The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
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DOI：
10.1093/nar/gkz997
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Osumi-Sutherland, David
中科院分区：
文献类型：
--
作者：
Shefchek, Kent A.;Harris, Nomi L.;Osumi-Sutherland, David
在生物学和生物医学中，将表型结果与遗传变异和环境因素联系起来仍然是一个挑战：患者表型可能与已知疾病不匹配，候选变异可能存在于尚未被表征的基因中，研究生物可能无法重现人类或兽医疾病，影响疾病结果的环境因素未知或未记录，并且必须查询许多资源以发现潜在的显著表型关联。Monarch Initiative（monarchinitiative.org）整合了各种物种的基因、变异、基因型、表型和疾病信息，并允许进行强大的基于本体的搜索。我们开发了许多广泛采用的本体论，这些本体论共同实现了孟德尔疾病的复杂计算分析、机械发现和诊断。我们的算法和工具被广泛用于通过表型相似性识别人类疾病的动物模型，用于差异诊断和促进转化研究。Monarch于2015年推出，在数据（新的生物体，更多的来源，更好的建模），新的API和标准，本体（新的Mondo统一疾病本体，HPO和uPheno等本体的改进），用户界面（重新设计的网站）和社区发展方面都有所发展。Monarch数据、算法和工具正在被GA4GH和NCATS Translator等资源使用和扩展，以帮助机械发现和诊断。
In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. 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.