ArticleBioinformatics (Oxford, England)2012
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
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- DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases.Oxidative medicine and cellular longevity · 2020Article
- HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.Journal of biomedical informatics · 2019Article
- Identification of pathways associated with chemosensitivity through network embedding.PLoS computational biology · 2019Article
- Literature-Based Enrichment Insights into Redox Control of Vascular Biology.Oxidative medicine and cellular longevity · 2019Review
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Inferring ontology graph structures using OWL reasoning.BMC bioinformatics · 2018Article
- Integrating phenotype ontologies with PhenomeNET.Journal of biomedical semantics · 2017Article
- Learning from biomedical linked data to suggest valid pharmacogenes.Journal of biomedical semantics · 2017Article
- Semantic prioritization of novel causative genomic variants.PLoS computational biology · 2017Article
- The Disease Ontology: fostering interoperability between biological and clinical human disease-related data.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases.Scientific reports · 2015Article
- KaBOB: ontology-based semantic integration of biomedical databases.BMC bioinformatics · 2015Article
- Mining Electronic Health Records using Linked Data.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2015Article
- HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.PloS one · 2015Article
- The functional therapeutic chemical classification system.Bioinformatics (Oxford, England) · 2014Article
- The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.Journal of biomedical semantics · 2014Article
- A rule-based ontological framework for the classification of molecules.Journal of biomedical semantics · 2014Article
- Enrichment analysis applied to disease prognosis.Journal of biomedical semantics · 2013Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationMany complex diseases are the result of abnormal pathway functions instead of single abnormalities. Disease diagnosis and intervention strategies must target these pathways while minimizing the interference with normal physiological processes. Large-scale identification of disease pathways and chemicals that may be used to perturb them requires the integration of information about drugs, genes, diseases and pathways. This information is currently distributed over several pharmacogenomics databases. An integrated analysis of the information in these databases can reveal disease pathways and facilitate novel biomedical analyses.
resultsWe demonstrate how to integrate pharmacogenomics databases through integration of the biomedical ontologies that are used as meta-data in these databases. The additional background knowledge in these ontologies can then be used to enable novel analyses. We identify disease pathways using a novel multi-ontology enrichment analysis over the Human Disease Ontology, and we identify significant associations between chemicals and pathways using an enrichment analysis over a chemical ontology. The drug-pathway and disease-pathway associations are a valuable resource for research in disease and drug mechanisms and can be used to improve computational drug repurposing. AVAILABILITY: http://pharmgkb-owl.googlecode.com
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.