Items referring to sequence-level data, including genomics, microbiomics, proteomics, etc.

molecular

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.

non-collection specific

(Simple) Released

JSON

FASTA

English

GNU AGPL v3

Charlton Callender

James Hadfield

Trevor Bedford

ORCID

Barney Potter

Jover Lee

Sarah Murata

Richard Neher

Eden Berga

Louise H Moncla

John Huddleston

fauna

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.

Influenza B virus

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.

Severe acute respiratory syndrome coronavirus 2

SARS-CoV2

Information about diagnostic tests, results, including serology tests, PCR, and other tests

diagnostic tests

Tests

An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.

host organism

Host

Homo sapiens

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.

human respiratory syncytial virus

The type species of MORBILLIVIRUS and the cause of the highly infectious human disease MEASLES, which affects mostly children.

Measles morbillivirus

Measles virus

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.

Influenza A virus

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.

Dengue virus

sequence collection

Sequence Collection

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.

Ebolavirus

The type species of RUBULAVIRUS that causes an acute infectious disease in humans, affecting mainly children. Transmission occurs by droplet infection.

Mumps orthorubulavirus

Mumps virus

 A count of simulated or physical individuals in a population.

Population count

Population Count

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.

Zika virus

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.

Viruses

An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.

pathogen

Pathogen

A collection of information in various types of structured or non-structured formats.

repository

The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability

about-property-structure

Apache 2.0

Schema.org vocabulary for structured data on the web

Schema.org

A structured data markup specification for describing datasets in the life sciences, extending schema.org Dataset

Bioschemas Dataset Profile

Dublin Core Metadata Initiative Terms - refined elements for precise resource description

DCMI Metadata Terms

W3C Data Catalog Vocabulary for describing data catalogs

Data Catalog Vocabulary

DataCite metadata schema for research data citation

DataCite Metadata Schema

W3C Provenance Ontology for describing provenance information

PROV Ontology

Provenance, Authoring and Versioning ontology for metadata about web resources

PAV Ontology

Custom MIDAS vocabulary for epidemiological data and modeling

MIDAS Metadata Vocabulary

OBO Foundry ontologies for life sciences and biomedical research

Open Biological and Biomedical Ontology

Health Level 7 Fast Healthcare Interoperability Resources

HL7 FHIR

Systematized Nomenclature of Medicine Clinical Terms

SNOMED Clinical Terms

LOINC database for laboratory and clinical observations

Logical Observation Identifiers Names and Codes

JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records

MIDAS Catalog JSON-LD Schema

Landing page where users can browse and download dataset files in various formats.

Identifier	URL: https://github.com/nextstrain/fauna
Type	Repository
Topics/About	Host Homo sapiens Pathogen Viruses Dengue virus Ebolavirus human respiratory syncytial virus Influenza A virus Influenza B virus Measles virus Mumps virus SARS-CoV2 Zika virus Population Count Tests Sequence Collection
Language	English
License	GNU AGPL v3
Accessible For Free	TRUE
Biological Scale	molecular
File Format	JSON, FASTA, PYP
Version	unspecified
HTTP Status Code	200
HTTP Checked On	2026/02/22