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MET network in PubMed: a text-mined network visualization and curation system

Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai, Ming-Siang Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui-Jou Chou, Marija Milacic, Onkar Singh, Shabbir Syed-Abdul, Wen-Lian Hsu
2016 Database: The Journal of Biological Databases and Curation  
MET network in PubMed: a text-mined network visualization and curation system.  ...  MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in  ...  Acknowledgements The authors would like to thank Cecilia Arighi, the organizer of the BioCreative V IAT, the curators for their annotation work and suggestions, and for their participation in our curation  ... 
doi:10.1093/database/baw090 pmid:27242035 pmcid:PMC4885604 fatcat:ezti4idx6ngktmesrtu5slzywa

Complex event extraction at PubMed scale

J. Bjorne, F. Ginter, S. Pyysalo, J. Tsujii, T. Salakoski
2010 Bioinformatics  
We introduce a system combining publicly available, state-of-theart methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed  ...  The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction.  ...  ACKNOWLEDGEMENTS We would like to thank Robert Leaman for providing us with advance access and assistance in using the most recent release of BANNER.  ... 
doi:10.1093/bioinformatics/btq180 pmid:20529932 pmcid:PMC2881365 fatcat:5vdmfc57hrh7zmwoazyriuac74

GeneView: a comprehensive semantic search engine for PubMed

P. Thomas, J. Starlinger, A. Vowinkel, S. Arzt, U. Leser
2012 Nucleic Acids Research  
We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts.  ...  Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature.  ...  ACKNOWLEDGEMENTS We thank the reviewers for their careful reading and helpful comments.  ... 
doi:10.1093/nar/gks563 pmid:22693219 pmcid:PMC3394277 fatcat:pdmdg5hdbvb4reroht5v6pzlsy

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

Jiao Li, Xiaoyan Zhu, Jake Yue Chen, Andrey Rzhetsky
2009 PLoS Computational Biology  
To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results.  ...  We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems.  ...  Harrison for his critical review and comments to the early versions of this manuscript, and thank Michael Grobe of the Pervasive Technology Institute at Indiana University for his comments and revision  ... 
doi:10.1371/journal.pcbi.1000450 pmid:19649302 pmcid:PMC2709445 fatcat:3fr3zhwflbdd7fdnev3iit3lry

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks

Anthony Deeter, Mark Dalman, Joseph Haddad, Zhong-Hui Duan, Frank Alexander Feltus
2017 PLoS ONE  
We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed  ...  We have created a system with which to combine the statistical power of Bayesian networks with the genetic information contained within citations accessible from the PubMed database in order to infer interactions  ...  Each publication that met this requirement became a row in the initial Bayesian network prior knowledge publication list.  ... 
doi:10.1371/journal.pone.0186004 pmid:29049295 pmcid:PMC5648141 fatcat:33xczuvkwbak3afyrapd7wx4xu

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, Juliane Fluck
2016 Database: The Journal of Biological Databases and Curation  
BELIEF provides a webbased curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks.  ...  The underlying UIMA-based text mining pipeline (BELIEF Pipeline) uses several named entity recognition processes and relationship extraction methods to detect concepts and BEL relationships in literature  ...  Various discussions and feedback rounds helped us to create a usable curation environment for the biocurators.  ... 
doi:10.1093/database/baw136 pmid:27694210 pmcid:PMC5045868 fatcat:fkuoxt7j6ffnxoknhsqmqjvdrq

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu (+15 others)
2019 Database: The Journal of Biological Databases and Curation  
In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine.  ...  To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task.  ...  Acknowledgements We thank the BioGRID database curators Rose Oughtred, Jennifer Rust, Christie S. Chang and Lorrie Boucher for annotating the evaluation data set. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay147 pmid:30689846 pmcid:PMC6348314 fatcat:jvsf4xwr7jbbnb75d3oqczrjrq

Mining Proteome Research Reports: A Bird's Eye View

Jagajjit Sahu
2021 Proteomes  
Here, with this article, an attempt has been made to provide a systematic analysis of all the available reports at PubMed on Proteome using text mining.  ...  Keyword link network and density visualizations were provided for the top 1000 frequent Mesh keywords.  ...  PubTator Central (PTC) is a well-maintained and curated service for automated annotation of bioconcepts from the text.  ... 
doi:10.3390/proteomes9020029 pmid:34200663 fatcat:g5ct7rhiznbfbe24vehq6yjl2q

LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models

Axel J Soto, Chrysoula Zerva, Riza Batista-Navarro, Sophia Ananiadou, Jonathan Wren
2017 Bioinformatics  
Results: We have developed LitPathExplorer, a visual text analytics tool that integrates advanced text mining, semi-supervised learning and interactive visualization, to facilitate the exploration and  ...  Their curation is typically carried out through manual inspection of published scientific literature to find information relevant to a model, which is a laborious and knowledge-intensive task.  ...  PathText2 utilized reactions from signalling pathway models to query three text mining-driven search systems, in order to retrieve and rank relevant documents.  ... 
doi:10.1093/bioinformatics/btx774 pmid:29228271 fatcat:gx33npwxprd6rn3jk6coe677oa

PINOT: An Intuitive Resource for Integrating Protein-Protein Interactions [article]

James E Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C Lovering, Patrick A Lewis, Liam J McGuffin, Claudia Manzoni
2019 biorxiv/medrxiv   pre-print
customised and/or directly uploaded in a network visualization software.  ...  The past decade has seen the rise of omics data, for the understanding of biological systems in health and disease.  ...  Funding Availability of data and materials This resource is available as a fully automated web-server at: http://www.; R scripts, which underlie this bioinformatics  ... 
doi:10.1101/788000 fatcat:cwyyefdt4fb3tihisq2e2hffdm

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  
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.  ...  Text mining (TM) is a semi-automatized, multi-step process, able to turn unstructured into structured data.  ...  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

PINOT: an intuitive resource for integrating protein-protein interactions

James E. Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C. Lovering, Patrick A. Lewis, Liam J. McGuffin, Claudia Manzoni
2020 Cell Communication and Signaling  
further customised and/or directly uploaded into network visualization software.  ...  The past decade has seen the rise of omics data for the understanding of biological systems in health and disease.  ...  Funding Availability of data and materials This resource is available as a fully automated web-server at: http://www.; R scripts, which underlie this bioinformatics  ... 
doi:10.1186/s12964-020-00554-5 pmid:32527260 pmcid:PMC7291677 fatcat:5e3xducnmfghbibewctqnxpcgm

The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology

Won-Yung Lee, Choong-Yeol Lee, Youn-Sub Kim, Chang-Eop Kim
2019 Biomolecules  
Overall, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was the most frequently employed network pharmacology database in THM-NP studies.  ...  Among the processes involved in THM-NP research, the methodology for constructing a compound–target network has shown the greatest change over time.  ...  resources and through text-mining method http://www.  ... 
doi:10.3390/biom9080362 pmid:31412658 pmcid:PMC6723118 fatcat:ne4yqk6ja5cajp3iiitxo6w5zq

A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions

A. P. Davis, T. C. Wiegers, P. M. Roberts, B. L. King, J. M. Lay, K. Lennon-Hopkins, D. Sciaky, R. Johnson, H. Keating, N. Greene, R. Hernandez, K. J. McConnell (+2 others)
2013 Database: The Journal of Biological Databases and Curation  
We describe Pfizer's text-mining process to collate the articles, and CTD's curation strategy, performance metrics, enhanced data content and new module to curate phenotype information.  ...  Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88 629 articles  ...  Acknowledgements We thank Michael Rosenstein and Roy McMorran for CTD maintenance, refinement and improvement; and Dr Cynthia Murphy for critical review of the manuscript and helpful comments.  ... 
doi:10.1093/database/bat080 pmid:24288140 pmcid:PMC3842776 fatcat:nrh4in5jbbdhtkhcxpjymu4wje

Calling on a million minds for community annotation in WikiProteins

Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert-Jan van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer (+11 others)
2008 Genome Biology  
WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources.  ...  Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated.  ...  ., and by the Centre for Medical Systems Biology, through the Biorange grant SP 3.5.1. of the Netherlands Bioinformatics Centre and the Netherlands Genomics Initiative.  ... 
doi:10.1186/gb-2008-9-5-r89 pmid:18507872 pmcid:PMC2441475 fatcat:jv3bo73psndqrjdrj4q4fvorr4
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