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Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows

Xiao Fu, Riza Batista-Navarro, Rafal Rak, Sophia Ananiadou
2015 Journal of Biomedical Semantics  
Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare.  ...  Conclusions: We describe in this work the means by which we aim to eventually support the process of COPD phenotype curation, i.e., by the application of various text mining tools integrated into an annotation  ...  Special mention goes to Andrea who has graciously contributed a significant amount of her time to provide us with annotations.  ... 
doi:10.1186/s13326-015-0004-6 pmid:25789153 pmcid:PMC4364458 fatcat:27zettictfbrbiswiabd62tmhi

The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research

Isaac Cano, Ákos Tényi, Christine Schueller, Martin Wolff, M Mercedes Huertas Migueláñez, David Gomez-Cabrero, Philipp Antczak, Josep Roca, Marta Cascante, Francesco Falciani, Dieter Maier
2014 Journal of Translational Medicine  
Previously we generated a chronic obstructive pulmonary disease (COPD) specific knowledge base ( from clinical and experimental data, text-mining results and public databases  ...  Integration with the Synergy-COPD Simulation Environment enables multi-scale integrated simulation of individual computational models while integration with a Clinical Decision Support System allows delivery  ...  and parts of the co-morbidity networks, respectively.  ... 
doi:10.1186/1479-5876-12-s2-s6 pmid:25471253 pmcid:PMC4255911 fatcat:t6lvuz4wffes5pjatwzssjkbv4

Argo: enabling the development of bespoke workflows and services for disease annotation

Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou
2016 Database: The Journal of Biological Databases and Curation  
With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest.  ...  Argo ( is a generic text mining workbench that can cater to a variety of use cases, including the semi-automatic annotation of literature.  ...  Acknowledgements We are grateful for the time and effort of Laurel Cooper, George Gkoutos, Raymund Stefancsik, Loukia Tsaprouni and Nicole Vasilevsky who carried out the COPD phenotype curation, as well  ... 
doi:10.1093/database/baw066 pmid:27189607 pmcid:PMC4869796 fatcat:6vi2iehkzjb7hbm7ke4f4yqg2i

Annotating and detecting phenotypic information for chronic obstructive pulmonary disease

Meizhi Ju, Andrea Short, Paul Thompson, Nawar Diar Bakerly, Georgios Gkoutos, Loukia Tsaprouni, Sophia Ananiadou
2019 JAMIA Open  
Chronic obstructive pulmonary disease (COPD) phenotypes cover a range of lung abnormalities.  ...  Our corpus of 30 full papers (available at: is annotated by experts with 27 030 phenotype-related concept mentions, most of which are automatically linked to UMLS Metathesaurus  ...  ACKNOWLEDGMENTS The authors thank John McNaught for his helpful comments on the manuscript. They also thank Piotr Przybyła for his help with the visualization of the annotations in the corpus.  ... 
doi:10.1093/jamiaopen/ooz009 pmid:31984360 pmcid:PMC6951876 fatcat:6wgkcujklrfqbfcs5imvxiop4q

Special issue on bio-ontologies and phenotypes

Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah
2015 Journal of Biomedical Semantics  
The selected papers span a wide range of topics including the automated re-use and update of ontologies, quality assessment of ontological resources, and the systematic description of phenotype variation  ...  The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent  ...  Acknowledgements As editors of this thematic issue, we thank all the authors who submitted papers, the Program Committee members and the reviewers for their excellent work.  ... 
doi:10.1186/s13326-015-0040-2 pmid:26682035 pmcid:PMC4682270 fatcat:7vupjwbtd5fzpojrh3tumhb2oq

Building a semantically annotated corpus for chronic disease complications using two document types

Noha Alnazzawi, Nicolas Fiorini
2021 PLoS ONE  
However, the development of text-mining tools depends on the availability of an annotated corpus.  ...  Text-mining tools provide efficient solutions to extract and integrate vital information related to disease complications hidden in the large volume of the narrative text.  ...  ., Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. Journal of biomedical semantics, 2015.  ... 
doi:10.1371/journal.pone.0247319 pmid:33735207 fatcat:2ymazoqfofcslgjhcr7hjalk6u

Knowledge management for Systems Biology a general and visually driven framework applied to translational medicine

Dieter Maier, Wenzel Kalus, Martin Wolff, Susana G Kalko, Josep Roca, Igor Marin de Mas, Nil Turan, Marta Cascante, Francesco Falciani, Miguel Hernandez, Jordi Villa-Freixa, Sascha Losko
2011 BMC Systems Biology  
From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular  ...  based on specific objects and their relations supporting annotations and ontologies.  ...  Acknowledgements We thank all the members of the BioBridge team for valuable discussions on the data model and their evaluation of BioXM.  ... 
doi:10.1186/1752-0509-5-38 pmid:21375767 pmcid:PMC3060864 fatcat:qtckdk6rbrabvecjbykgyv6gpu

Overview of the interactive task in BioCreative V

Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai (+44 others)
2016 Database: The Journal of Biological Databases and Curation  
The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey.  ...  Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents.  ...  Acknowledgements We would like to acknowledge all the users and team members who have participated in this activity throughout BioCreative. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw119 pmid:27589961 pmcid:PMC5009325 fatcat:ldpn6gjxircjlibqtysi57cztq

Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: A Systems Biology Approach

Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad-Reza Nourani, Ali Moeini, Daniel J. Tschumperlin
2014 PLoS ONE  
Airway remodeling is a pathophysiologic process at the clinical, cellular, and molecular level relating to chronic obstructive airway diseases such as chronic obstructive pulmonary disease (COPD), asthma  ...  These diseases are associated with the dysregulation of multiple molecular pathways in the airway cells.  ...  Airway remodeling is reported in complex diseases such as asthma, chronic obstructive pulmonary disease (COPD), and Mustard Lung as the main respiratory clinical sign.  ... 
doi:10.1371/journal.pone.0100094 pmid:24978043 pmcid:PMC4076832 fatcat:daghvah4ubgcxenrcrt5tlorpm

Biomedical Informatics on the Cloud

Peipei Ping, Henning Hermjakob, Jennifer S. Polson, Panagiotis V. Benos, Wei Wang
2018 Circulation Research  
By introducing several established resources and state-of-the-art workflows, we share with our readers a broadly-defined informatics framework to phenotype cardiovascular health and disease.  ...  practical scenarios of machine learning-supported molecular signature extraction.  ...  Ding Wang and Bilal Mirza, as well as Anders Garlid, Chelsea Ju, Jessica Lee, Zeyu Li, Patrick Tan, and Justin Wood at the University of California, Los Angeles (UCLA) for their critical input on the content  ... 
doi:10.1161/circresaha.117.310967 pmid:29700073 pmcid:PMC6192708 fatcat:kekqc3gegvcc3hm56xzw3cosmu

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures

2018 Briefings in Bioinformatics  
Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes.  ...  The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous  ...  The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking eTRIKS Project (Grant Number: IMI 115446) resources of which are composed of a financial  ... 
doi:10.1093/bib/bby025 pmid:29684165 pmcid:PMC6556902 fatcat:iyfard4tdzgnnmhhiqibld756a

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report

Russell P. Bowler, Chris H. Wendt, Michael B. Fessler, Matthew W. Foster, Rachel S. Kelly, Jessica Lasky-Su, Angela J. Rogers, Kathleen A. Stringer, Brent W. Winston
2017 Annals of the American Thoracic Society  
and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis  ...  The major findings and conclusions of this workshop are summarized at the end of the report, and outline the progress and challenges that face these rapidly advancing fields.  ...  Acknowledgment: The authors gratefully acknowledge support from the following organizations and individuals who made the workshop possible: the American Thoracic Society (ATS), the National Institutes  ... 
doi:10.1513/annalsats.201710-770ws pmid:29192815 pmcid:PMC5946579 fatcat:pjzokf6ej5dlfdxfzztttunnca

CSEO – the Cigarette Smoke Exposure Ontology

Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris Coggins, Julia Hoeng, Martin Hofmann-Apitius, Manuel C Peitsch
2014 Journal of Biomedical Semantics  
The ontology in its current form is able to capture a wide range of cigarette smoke exposure concepts within the knowledge domain of exposure science with a reasonable sensitivity and specificity.  ...  Mainly because of the emerging need of systems toxicology to controlled vocabularies and also the lack of suitable ontologies for this domain, the CSEO prepares the ground for integrative systems-based  ...  Acknowledgements The authors wish to thank PMI  ... 
doi:10.1186/2041-1480-5-31 pmid:25093069 pmcid:PMC4120729 fatcat:jziaxyi775davpputqpq3ipzne

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives

Sebastian Gehrmann, Franck Dernoncourt, Yeran Li, Eric T. Carlson, Joy T. Wu, Jonathan Welt, John Foote, Edward T. Moseley, David W. Grant, Patrick D. Tyler, Leo A. Celi, Jen-Hsiang Chuang
2018 PLoS ONE  
Lung Disease 167 0.81 Severe chronic obstructive pulmonary disease (COPD) defined as Gold Stage III-IV, or with a forced expiratory volume during first breath (FEV1) < 50% of normal, or forced vital capacity  ...  We hope that the release of our annotations will support work towards a more comparable performance in text-based phenotyping.  ... 
doi:10.1371/journal.pone.0192360 pmid:29447188 pmcid:PMC5813927 fatcat:4cssnvp3ircfrlvxcqygp442ke

ChainRank, a chain prioritisation method for contextualisation of biological networks

Ákos Tényi, Pedro de Atauri, David Gomez-Cabrero, Isaac Cano, Kim Clarke, Francesco Falciani, Marta Cascante, Josep Roca, Dieter Maier
2016 BMC Bioinformatics  
Specifically, we recreated skeletal muscle specific signaling networks in healthy and chronic obstructive pulmonary disease (COPD) contexts.  ...  An improvement of up to factor 2.5 was shown in the precision of finding proteins of the recreated pathways compared to random simulation.  ...  Acknowledgements We would like to thank Peter Davidson who provided the analysis results on the study of inactivity-induced wasting in mouse glycolytic muscle.  ... 
doi:10.1186/s12859-015-0864-x pmid:26729273 pmcid:PMC4700624 fatcat:qvmpp35t5vc6ndczwryph57omq
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