The fauna database stores viral sequences and serological data in RethinkDB. The current database and scripts are designed around influenza, Ebola and Zika viruses, but with the intention of provided a general purpose tool.
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
JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records
A collection of information in various types of structured or non-structured formats.
A contagious viral infection caused by the mumps virus. Symptoms include swollen and tender parotid glands, fever, muscle aches and fatigue. Due to vaccination programs, mumps has become a rare disease.
Dengue fever (DF), caused by dengue virus, is an arboviral disease characterized by an initial non-specific febrile illness that can sometimes progress to more severe forms manifesting capillary leakage and hemorrhage (dengue hemorrhagic fever, or DHF) and shock (dengue shock syndrome, or DSS).
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.
Mosquito-born virus disease characterized by a clinical course that may be asymptomatic or mild with fever, conjunctivitis, muscle and joint pain, headache, exanthema, but may also be associated with severe neurological (meningitis, meningoencephalitis and myelitis) and auto-immune (Guillain-Barre syndrome) complications, as well as a potential increase of birth defects (microcephaly) if the infection occurs during pregnancy.
An acute viral infection of the respiratory tract, occurring in isolated cases, in epidemics, or in pandemics; it is caused by serologically different strains of viruses (influenzaviruses) designated A, B, and C, has a 3-day incubation period, and usually lasts for 3 to 10 days. It is marked by inflammation of the nasal mucosa, pharynx, and conjunctiva; headache; myalgia; often fever, chills, and prostration; and occasionally involvement of the myocardium or central nervous system.
An arbovirus in the FLAVIVIRUS genus of the family FLAVIVIRIDAE. Originally isolated in the Zika Forest of UGANDA it has been introduced to Asia and the Americas.
Vaccine preventable diseases are those infectious diseases that can be prevented by vaccination
A highly contagious viral infection caused by the measles virus. Symptoms appear 8-12 days after exposure and include a rash, cough, fever and muscle pains that can last 4-7 days. Measles vaccines are available to provide prophylaxis, usually combined with mumps and rubella vaccines (MMR).
Severe acute respiratory syndrome coronavirus 2
A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis.
The type species of the genus ALPHAINFLUENZAVIRUS that causes influenza and other diseases in humans and animals. Antigenic variation occurs frequently between strains, allowing classification into subtypes and variants. Transmission is usually by aerosol (human and most non-aquatic hosts) or waterborne (ducks). Infected birds shed the virus in their saliva, nasal secretions, and feces.
A viral hemorrhagic fever that is caused by the Ebola virus, which is transmitted by contact with infected animals or humans; it is characterized by high fever, unexplained bleeding, and a high mortality rate.
A respiratory tract infection caused by a virus. Viruses represent the most common causes of upper and lower respiratory tract infections and include rhinoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial virus.
An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
An infectious disease where a pathogen is carried and transmitted by another organism that acts as disease vector.
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.
A collection of discontinuous sequences.
Unidentified influenza virus is a species of ssRNA(-) virus in the family Orthomyxoviridae.
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 disease whose physical basis is an infectious disorder
A count of simulated or physical individuals in a population.
A genus in the family FILOVIRIDAE consisting of several distinct species of Ebolavirus, each containing separate strains. These viruses cause outbreaks of a contagious, hemorrhagic disease (HEMORRHAGIC FEVER, EBOLA) in humans, usually with high mortality.
The type species of RUBULAVIRUS that causes an acute infectious disease in humans, affecting mainly children. Transmission occurs by droplet infection.
A viral infectious disease caused by RNA viruses in the Arenaviridae, Bunyaviridae, Filoviridae, or Flaviviridae family, and characterized by a severe multisystem syndrome, with damage to the vascular system and hemorrhaging.
Infection by an etiologic agent that can be passed between animals and humans.
The type species of PNEUMOVIRUS and an important cause of lower respiratory disease in infants and young children. It frequently presents with bronchitis and bronchopneumonia and is further characterized by fever, cough, dyspnea, wheezing, and pallor.
The type species of MORBILLIVIRUS and the cause of the highly infectious human disease MEASLES, which affects mostly children.
A species of the genus FLAVIVIRUS which causes an acute febrile and sometimes hemorrhagic disease in man. Dengue is mosquito-borne and four serotypes are known.
Species of the genus BETAINFLUENZAVIRUS that cause HUMAN INFLUENZA and other diseases primarily in humans. Antigenic variation is less extensive than in type A viruses (INFLUENZA A VIRUS) and consequently there is no basis for distinct subtypes or variants. Epidemics are less likely than with INFLUENZA A VIRUS and there have been no pandemics. Previously only found in humans, Influenza B virus has been isolated from seals which may constitute the animal reservoir from which humans are exposed.
Neglected tropical diseases (NTDs) are a diverse group of conditions caused by a variety of pathogens (including viruses, bacteria, parasites, fungi and toxins) and associated with devastating health, social and economic consequences.
Information about diagnostic tests, results, including serology tests, PCR, and other tests
Landing page where users can browse and download dataset files in various formats.
National Institute of General Medical Sciences
Trevor Bedford, Charlton Callender, Barney Potter, Jover Lee, James Hadfield, Louise H Moncla, John Huddleston, Richard Neher, Sarah Murata, Eden Berga. nextstrain: fauna. 2021. Available from: https://github.com/nextstrain/fauna
The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability