Challenges in the construction of knowledge bases for human microbiome-disease associations
Published 2019 View Full Article
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Title
Challenges in the construction of knowledge bases for human microbiome-disease associations
Authors
Keywords
Natural language processing, Knowledge base, Microbes, Disease, Human, Model organisms, Microbiome, Microbiome dynamics
Journal
Microbiome
Volume 7, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-09-06
DOI
10.1186/s40168-019-0742-2
References
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- (2018) Dachao Liang et al. Gut Pathogens
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- (2018) QuanQiu Wang et al. Scientific Reports
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- (2018) Jian-Yu Shi et al. BMC BIOINFORMATICS
- Regional variation limits applications of healthy gut microbiome reference ranges and disease models
- (2018) Yan He et al. NATURE MEDICINE
- Qiita: rapid, web-enabled microbiome meta-analysis
- (2018) Antonio Gonzalez et al. NATURE METHODS
- The Comparative Toxicogenomics Database: update 2019
- (2018) Allan Peter Davis et al. NUCLEIC ACIDS RESEARCH
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- A method of inferring the relationship between Biomedical entities through correlation analysis on text
- (2018) Hye-Jeong Song et al. Biomedical Engineering Online
- Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human
- (2018) Guangyi Niu et al. NUCLEIC ACIDS RESEARCH
- gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data
- (2018) Wenyu Shi et al. NUCLEIC ACIDS RESEARCH
- The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019
- (2018) Annalisa Buniello et al. NUCLEIC ACIDS RESEARCH
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- (2018) Raphael Eisenhofer et al. TRENDS IN MICROBIOLOGY
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- (2017) QuanQiu Wang et al. JOURNAL OF BIOMEDICAL INFORMATICS
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use
- (2017) Bryony N. Parsons et al. PLoS Pathogens
- Enterotypes in the landscape of gut microbial community composition
- (2017) Paul I. Costea et al. Nature Microbiology
- A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network
- (2017) Shuai Zou et al. PLoS One
- @MInter: automated text-mining of microbial interactions
- (2016) Kun Ming Kenneth Lim et al. BIOINFORMATICS
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- (2016) Robert Leaman et al. BIOINFORMATICS
- Protein complex prediction for large protein protein interaction networks with the Core&Peel method
- (2016) Marco Pellegrini et al. BMC BIOINFORMATICS
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- (2016) Rong Xu et al. BMC Systems Biology
- An analysis of human microbe–disease associations
- (2016) Wei Ma et al. BRIEFINGS IN BIOINFORMATICS
- Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness
- (2016) Paul E. Wischmeyer et al. Current Opinion in Critical Care
- Microbiome-wide association studies link dynamic microbial consortia to disease
- (2016) Jack A. Gilbert et al. NATURE
- KEGG: new perspectives on genomes, pathways, diseases and drugs
- (2016) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- BioCreative V CDR task corpus: a resource for chemical disease relation extraction
- (2016) Jiao Li et al. Database-The Journal of Biological Databases and Curation
- Gut biogeography of the bacterial microbiota
- (2015) Gregory P. Donaldson et al. NATURE REVIEWS MICROBIOLOGY
- BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
- (2015) Zachary A. King et al. NUCLEIC ACIDS RESEARCH
- Synthesis of phylogeny and taxonomy into a comprehensive tree of life
- (2015) Cody E. Hinchliff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2015) Robert G. Beiko TRENDS IN MICROBIOLOGY
- Systems biology of host-microbe metabolomics
- (2015) Almut Heinken et al. Wiley Interdisciplinary Reviews-Systems Biology and Medicine
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- (2014) Susannah J Salter et al. BMC BIOLOGY
- Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome
- (2014) Amir Zarrinpar et al. Cell Metabolism
- NCBI disease corpus: A resource for disease name recognition and concept normalization
- (2014) Rezarta Islamaj Doğan et al. JOURNAL OF BIOMEDICAL INFORMATICS
- Replenishing our defensive microbes
- (2013) Luke K. Ursell et al. BIOESSAYS
- DNorm: disease name normalization with pairwise learning to rank
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- PubTator: a web-based text mining tool for assisting biocuration
- (2013) Chih-Hsuan Wei et al. NUCLEIC ACIDS RESEARCH
- The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
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- The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
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- (2012) Catherine A. Lozupone et al. NATURE
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- (2012) Tanya Yatsunenko et al. NATURE
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- (2012) Marco Candela et al. TRENDS IN MICROBIOLOGY
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- Normalized names for clinical drugs: RxNorm at 6 years
- (2011) Stuart J Nelson et al. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
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- LINNAEUS: A species name identification system for biomedical literature
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- (2009) P. A. Crawford et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Evolution of Mammals and Their Gut Microbes
- (2008) R. E. Ley et al. SCIENCE
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