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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  ...  The only system that we are aware of that has an explicit focus on extracting metabolic pathway information from free text is the template-based EMPathIE [9] , which is no longer under active development  ...  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

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

Andres Cañada, Salvador Capella-Gutierrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
2017 Nucleic Acids Research  
This system processes scientific abstracts, a set of full text articles and medical agency assessment reports.  ...  Here we present LimTox (Literature Mining for Toxicology), a webbased online biomedical search tool with special focus on adverse hepatobiliary reactions.  ...  ACKNOWLEDGEMENTS Many thanks to Florian Leitner, Miguel Vazquez, Montse Cases, Nicole Dolker and Analia Lourenc ¸o for useful feedback and input.  ... 
doi:10.1093/nar/gkx462 pmid:28531339 pmcid:PMC5570141 fatcat:q75q5tllbzdxnltcnlpjvpqqz4

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways

Irena Spasić, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, Douglas B. Kell
2009 Computer applications in the biosciences : CABIOS  
The baseline recall is improved by 36% for abstracts and by 100% for full text. It appears that full-text articles are a much richer source of information on kinetic data than are their abstracts.  ...  It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given  ...  ACKNOWLEDGEMENTS We thank many colleagues in Manchester for the most useful discussions. Particular thanks to Goran Nenadic for his help in testing the software.  ... 
doi:10.1093/bioinformatics/btp175 pmid:19336445 fatcat:cbdqvfmdpjgdlnuiw3jvwzddmu

Semantic annotation of biological concepts interplaying microbial cellular responses

Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C Ferreira, Anália Lourenço
2011 BMC Bioinformatics  
Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks.  ...  Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.  ...  In this paper, we explore the issues that text mining systems will need to face in order to handle the knowledge contained within full-text articles.  ... 
doi:10.1186/1471-2105-12-460 pmid:22122862 pmcid:PMC3259143 fatcat:mj6to5arrfav5mkn6fddhy7lgy

tcTKB: an integrated cardiovascular toxicity knowledge base for targeted cancer drugs

Rong Xu, QuanQiu Wang
2015 AMIA Annual Symposium Proceedings  
), published biomedical literature (21,354,075 records), and published full-text articles from the Journal of Oncology (JCO) (13,855 articles). tcTKB contains 14,351 drug-CV pairs for 45 targeted anticancer  ...  In this study, we built tcTKB, a comprehensive CV toxicity knowledge base for targeted cancer drugs, by extracting drug-CV pairs from five large-scale and complementary data sources.  ...  We would like to thank the three curators from ThinTek for the manual curation.  ... 
pmid:26958275 pmcid:PMC4765587 fatcat:geujs4hwl5bzvbzds3ai6a6ob4

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  
Thus, the full utilization of text mining to facilitate cancer systems biology research is fast becoming a major concern.  ...  The immense body and rapid growth of biomedical text on cancer has led to the appearance of a large number of text mining techniques aimed at extracting novel knowledge from scientific text.  ...  Consequently, the full utilization of text mining to facilitate cancer systems biology research is a new hot topic.  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

An integrated text mining framework for metabolic interaction network reconstruction

Preecha Patumcharoenpol, Narumol Doungpan, Asawin Meechai, Bairong Shen, Jonathan H. Chan, Wanwipa Vongsangnak
2016 PeerJ  
Text mining (TM) in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals) as well as their relationships  ...  Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module—MEE) and for the construction of a metabolic interaction network  ...  Yutthanattee Tohreh for assisting in the manual annotation process and Mr. Sean Kortschot for proofreading the draft version of the manuscript. We also would like to thank Mr. David H.  ... 
doi:10.7717/peerj.1811 pmid:27019783 pmcid:PMC4806637 fatcat:72y36huwjbf7tglk24fznwoaia

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

Sanna M. Kreula, Suwisa Kaewphan, Filip Ginter, Patrik R. Jones
2018 PeerJ  
The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to  ...  Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network  ...  We would like to thank Sofie Van Landeghem (Ghent University) and Tero Aittokallio (FIMM) for their insight and valuable comments on text-mining, systems and network biology.  ... 
doi:10.7717/peerj.4806 pmid:29844966 pmcid:PMC5970561 fatcat:7ygfmgo7ybbpfjhgbasd7kei6u

Padhoc: a computational pipeline for pathway reconstruction on the fly

Salvador Casaní-Galdón, Cecile Pereira, Ana Conesa
2020 Bioinformatics  
Results Here we present Padhoc, a pipeline for pathway ad hoc reconstruction.  ...  Based on a set of user-provided keywords, Padhoc combines natural language processing, database knowledge extraction, orthology search and powerful graph algorithms to create navigable pathways tailored  ...  Knowledge extraction from scientific literature falls within the domain of text mining.  ... 
doi:10.1093/bioinformatics/btaa811 pmid:33381819 fatcat:e7te5paykvegvdvdq3mclmssa4

Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India

Abhishek Gupta, Avishek Dutta, Jayeeta Sarkar, Mruganka Kumar Panigrahi, Pinaki Sar
2018 Frontiers in Microbiology  
The present study investigated the scope for increasing the abundance and activity of inhabitant sulfate- and iron-reducing bacterial populations of an AIS from Malanjkhand Copper Project.  ...  stimulated for in situ bioremediation of an AMD impacted soil (AIS).  ...  DNA Extraction From Enrichment Total DNA from enriched populations was extracted from 4 ml of each enrichment.  ... 
doi:10.3389/fmicb.2018.02882 pmid:30619102 pmcid:PMC6297179 fatcat:b2sps3s6gffnrj2mlfl4ydfsbu

Recent progress in automatically extracting information from the pharmacogenomic literature

Yael Garten, Adrien Coulet, Russ B Altman
2010 Pharmacogenomics (London)  
Acknowledgements The authors would like to thank Connie M Oshiro for comments on the manuscript and Nicholas P Tatonetti for useful discussions and assistance creating the figures.  ...  We also thank the three anonymous reviewers for their excellent comments.  ...  of full text pharmacogenomic articles [19, 20] .  ... 
doi:10.2217/pgs.10.136 pmid:21047206 pmcid:PMC3035632 fatcat:7g3jwc4hjfetbb5phmzstzhjeu

BRENDA in 2015: exciting developments in its 25th year of existence

Antje Chang, Ida Schomburg, Sandra Placzek, Lisa Jeske, Marcus Ulbrich, Mei Xiao, Christoph W. Sensen, Dietmar Schomburg
2014 Nucleic Acids Research  
The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms.  ...  They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation.  ...  KENDA (Kinetic ENzyme DAta) is a database containing kinetic enzyme data, extracted from PubMed literature abstracts via text mining methods.  ... 
doi:10.1093/nar/gku1068 pmid:25378310 pmcid:PMC4383907 fatcat:sdwv66mdaffetnkky63xabh3jm

BRENDA, the enzyme information system in 2011

M. Scheer, A. Grote, A. Chang, I. Schomburg, C. Munaretto, M. Rother, C. Sohngen, M. Stelzer, J. Thiele, D. Schomburg
2010 Nucleic Acids Research  
The disease text mining part is strongly enhanced.  ...  The majority of the data are manually extracted from the primary literature.  ...  ACKNOWLEDGEMENTS We wish to thank all collaborating scientists who performed the literature annotation and created the molecular structures for the enzyme ligands.  ... 
doi:10.1093/nar/gkq1089 pmid:21062828 pmcid:PMC3013686 fatcat:sf363c4w7fbidmu7fpgzuqrpye

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg
2016 Nucleic Acids Research  
The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms.  ...  Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations.  ...  Text mining Since it is impossible to perform a manual annotation for the complete literature for each enzyme class, text mining procedures have been developed to include more information and give a complete  ... 
doi:10.1093/nar/gkw952 pmid:27924025 pmcid:PMC5210646 fatcat:kltw4gqvqvfc5ijvwuddbe4vhi

ISMB 2003 Text Mining SIG Meeting Report

Christian Blaschke, Alexander Yeh, Lynette Hirschman, Alfonso Valencia
2003 Comparative and Functional Genomics  
Society for Computational Biology) for organizing the logistics and the infrastructure, and the EU projects ORIEL (Contract number: IST-2001-32688) and TEMBLOR (Contract number: VEQLRT 2001 00015) for  ...  Acknowledgements The organizers of the workshop would like to thank especially all the speakers for their presentations, Marc Light for co-organizing the event, Steven Leard and the ISCB (The International  ...  PASTA, for Protein Active Site Template Acquisition system, is a text mining system for the automatic extraction of information relating to protein structures from the biological literature.  ... 
doi:10.1002/cfg.338 pmid:18629019 pmcid:PMC2447301 fatcat:vmqqau3myrgsfdfhwotqljapje
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