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Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows
2015
Journal of Biomedical Semantics
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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
2014
Journal of Translational Medicine
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Previously we generated a chronic obstructive pulmonary disease (COPD) specific knowledge base (http://www.copdknowledgebase.eu) 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
2016
Database: The Journal of Biological Databases and Curation
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With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest. ...
Argo (http://argo.nactem.ac.uk) 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
2019
JAMIA Open
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Chronic obstructive pulmonary disease (COPD) phenotypes cover a range of lung abnormalities. ...
Our corpus of 30 full papers (available at: http://www.nactem.ac.uk/COPD) 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
2015
Journal of Biomedical Semantics
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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
2021
PLoS ONE
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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
2011
BMC Systems Biology
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2014
PLoS ONE
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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
2018
Circulation Research
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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
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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
2017
Annals of the American Thoracic Society
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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
2014
Journal of Biomedical Semantics
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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
2018
PLoS ONE
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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
2016
BMC Bioinformatics
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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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