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The Monarch Initiative (https:\/\/monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.<\/jats:p>","DOI":"10.1093\/nar\/gkz997","type":"journal-article","created":{"date-parts":[[2019,10,15]],"date-time":"2019-10-15T12:09:30Z","timestamp":1571141370000},"page":"D704-D715","source":"Crossref","is-referenced-by-count":246,"title":["The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6439-2224","authenticated-orcid":false,"given":"Kent A","family":"Shefchek","sequence":"first","affiliation":[{"name":"Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA"}]},{"given":"Nomi L","family":"Harris","sequence":"first","affiliation":[{"name":"Environmental Genomics and Systems 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