Awesome Parasite

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. Contents

Databases

Museums & Collections

Citizen Science Projects

Reporting Systems

Taxonomy

Scientific Journals

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.

Human Virus Database (HVD) - A database of human viruses, including information on infected tissues. See description and use in a predictive model in Ye et al. 2022

Interaction Web Data (iwdb) - 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 originally developed in 2003 by NCEAS and is now hosted by the Department of Ecology at the University of São Paulo, Brazil.

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.

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.

Shaw et al. 2020 - A human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species. Analysis published in Molecular Ecology.

Awesome Parasite

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
Museums & Collections
Citizen Science Projects
Reporting Systems
Taxonomy
Scientific Journals

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.
Human Virus Database (HVD) - A database of human viruses, including information on infected tissues. See description and use in a predictive model in Ye et al. 2022
Interaction Web Data (iwdb) - 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 originally developed in 2003 by NCEAS and is now hosted by the Department of Ecology at the University of São Paulo, Brazil.
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.
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.
Shaw et al. 2020 - A human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species. Analysis published in Molecular Ecology.