the Monarch Initiative

{{Infobox biodatabase|description=Bioinformatics database of genetic disease data|title=The Monarch Initiative|scope=genotype, phenotype, variant, disease, species|organism=Metazoa|citation=Mungall et al. 2017|url=https://monarchinitiative.org|released=July 12, 2015}}

The Monarch Initiative{{Cite journal|last1=Mungall|first1=Christopher J.|last2=McMurry|first2=Julie A.|last3=Köhler|first3=Sebastian|last4=Balhoff|first4=James P.|last5=Borromeo|first5=Charles|last6=Brush|first6=Matthew|last7=Carbon|first7=Seth|last8=Conlin|first8=Tom|last9=Dunn|first9=Nathan|date=2017-01-04|title=The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species|journal=Nucleic Acids Research|volume=45|issue=D1|pages=D712–D722|doi=10.1093/nar/gkw1128|issn=1362-4962|pmc=5210586|pmid=27899636}} 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

[https://mondo.monarchinitiative.org/ Mondo ontology] is product of the Monarch Initiative and provides harmonized disease content for diseases and disorders, both rare and common.{{cite journal |last1=Shefchek |first1=Kent A |last2=Harris |first2=Nomi L |last3=Gargano |first3=Michael |last4=Matentzoglu |first4=Nicolas |last5=Unni |first5=Deepak |last6=Brush |first6=Matthew |last7=Keith |first7=Daniel |last8=Conlin |first8=Tom |last9=Vasilevsky |first9=Nicole |last10=Zhang |first10=Xingmin Aaron |last11=Balhoff |first11=James P |last12=Babb |first12=Larry |last13=Bello |first13=Susan M |last14=Blau |first14=Hannah |last15=Bradford |first15=Yvonne |last16=Carbon |first16=Seth |last17=Carmody |first17=Leigh |last18=Chan |first18=Lauren E |last19=Cipriani |first19=Valentina |last20=Cuzick |first20=Alayne |last21=Rocca |first21=Maria D |last22=Dunn |first22=Nathan |last23=Essaid |first23=Shahim |last24=Fey |first24=Petra |last25=Grove |first25=Chris |last26=Gourdine |first26=Jean-Phillipe |last27=Hamosh |first27=Ada |last28=Harris |first28=Midori |last29=Helbig |first29=Ingo |last30=Hoatlin |first30=Maureen |last31=Joachimiak |first31=Marcin |last32=Jupp |first32=Simon |last33=Lett |first33=Kenneth B |last34=Lewis |first34=Suzanna E |last35=McNamara |first35=Craig |last36=Pendlington |first36=Zoë M |last37=Pilgrim |first37=Clare |last38=Putman |first38=Tim |last39=Ravanmehr |first39=Vida |last40=Reese |first40=Justin |last41=Riggs |first41=Erin |last42=Robb |first42=Sofia |last43=Roncaglia |first43=Paola |last44=Seager |first44=James |last45=Segerdell |first45=Erik |last46=Similuk |first46=Morgan |last47=Storm |first47=Andrea L |last48=Thaxon |first48=Courtney |last49=Thessen |first49=Anne |last50=Jacobsen |first50=Julius O B |last51=McMurry |first51=Julie A |last52=Groza |first52=Tudor |last53=Köhler |first53=Sebastian |last54=Smedley |first54=Damian |last55=Robinson |first55=Peter N |last56=Mungall |first56=Christopher J |last57=Haendel |first57=Melissa A |last58=Munoz-Torres |first58=Monica C |last59=Osumi-Sutherland |first59=David |title=The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species |journal=Nucleic Acids Research |date=8 November 2019 |volume=48 |issue=D1 |pages=D704–D715 |doi=10.1093/nar/gkz997 |pmid=31701156 |pmc=7056945 |ref=fg|doi-access=free }} The rare disease subset has been published with >10.5 rare diseases,{{Cite journal |last1=Haendel |first1=Melissa |last2=Vasilevsky |first2=Nicole |last3=Unni |first3=Deepak |last4=Bologa |first4=Cristian |last5=Harris |first5=Nomi |last6=Rehm |first6=Heidi |last7=Hamosh |first7=Ada |last8=Baynam |first8=Gareth |last9=Groza |first9=Tudor |last10=McMurry |first10=Julie |last11=Dawkins |first11=Hugh |last12=Rath |first12=Ana |last13=Thaxon |first13=Courtney |last14=Bocci |first14=Giovanni |last15=Joachimiak |first15=Marcin P. |date=February 2020 |title=How many rare diseases are there? |journal=Nature Reviews. Drug Discovery |volume=19 |issue=2 |pages=77–78 |doi=10.1038/d41573-019-00180-y |issn=1474-1776 |pmc=7771654 |pmid=32020066}} and is maintained by the community.{{Cite web |title=Rare disease subset - Mondo Documentation |url=https://mondo.readthedocs.io/en/latest/editors-guide/rare-disease-subset/ |access-date=2024-09-05 |website=mondo.readthedocs.io}}

References

External links

[http://www.informatics.jax.org/ Mouse Genome Informatics]
[http://zfin.org/ Zebrafish Information Network]
[http://www.wormbase.org/ WormBase database of nematode biology]
[http://flybase.org/ FlyBase]
[http://www.mousephenotype.org International Mouse Phenotyping Consortium]
[http://phenome.jax.org/ Mouse Phenome Database]
[http://omia.angis.org.au/ Online Mendelian Inheritance in Animals]
[https://www.ncbi.nlm.nih.gov/clinvar/ ClinVar]
[http://omim.org Mendelian Inheritance in Man]
[http://www.orpha.net ORPHANET]
[http://www.pantherdb.org/ Protein ANalysis THrough Evolutionary Relationships Classification System]
[http://ccr.coriell.org/ Coriell Institute for Medical Research]
[http://www.ctdbase.org Comparative Toxicogenomics Database]
[https://human-phenotype-ontology.github.io Human Phenotype Ontology]
[http://www.genome.ad.jp/kegg/ Kyoto Encyclopedia of Genes and Genomes]
[http://mygene.info/v2/query?q= MyGene.info]
[https://www.ncbi.nlm.nih.gov/ National Center for Biotechnology Information]
[http://www.thebiogrid.org BioGRID]
[http://www.ebi.ac.uk/gwas/ GWAS Catalog]
[http://www.animalgenome.org AnimalQTLdb]
[http://www.ensembl.org/ Ensembl database of automatically annotated genomic data]
[http://amigo.geneontology.org/ Gene Ontology Database]
[https://www.ncbi.nlm.nih.gov/books/NBK1116/ Gene Reviews]
[https://www.genenames.org/ HUGO Gene Nomenclature Committee]
[http://www.mmrrc.org Mutant Mouse Resource and Research Centers]
[http://www.reactome.org/ Reactome - a curated knowledgebase of biological pathways]
[https://www.genome.gov/27544402/the-undiagnosed-diseases-program/ Undiagnosed Diseases Program (UDP)]
[http://string-db.org STRING]

Category:Biological databases

Category:Ontology (information science)