Data we accept

PHAROS collects data on pathogen testing or parasite sampling in wild animals, with a standardized format that captures taxonomic data and geospatial metadata. We particularly encourage you to submit negative data, i.e., lack of detection of a particular parasite or pathogen.

Data requirements

Data submitted to PHAROS must:

  • Be collected from wild animals

  • Include information on host and pathogen identity (not necessarily to species level)

  • Include a location in longitude-latitude format

  • Include a complete date

  • Be yours

Examples of data we accept

Example projects that could contribute data would include:

  • A longitudinal dataset that captures seven years of repeat sampling for rabies virus in cave-dwelling bats

  • A descriptor of the first frog recorded with a newly-discovered fungal infection

  • A negative test for rabies for an opportunistically-collected raccoon carcass

  • Regular screening of fecal samples for parasites in a monitored ungulate population

  • Hantavirus screening in urban rats during an investigation of a human outbreak

  • Ticks tested for Lyme disease and viral pathogens after being removed from trapped rodents in a forest-suburb mosaic

Data we don't accept

  • Human clinical data. We do not accept any data on human disease surveillance. We encourage you to consider whether the project to build an open database of human epidemiological line data would be appropriate for your needs.

  • Livestock or companion animal disease data. At this time, we don't accept data on any captive, domestic, or livestock animal disease. These tend to fall under the jurisdiction of the World Organization for Animal Health, which shares data submitted by member states through the WAHIS system. Data on feral cats, dogs, or other domesticated species is currently permissible.

  • Animal disease in captivity. No experimental infections in laboratory settings, infection data from zoo animals, wildlife trade supply chain data, etc.

  • Data on livestock select agents. We ask that you not deposit any original data (i.e., data not already published elsewhere) for any animal pathogens on the USDA Veterinary Services list of Select Agents.

  • Pathogen genetic or genomic sequence data. There are other repositories that are more appropriate for these data, and we strongly encourage you to deposit data in submissions that are cross-linked. Any nucleotide sequence can be deposited in NCBI's GenBank database; some pathogen sequence data (e.g., for influenza, SARS-CoV-2, and monkeypox) can also be deposited in GISAID. Metagenomic or metatranscriptomic data - including any samples meant to describe an entire animal microbiome - should be deposited in the NCBI Sequence Read Archive.

  • Data on pathogen free-living stages or most environmental samples. These are appropriate for several other databases, including GBIF. All records submitted to PHAROS should include an association with a host; do not submit data that document occurrences of e.g., questing ticks, hunting leeches, soil samples of environmentally-persistent bacteria, etc. Exceptions on environmental samples can be made if host associations are still known (e.g., parasites in nest boxes, or fecal samples from monitored animal populations).

  • Data you've digitized from the literature or accessed from other public sources (that isn't yours). For now, we're not allowing data rescue or digitization projects into PHAROS. This is an ethics question, not a feasibility question: We're currently deciding the best way to recover large quantities of data from the published literature, while also honoring the principles around credit and equity that have shaped our approach. We will seek input from the community on this issue in the future, and may eventually develop a revised policy.