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jamesamcl authored Mar 27, 2024
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| Category | Example datasets | Example phenotype |
|-------------------------------------------|-----------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------|
| Gene to phenotype associations | [Online Mendelian Inheritance in Man (OMIM)](https://www.omim.org/), [Human Phenotype Ontology (HPO)](https://hpo.jax.org/app/), [Gene Ontology (GO)](http://geneontology.org/) | Achondroplasia (associated with FGFR3 gene mutations) |
| Gene to disease associations | [The Cancer Genome Atlas (TCGA)](https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga), [Online Mendelian Inheritance in Man (OMIM)](https://www.omim.org/), [GWAS Catalog](https://www.ebi.ac.uk/gwas/) | Breast invasive carcinoma (associated with BRCA1/BRCA2 mutations) |
| Phenotype-phenotype semantic similarity | [Human Phenotype Ontology (HPO)](https://hpo.jax.org/app/), [Unified Medical Language System (UMLS)](https://www.nlm.nih.gov/research/umls/index.html), [Disease Ontology (DO)](http://disease-ontology.org/) | Cardiac abnormalities (semantic similarity with congenital heart defects) |
| Quantified trait data (QTL etc) | [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/), [Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/), [The Human Protein Atlas](https://www.proteinatlas.org/) | Height (quantified trait associated with SNPs in genomic regions) |
| Electronic health records | [Medical Information Mart for Intensive Care III (MIMIC-III)](https://mimic.physionet.org/), [UK Biobank](https://www.ukbiobank.ac.uk/), [IBM Watson Health](https://www.ibm.com/watson-health) | Acute kidney injury (recorded diagnosis during ICU stay) |
| Epidemiological datasets | [Framingham Heart Study](https://framinghamheartstudy.org/), [National Health and Nutrition Examination Survey (NHANES)](https://www.cdc.gov/nchs/nhanes/index.htm), [Global Burden of Disease Study (GBD)](http://www.healthdata.org/gbd) | Cardiovascular disease (epidemiological study of risk factors and disease incidence) |
| Clinical trial datasets | [ClinicalTrials.gov](https://clinicaltrials.gov/), [European Union Clinical Trials Register (EUCTR)](https://www.clinicaltrialsregister.eu/), [International Clinical Trials Registry Platform (ICTRP)](https://www.who.int/ictrp/en/) | Treatment response (clinical trial data on efficacy and safety outcomes) |
| Environmental exposure datasets | [Environmental Protection Agency Air Quality System (EPA AQS)](https://www.epa.gov/outdoor-air-quality-data), [Global Historical Climatology Network (GHCN)](https://www.ncdc.noaa.gov/data-access/land-based-station-data/land-based-datasets/global-historical-climatology-network-ghcn), [National Centers for Environmental Information Climate Data Online (NCEI CDO)](https://www.ncdc.noaa.gov/cdo-web/) | Respiratory diseases (association with air pollutant exposure) |
| Population surveys e.g., UK Biobank | [UK Biobank](https://www.ukbiobank.ac.uk/), [National Health Interview Survey (NHIS)](https://www.cdc.gov/nchs/nhis/index.htm), [National Health and Nutrition Examination Survey (NHANES)](https://www.cdc.gov/nchs/nhanes/index.htm) | Chronic diseases (population-based study on disease prevalence and risk factors) |
| Behavioral observation datasets | [National Survey on Drug Use and Health (NSDUH)](https://www.samhsa.gov/data/data-we-collect/nsduh-national-survey-drug-use-and-health), [Add Health](https://www.cpc.unc.edu/projects/addhealth), [British Cohort Study (BCS)](http://cls.ucl.ac.uk/cls-studies/) | Substance abuse disorders (survey data on drug consumption and addiction) |

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