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

Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; Balhoff, James P.; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin D.; Gourdine, JP; Jacobsen, Julius O. B.; Keith, Daniel; Laraway, Bryan; Lewis, Suzanna; Xuan, Jeremy Nguyen; Shefchek, Kent; Vasilevsky, Nicole; Zhou, Yuan; Washington, Nicole; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter N.; Haendel, Melissa

doi:10.1101/055756

Cited by 29 publications

(36 citation statements)

References 56 publications

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“…Easy access to orthologous genes across species is provided by the well-established OrthoDB and the new arrival HieranoiDB which offers beautifully presented trees of orthologues. Another important cross-species analysis is represented by the Monarch Initiative, highlighted by NAR reviewers and editors as a ‘Breakthrough’ article (2). Working with the Human Phenotype Ontology, also reporting an update in this issue, Monarch Initiative aims to link mutations in orthologous genes to the similar phenotypes often observed in different species.…”

Section: New and Updated Databasesmentioning

confidence: 99%

“…Working with the Human Phenotype Ontology, also reporting an update in this issue, Monarch Initiative aims to link mutations in orthologous genes to the similar phenotypes often observed in different species. This ambitious objective requires the careful use and integration of ontologies to precisely describe anatomy, diseases and phenotypes, but the pay-off is an ability to link from human diseases to disease models in various model organisms, maximizing the value of data obtained for any given organism (2). …”

Section: New and Updated Databasesmentioning

confidence: 99%

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The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

2017

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This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.

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Section: New and Updated Databasesmentioning

confidence: 99%

Section: New and Updated Databasesmentioning

confidence: 99%

The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

2017

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“…41,43 Although the similarities between human and model organism mutant phenotype can be informative, this approach may miss numerous opportunities in which the protein functions are part of conserved pathways among organisms when the orthologous phenotypes are not obviously analogous. 44 For example, a yeast model for angiogenesis 44 and a worm model for breast cancer 44 revealed molecular pathways that contribute to these disorders based on the ''phenology'' concept.…”

Section: Discussionmentioning

confidence: 99%

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

Wang¹,

Al‐Ouran²,

Hu³

et al. 2017

The American Journal of Human Genetics

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195

146

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One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research.

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“…matchbox uses the Exomiser (Smedley et al., ) Phenodigm (Smedley et al., ) phenotype matching module available from the Monarch Initiative (Mungall et al., ) to calculate the similarity between sets of phenotypes between two patients. The Phenodigm algorithm compares all query phenotypes encoded using the Human Phenotype Ontology (HPO) (Kohler et al., ) against the set of all HPO disease profiles to produce the best possible match.…”

Section: The Genotype Scoring Strategymentioning

confidence: 99%

matchbox: An open-source tool for patient matching via the Matchmaker Exchange

et al. 2018

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Rare disease investigators constantly face challenges in identifying additional cases to build evidence for gene-disease causality. The Matchmaker Exchange (MME) addresses this limitation by providing a mechanism for matching patients across genomic centers via a federated network. The MME has revolutionized searching for additional cases by making it possible to query across institutional boundaries, so that what was once a laborious and manual process of contacting researchers is now automated and computable. However, while the MME network is beginning to scale, the growth of additional nodes is limited by the lack of easy-to-use solutions that can be implemented by any rare disease database owner, even one without significant software engineering resources. Here we describe matchbox, which is an open-source, platform-independent, portable bridge between any given rare disease genomic center and the MME network, which has already led to novel gene discoveries. We also describe how matchbox greatly reduces the barrier to participation by overcoming challenges for new databases to join the MME.

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

Abstract: The correlation of phenotypic outcomes with genetic

Cited by 29 publications

References 56 publications

The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

matchbox: An open-source tool for patient matching via the Matchmaker Exchange

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