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Monarch Initiative specifications


Unique identifier OMICS_14548
Name Monarch Initiative
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes



  • person_outline Melissa Haendel

Publications for Monarch Initiative

Monarch Initiative citations


Disease Model Discovery from 3,328 Gene Knockouts by The International Mouse Phenotyping Consortium

Nat Genet
PMCID: 5546242
PMID: 28650483
DOI: 10.1038/ng.3901

[…] The automated phenotype comparisons were performed using the open-source OWLtools package provided by the Monarch Initiative. […]


Naming CRISPR alleles: endonuclease mediated mutation nomenclature across species

Mamm Genome
PMCID: 5569137
PMID: 28589392
DOI: 10.1007/s00335-017-9698-3

[…] en six major model organism databases (MGI, RGD, SGD, ZFIN, FlyBase and WormBase), aims to allow for cross species comparison for analysis of genetic, phenotypic, and disease-related annotations. The Monarch Initiative (; Mungall et al. ) integrates genotype to phenotype data across multiple species to support biomedical research. MouseNet2 (; K […]


The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

Nucleic Acids Res
PMCID: 5210597
PMID: 28053160
DOI: 10.1093/nar/gkw1188

[…] cies 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 (). Working with the Human Phenotype Ontology, also reporting an update in this issue, Monarch Initiative aims […]


Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

PMCID: 5060938
PMID: 27785453
DOI: 10.3389/fmed.2016.00039

[…] ia Bench Lab NGS. HH and MH performed usability evaluation for UDPICS and PhenoTips. MH, CM, DS, and HH provided cross species phenotype comparison, ontological algorithms, and visualization from the Monarch Initiative. AL, CB, and MS wrote the manuscript. All authors read and approved the final manuscript. […]


Omics Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations

Int J Mol Sci
PMCID: 5037827
PMID: 27649151
DOI: 10.3390/ijms17091555

[…] his solution allows accessible visualization of multi-omics data following effective dimension reduction. The strategy has been successfully applied to chronic obstructive lung disease (COPD) []. The Monarch initiative is an impressive global endeavor that provides computational tools for genotype–phenotype analysis, genomic diagnostics, and PM across broad areas of disease. Thus, the Monarch init […]


Laying a Community Based Foundation for Data Driven Semantic Standards in Environmental Health Sciences

Environ Health Perspect
PMCID: 4977056
PMID: 26871594
DOI: 10.1289/ehp.1510438

[…] ta entry and automated validation tools for quality control assessment were recommended as part of the toolkit. One example of a validation tool is the Annotation Sufficiency Meter () provided by the Monarch Initiative (), which leverages diverse large-scale semantically integrated data. This validation tool allows clinicians or model organism researchers to enter phenotypic data at the point of c […]


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Monarch Initiative institution(s)
Department of Medical Informatics and Epidemiology, and Oregon Health and Science University Library, Oregon Health and Science University, Portland, OR, USA; Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Germany; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, CA, USA; RTI International, Durham, NC, USA; Department of Biomedical Informatics, University of Pittsburgh, PA, USA; Wellcome Trust Sanger Institute, Cambridge, UK; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia; William Harvey Research Institute, Barts, London, UK; The London School of Medicine and Dentistry, London, UK; Queen Mary University of London, London, UK

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