The Genomic Epidemiology of Monkeypox Dashboard contains phylogenetic trees that can be displayed by clades, sampling dates, genotypes, regions, countries, hosts, genomic composition, etc of the monkeypox virus. The output is visible with a phylogenic tree, on a map, and with a graph of sequence diversity and is available in multiple languages. The phylogenetic tree (NEXUS, NWK, SVG) and the metadata (TSV) are downloadable in multiple formats. Link to curated sequences and metadata, andpPairwise alignments with Nextclade against the reference sequence MPXV-M5312_HM12_Rivers, insertions relative to the reference, and translated ORFs are also available The data here focuses on recent viruses transmitting from human-to-human and includes viruses belonging to the hMPXV1 clade as denoted by Happi et al. They conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year). All source code for Nextstrain is freely available under the terms of an open-source license, typically AGPL-3.0 or MIT. Refer to specific projects for details. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.
Schema.org vocabulary for structured data on the web
A structured data markup specification for describing datasets in the life sciences, extending schema.org Dataset
Dublin Core Metadata Initiative Terms - refined elements for precise resource description
W3C Data Catalog Vocabulary for describing data catalogs
DataCite metadata schema for research data citation
W3C Provenance Ontology for describing provenance information
Provenance, Authoring and Versioning ontology for metadata about web resources
Custom MIDAS vocabulary for epidemiological data and modeling
OBO Foundry ontologies for life sciences and biomedical research
Health Level 7 Fast Healthcare Interoperability Resources
Systematized Nomenclature of Medicine Clinical Terms
Logical Observation Identifiers Names and Codes
LOINC database for laboratory and clinical observations
A disease whose physical basis is an infectious disorder
A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy.
An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
A species of ORTHOPOXVIRUS that is the etiological agent of MPOX, MONKEYPOX.
Infection by an etiologic agent that can be passed between animals and humans.
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
Construction and/or visualization of phylogenetic trees based on sequence data
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.
A collection of discontinuous sequences.
Landing page where users can browse and download dataset files in various formats.
National Institute of General Medical Sciences
TreeTime: Maximum-likelihood phylodynamic analysis
Nextstrain: real-time tracking of pathogen evolution
Nextstrain. Genomic epidemiology of monkeypox virus. 2022. Available from: https://nextstrain.org/monkeypox/hmpxv1
The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability