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A text-mining system for extracting metabolic reactions from full-text articles
2012
BMC Bioinformatics
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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
2017
Nucleic Acids Research
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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
2009
Computer applications in the biosciences : CABIOS
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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
2011
BMC Bioinformatics
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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
2015
AMIA Annual Symposium Proceedings
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), 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
2013
Journal of Biomedical Informatics
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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
2016
PeerJ
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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
2018
PeerJ
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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
2020
Bioinformatics
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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
2018
Frontiers in Microbiology
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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
2010
Pharmacogenomics (London)
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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
2014
Nucleic Acids Research
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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
2010
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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
2003
Comparative and Functional Genomics
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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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