Parasite

Awesome Parasite Awesome =========

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.

Awesome parasite was created by Anna Willoughby and is maintained in partnership with EcoHealth Alliance. Contributions welcome, please read the contributing guidelines.


Databases

  • Arbovirus Catalog (ARBOCAT) - The CDC-curated arbovirus information including dates of first isolation and wildlife hosts.
  • Arctos - A collective management database for museum specimens. See below for specific collections. Data includes locality and collection dates, and is downloadable for any registered accounts.
  • Benesh et al. 2017, Ecology - Extensive database with 8,510 host species associations of parasites with complex life cycles (acanthocephalans, cestodes, and nematodes). Includes life‐history data such as development time and body size for each life cycle stage of the parasites.
  • ENHanCEd Infectious Diseases Database (EID2) - A database that pulls organism associations from NCBI sequences and PubMed. See database and brief analysis in Wardeh et al. 2015.
  • Global Biotic Interactions (GloBI) - A species interaction repository that can be searched by 'parasite of', 'pathogen of', or 'host of'.
  • Global Mammal Parasite Database 2.0 - A database of the parasites of wild ungulates (artiodactyls and perissodactyls), carnivores, and primates.
  • 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.
  • MalAvi - A database of avian blood parasites from the Plasmodium, Haemoproteus and Leucocytozoon genera including select host and vector information. See database description by Bensch et al. 2009.
  • NCEAS Interaction Web data - Collation of fish host and parasites datasets from several Canadain liminological sites, including information on prevalence and intensity. Part of a larger database of species interactions in food webs and plant relationships.
  • NHM Host-parasite database - A database of parasitic worms extracted from the scientific literature maintained by London Natural History Museum. Compilation started in 1922 by Dr H.A. Baylis, with curation through 2003 by LNHM staff. Wells et al. 2018 provides a broad analysis of this database, and you can access data through the R package helminthR.
  • Olival et al. 2017, Nature - Mammal-virus database with analysis.
  • PEARL - Conservation assessments of macroparasitic invertebrates.
  • 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.
  • 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.
  • Virus-Host DB - A synthesis of host-virus associations from genomes posted in NCBI/RefSeq and GenBank.

Museums & Collections

Citizen Science Projects

  • Garden Wildlife Health - This is a UK collaborative project between the Zoological Society of London (ZSL), the British Trust for Ornithology (BTO), Froglife and the Royal Society for the Protection of Birds (RSPB) that historically has been running since the 1980's (previously as Garden Bird Health initiative and Frog Mortality Project). Citizens can submit sickness and mortality reports, as well as animal wildlife samples, for wild birds, amphibians, reptiles, and hedgehogs.
  • Project Monarch Health - A citizen science project running since 2006 to test adult monarch butterflies from the U.S. and Canada for the protozoan parasite Ophryocystis elektroscirrha. Participants submit spore samples collected from adult abdomems with tape for laboratory assessment at University of Georgia.

Reporting Systems

  • 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. EIDR-Connect parses ProMed reports into disease outbreak events, curated by disease experts.
  • The Contagion Outbreak Monitor - An interactive map of human bloodborne or foodborne outbreaks in the past two years. Targeted to practitioners and clinicians.
  • WHISPers - Wildlife Health Information Sharing Partnership event reporting system managed by USGS National Wildlife Health Center. Events of North American wildlife mortality (death) and morbidity (illness) involving five or more individuals are reported.
  • 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.

Taxonomy

  • GBIF Backbone Taxonomy - Aggregation and synonymization of taxonomy for animals, bacteria, protozoa, and viruses that synthesizes 56 taxonomy sources.
  • 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 rredlist and the API to access the data directly.
  • 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.

Scientific Journals

License

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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.