The Monarch Initiative
 | This article includes a list of general references, but it lacks sufficient corresponding inline citations. (February 2018) |
| Content | |
|---|---|
| Description | Bioinformatics database of genetic disease data |
| Data types captured | genotype, phenotype, variant, disease, species |
| Organisms | Metazoa |
| Contact | |
| Primary citation | Mungall et al. 2017 |
| Release date | July 12, 2015 |
| Access | |
| Website | https://monarchinitiative.org |
The Monarch Initiative[1] is a large scale bioinformatics web resource focused on leveraging existing biomedical knowledge to connect genotypes with phenotypes in an effort to aid research that combats genetic diseases. Monarch does this by integrating multi-species genotype, phenotype, genetic variant and disease knowledge from various existing biomedical data resources into a centralized and structured database. While this integration process has been traditionally done manually by basic researchers and clinicians on a case-by-case basis, The Monarch Initiative provides an aggregated and structured collection of data and tools that make biomedical knowledge exploration more efficient and effective.
Mondo ontology
[edit]Mondo ontology is product of the Monarch Initiative and provides harmonized disease content for diseases and disorders, both rare and common.[2] The rare disease subset has been published with >10.5 rare diseases,[3] and is maintained by the community.[4]
References
[edit]- ^ Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; Balhoff, James P.; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan (2017-01-04). "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species". Nucleic Acids Research. 45 (D1): D712–D722. doi:10.1093/nar/gkw1128. ISSN 1362-4962. PMC 5210586. PMID 27899636.
- ^ Shefchek, Kent A; Harris, Nomi L; Gargano, Michael; Matentzoglu, Nicolas; Unni, Deepak; Brush, Matthew; Keith, Daniel; Conlin, Tom; Vasilevsky, Nicole; Zhang, Xingmin Aaron; Balhoff, James P; Babb, Larry; Bello, Susan M; Blau, Hannah; Bradford, Yvonne; Carbon, Seth; Carmody, Leigh; Chan, Lauren E; Cipriani, Valentina; Cuzick, Alayne; Rocca, Maria D; Dunn, Nathan; Essaid, Shahim; Fey, Petra; Grove, Chris; Gourdine, Jean-Phillipe; Hamosh, Ada; Harris, Midori; Helbig, Ingo; Hoatlin, Maureen; Joachimiak, Marcin; Jupp, Simon; Lett, Kenneth B; Lewis, Suzanna E; McNamara, Craig; Pendlington, Zoë M; Pilgrim, Clare; Putman, Tim; Ravanmehr, Vida; Reese, Justin; Riggs, Erin; Robb, Sofia; Roncaglia, Paola; Seager, James; Segerdell, Erik; Similuk, Morgan; Storm, Andrea L; Thaxon, Courtney; Thessen, Anne; Jacobsen, Julius O B; McMurry, Julie A; Groza, Tudor; Köhler, Sebastian; Smedley, Damian; Robinson, Peter N; Mungall, Christopher J; Haendel, Melissa A; Munoz-Torres, Monica C; Osumi-Sutherland, David (8 November 2019). "The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species". Nucleic Acids Research. 48 (D1): D704–D715. doi:10.1093/nar/gkz997. PMC 7056945. PMID 31701156.
- ^ Haendel, Melissa; Vasilevsky, Nicole; Unni, Deepak; Bologa, Cristian; Harris, Nomi; Rehm, Heidi; Hamosh, Ada; Baynam, Gareth; Groza, Tudor; McMurry, Julie; Dawkins, Hugh; Rath, Ana; Thaxon, Courtney; Bocci, Giovanni; Joachimiak, Marcin P. (February 2020). "How many rare diseases are there?". Nature Reviews. Drug Discovery. 19 (2): 77–78. doi:10.1038/d41573-019-00180-y. ISSN 1474-1776. PMC 7771654. PMID 32020066.
- ^ "Rare disease subset - Mondo Documentation". mondo.readthedocs.io. Retrieved 2024-09-05.
External links
[edit]- Mouse Genome Informatics
- Zebrafish Information Network
- WormBase database of nematode biology
- FlyBase
- International Mouse Phenotyping Consortium
- Mouse Phenome Database
- Online Mendelian Inheritance in Animals
- ClinVar
- Mendelian Inheritance in Man
- ORPHANET
- Protein ANalysis THrough Evolutionary Relationships Classification System
- Coriell Institute for Medical Research
- Comparative Toxicogenomics Database
- Human Phenotype Ontology
- Kyoto Encyclopedia of Genes and Genomes
- MyGene.info
- National Center for Biotechnology Information
- BioGRID
- GWAS Catalog
- AnimalQTLdb
- Ensembl database of automatically annotated genomic data
- Gene Ontology Database
- Gene Reviews
- HUGO Gene Nomenclature Committee
- Mutant Mouse Resource and Research Centers
- Reactome - a curated knowledgebase of biological pathways
- Undiagnosed Diseases Program (UDP)
- STRING
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