A curated list of amazingly awesome information and open-access databases related to parasites and host-pathogen interactions.
Parasites are unique organisms studied in a variety of disciplines due to their health burden, diversity, and complex ecologies.
- Olival et al. 2017 - Mammal-virus database with analysis.
- PREDICT - Field data from the USAID PREDICT project 2008-2019, a global emerging virus surveillance program. This data is downloadable if you have a healthmap account.
- Global Mammal Parasite Database 2.0- A database of the parasites of wild ungulates (artiodactyls and perissodactyls), carnivores, and primates.
- PEARL - Conservation assessments of macroparasitic invertebrates.
- Virus-Host DB - A synthesis of host-virus associations from genomes posted in NCBI/RefSeq and GenBank.
- NHM Host-parasite database - A database of parasitic worms maintained by London Natural History Museum. Wells et al. 2018 provides a broad analysis of this database, and you can access data through the R package helmithR.
- Arctos - A collective management database for museum specimens. This contains parasite samples from Denver Museum of Nature and Science, Harold W. Manter Laboratory of Parasitology Collection, Museum of Southwestern Biology, and the U.S. National Parasite Collection. Data includes locality and collection dates, and is downloadable for any registered accounts.
- ENHanCEd Infectious Diseases Database (EID2) - A database that pulls organism associations from NCBI sequences and PubMed.
- Arbovirus Catalog (ARBOCAT) - The CDC-curated arbovirus information including dates of first isolation and wildlife hosts.
- Global Biotic Interactions (GloBI) - A species interaction repository that can be searched by 'parasite of', 'pathogen of', or 'host of'.
- DBatVir - A bat virus database curated from Genbank with host traits and summaries by location.
- DRodVir - A rodent virus database curated from Genbank with host traits.
- PHI-base - A database with information on specific genes of fungal, Oomycete and bacterial pathogens that affect pathogenicity. Focused on agricultural and medical pathogens of importance.
- World Animal Health Information System (WAHIS) - The OIE archive of country alerts and regular reports of certain pathogens. They also have some nice interfaces to show disease distribution and timelines.
- Healthmap - A web platform that provides infectious disease outbreak alerts for humans and animals.
- Program for Monitoring Emerging Diseases (ProMed) - An early warning of outbreaks of emerging and re-emerging diseases. Sources of information include media reports, official reports, online summaries, local observers, and others.
- NCBI Taxonomy - The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases, both parasites and hosts.
- ICTV - The viral taxonomy authority with excellent archives and open reports.
- IUCN Redlist - Online database that provides taxonomic information for wild hosts. You can use the R package
rredlistand the API to access the data directly.
- Journal of Wildlife Diseases - JWD provides many open-access articles on new parasite expansions or discoveries.
- American Journal of Tropical Medicine and Hygiene - AJTMH publishes a broad range of papers covering topics in tropical medicine. Their archive is open-access after a 12-month embargo.
- Emerging Infectious Diseases - The CDC open-access journal.
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