from the National Institutes of Health (RO1LM11829, RO1GM102282, RO1LM11934, RO1LM11369). Conflict of interest. None declared.  ... 
doi:10.1093/database/baw156 pmid:28365720 pmcid:PMC5467463 fatcat:g3hvapwchbcnpb33g6d4rmogke

Mining experimental evidence of molecular function claims from the literature

C. E. Crangle, J. M. Cherry, E. L. Hong, A. Zbyslaw
2007 Bioinformatics  
Motivation- The rate at which gene-related findings appear in the scientific literature makes it difficult if not impossible for biomedical scientists to keep fully informed and up to date.  ...  to an examination of the different kinds of errors.  ...  The Saccharomyces Genome Database project is  ... 
doi:10.1093/bioinformatics/btm495 pmid:17942445 pmcid:PMC3041023 fatcat:iuoqlispzfg2xfsu5cn3ydj7z4

SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics

Dietrich Rebholz-Schuhman, Graham Cameron, Dominic Clark, Erik van Mulligen, Jean-Louis Coatrieux, Eva Del Hoyo Barbolla, Fernando Martin-Sanchez, Luciano Milanesi, Ivan Porro, Francesco Beltrame, Ioannis Tollis, Johan Van der Lei
2007 BMC Bioinformatics  
To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics.  ...  As part of the project experts in both research fields will be identified and approached through a survey.  ...  Medline abstracts are provided from the National Library of Medicine (NLM, Bethesda, MD, USA) and PubMed http:/ /www.pubmed.org is the premier Web portal to access the data.  ... 
doi:10.1186/1471-2105-8-s1-s18 pmid:17430562 pmcid:PMC1885847 fatcat:oub64mrzu5c5pfihydiq2uacki

Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature

Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B. Bajic, Jun S. Liu, Peter Csermely
2012 PLoS ONE  
Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality  ...  connected proteinpairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface.  ...  We would like to thank the authors of the scientific knowledge resources that we have used in this study and that have made this study possible. We thank Ryan Frahm for providing server support.  ... 
doi:10.1371/journal.pone.0034480 pmid:22493694 pmcid:PMC3321019 fatcat:7ug7ftxnyrfgng7yfafzj6ze5a

Enhanced semantic access to the protein engineering literature using ontologies populated by text mining

Rene Witte, Thomas Kappler, Christopher J.O. Baker
2007 International Journal of Bioinformatics Research and Applications  
We demonstrate the feasibility of this approach with a system targeting the protein mutation literature. , where he heads the Text Mining group.  ...  We investigate a novel approach employing description logics (DL)-based queries made to formal ontologies that have been created using the results of text mining full-text research papers.  ...  Acknowledgements The authors would like to thank Vladislav Ryzhikov for his contributions to the Mutation Miner NLP subsystem.  ... 
doi:10.1504/ijbra.2007.015009 pmid:18048198 fatcat:u5ht7swye5bd3kx5nwrljw2cjq

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

M. Torii, G. Li, Z. Li, R. Oughtred, F. Diella, I. Celen, C. N. Arighi, H. Huang, K. Vijay-Shanker, C. H. Wu
2014 Database: The Journal of Biological Databases and Curation  
The utility of the RLIMS-P Web site has been evaluated by curators from Phospho.ELM, PhosphoGRID/BioGrid and Protein Ontology as part of the BioCreative IV user interactive task (IAT).  ...  We have developed Rule-based Literature Mining System for protein Phosphorylation (RLIMS-P), an online text-mining tool to help curators identify biomedical research articles relevant to protein phosphorylation  ...  The text evidence page contains two panels, one containing tables for the article general information, the RLIMS-P annotation, the normalization and UniProtKB mapping (a); the other containing the text  ... 
doi:10.1093/database/bau081 pmid:25122463 pmcid:PMC4131691 fatcat:ptfbobrhkbdrbovnwydi3t6pbu

An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database

Fabio Rinaldi, Oscar Lithgow-Serrano, Alejandra López-Fuentes, Socorro Gama-Castro, Yalbi I. Balderas-Martínez, Hilda Solano-Lira, Julio Collado-Vides
2015 POLIBITS Research Journal on Computer Science and Computer Engineering With Applications  
The aim of our activity is to improve the efficiency of this process by leveraging upon natural language processing technologies in a text mining system.  ...  As part of a large-scale biocuration project, we are developing innovative techniques to process the biomedical literature and extract information relevant to specific biological investigations.  ...  Biomedical text mining can be used to partially automate the process of biomedical literature curation by using sophisticated algorithms for discovering biomedical entities together with interaction and  ... 
doi:10.17562/pb-52-3 fatcat:akvxswq7u5havf45rrx56sfjna

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 http://gen-es.org  ... 
doi:10.1186/gb-2008-9-s2-s7 pmid:18834498 pmcid:PMC2559991 fatcat:6cerr44envaqrfatnatmiy5nbq
« Previous Showing results 1 — 15 out of 294 results