The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

By C. Mungall, J. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, S. Carbon, Tom Conlin, Nathan A. Dunn, M. Engelstad and 16 more. bioRxiv, 2016

450 citations recorded by the source corpus.

The principles of genetics apply across the whole tree of life: on a cellular level, we share mechanisms with species from which we diverged millions or even billions of years ago. We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species. Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these multimodal data to inform interpretations by geneticists and to suggest experiments. However, the distribution and heterogeneity of databases is a major impediment: databases tend to focus either on a single data type across species, or on single species across data types. Although each database provides rich, high-quality information, no single one provides unified data that is comprehensive across species, biological scales, and data types. Without a big-picture view of the data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/954de156179b313a2988871464ad786220317bb8

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Citations in the corpus

From Big Data to Precision Medicine (2019, unknown): “There have been several initiatives to standardize phenotypic terminology including Human Phenotype Ontology (HPO), Monarch Initiative, among others (61, 62).”
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources (2018, background): “Members of the Monarch Initiative are contributing to community tools for pattern-based development using Dead Simple Ontology Design Patterns (DOSDP, (52)) and the Ontology Development Kit (ODK).”
Enabling semantic queries across federated bioinformatics databases (2019, background): “For instance, by comparing disease phenotypes in humans with phenotypes produced by particular mutations in model species, it is possible to infer which human genes are involved in the disease (3).”
Open Targets Platform: supporting systematic drug–target identification and prioritisation (2020, unknown): “By liaising with the Monarch Disease Ontology (MonDO) (26), EFO v3 provides a comprehensive ontology of diseases and phenotypes as well as cutting-edge algorithmic and manual curation to classify them using different ontologies.”