Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

@article{Ong2020ModellingKD,
  title={Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project},
  author={Edison Ong and Lucy Lu Wang and Jennifer A. Schaub and John F. O'Toole and Becky Steck and Avi Z. Rosenberg and Frederick Dowd and Jens Hansen and Laura Barisoni and Sanjay Jain and Ian H. de Boer and M. Todd Valerius and Sushrut S. Waikar and Christopher Park and Dana C. Crawford and Theodore Alexandrov and Christopher R. Anderton and Christian J. Stoeckert and Chunhua Weng and Alexander D. Diehl and Chris J. Mungall and Melissa A. Haendel and Peter N. Robinson and Jonathan Himmelfarb and Ravi Iyengar and Matthias Kretzler and Sean D. Mooney and Yongqun Oliver He},
  journal={Nature Reviews Nephrology},
  year={2020},
  volume={16},
  pages={686 - 696}
}
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling… 
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research.
TLDR
The usage of the term 'precision omics' is proposed to represent the combinatorial strategy that applies omics to translate large-scale molecular omics data for precision disease understanding and accurate disease diagnosis, treatment and prevention.
A reference tissue atlas for the human kidney
TLDR
This reference atlas provides an initial framework for molecular classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.
TLDR
The representation of prenatal phenotypes in HPO was expanded by adding 95 new phenotype terms under the Abnormality of prenatal development or birth grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort.
Non-invasive molecular imaging of kidney diseases
TLDR
Non-invasive visualization of the kidneys through molecular imaging can be used to detect and longitudinally monitor disease activity and can therefore provide companion diagnostics to guide clinical trials, as well as the safe and effective use of drugs.
Fine-Grained ICD Code Assignment Using Ontology-Based Classification
TLDR
This paper uses ontology-based human knowledge to extract semantically related sentences from doctor’s notes to support the use of deep learning for reliable training and classification and proposes a fine-grained approach that focuses on one diagnosis at a time.
Precision medicine for the treatment of glomerulonephritis: a bold goal but not yet a transformative achievement
TLDR
A sustained and highly collaborative engagement with this new paradigm will be required for this field, full of hope and high expectations, to realize its goal of transforming glomerular therapeutics from one size fits all (or many) to a true individualized management principle.
A multiscale lipid and cellular atlas of the human kidney
TLDR
An extensive lipid and cellular atlas of the human kidney is developed and the lipid profiles obtained from imaging mass spectrometry to distinct cell types obtained from immunofluorescence allowed us to hypothesize the functional role of specific phospholipids that have not been described.
...
...

References

SHOWING 1-10 OF 73 REFERENCES
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration
TLDR
A Kidney Tissue Atlas Ontology is developed that reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology and generates new semantic axioms to logically link terms of entities in different domains.
OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis
TLDR
The case studies showed that OPMI is able to semantically and precisely represent the OHDSI CDM, various KPMP clinical forms, and their associated data and metadata.
An ontological approach to identifying cases of chronic kidney disease from routine primary care data: a cross-sectional study
TLDR
Finding cases of CKD from primary care data using an ontological approach may have greater sensitivity than less comprehensive methods, particularly for identifying those receiving renal replacement therapy or with CKD stages 1 or 2.
The Ontology for Biomedical Investigations
TLDR
The state of OBI and several applications that are using it are described, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources.
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
TLDR
The current version of the Human Disease Ontology (DO), a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology, is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language.
Integrated multi-omics approaches to improve classification of chronic kidney disease
TLDR
The success of targeting molecular pathways identified through approaches that involve the integration of various datasets has been demonstrated in clinical trials and puts nephrology in a position to test the concept of precision medicine.
Building a drug ontology based on RxNorm and other sources
TLDR
DrOn is a modular, extensible ontology of drug products, their ingredients, and their biological activity that avoids many of the fundamental flaws found in other, similar artifacts and meets the requirements of the comparative-effectiveness research use-case.
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications
TLDR
Use of these vocabularies to standardize data representation for quantitative phenotypes and quantitative trait loci across databases for multiple species has demonstrated their utility for integrating diverse data types from multiple sources.
...
...