awesome-awesomeness/html/parasite.html

<h1 id="awesome-parasite-awesome">Awesome Parasite <a
href="https://awesome.re"><img src="https://awesome.re/badge.svg"
alt="Awesome" /></a></h1>
<blockquote>
<p>A curated list of amazingly awesome information and open-access
databases related to parasites and host-pathogen interactions.</p>
</blockquote>
<p>Parasites are unique organisms studied in a variety of disciplines
due to their health burden, diversity, and complex ecologies.</p>
<p>Awesome parasite was created by <a
href="https://arw36.github.io/">Anna Willoughby</a> and is maintained in
partnership with <a href="www.ecohealthalliance.org">EcoHealth
Alliance</a>. Contributions welcome, please read the <a
href="contributing.md">contributing guidelines</a>.</p>
<h2 id="contents">Contents</h2>
<ul>
<li><a href="#databases">Databases</a></li>
<li><a href="#museums-collections">Museums &amp; Collections</a></li>
<li><a href="#citizen-science-projects">Citizen Science
Projects</a></li>
<li><a href="#reporting-systems">Reporting Systems</a></li>
<li><a href="#taxonomy">Taxonomy</a></li>
<li><a href="#scientific-journals">Scientific Journals</a> - - - ##
Databases</li>
<li><a href="https://wwwn.cdc.gov/arbocat/">Arbovirus Catalog
(ARBOCAT)</a> - The CDC-curated arbovirus information including dates of
first isolation and wildlife hosts.</li>
<li><a
href="http://arctos.database.museum/SpecimenSearch.cfm">Arctos</a> - 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.</li>
<li><a
href="https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.1680">Benesh
et al. 2017, Ecology</a> - 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.</li>
<li><a href="https://eid2.liverpool.ac.uk/">ENHanCEd Infectious Diseases
Database (EID2)</a> - A database that pulls organism associations from
NCBI sequences and PubMed. See database and brief analysis in <a
href="https://www.nature.com/articles/sdata201549">Wardeh et
al. 2015</a>.</li>
<li><a href="https://www.globalbioticinteractions.org/data.html">Global
Biotic Interactions (GloBI)</a> - A species interaction repository that
can be searched by ‘parasite of’, ‘pathogen of’, or ‘host of’.</li>
<li><a
href="https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.1799">Global
Mammal Parasite Database 2.0</a> - A database of the parasites of wild
ungulates (artiodactyls and perissodactyls), carnivores, and
primates.</li>
<li><a href="http://computationalbiology.cn/humanVirusBase/#/">Human
Virus Database (HVD)</a> - A database of human viruses, including
information on infected tissues. See description and use in a predictive
model in <a
href="https://academic.oup.com/bioinformatics/article-abstract/38/11/3087/6569817?redirectedFrom=fulltext">Ye
et al. 2022</a></li>
<li><a
href="https://iwdb.nceas.ucsb.edu/resources.html#host_parasite">Interaction
Web Data (iwdb)</a> - 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.</li>
<li><a href="http://130.235.244.92/Malavi/">MalAvi</a> - A database of
avian blood parasites from the Plasmodium, Haemoproteus and
Leucocytozoon genera including select host and vector information. See
database description by <a
href="https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1755-0998.2009.02692.x">Bensch
et al. 2009</a>.</li>
<li><a
href="http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/">NHM
Host-parasite database</a> - 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. <a
href="http://nicholasjclark.weebly.com/uploads/4/4/9/4/44946407/wells_etal_2018_globchangbiol.pdf">Wells
et al. 2018</a> provides a broad analysis of this database, and you can
access data through the R package <a
href="https://github.com/ropensci/helminthR">helminthR</a>.</li>
<li><a href="https://zenodo.org/record/807517#.Wv7kuFMvzOQ">Olival et
al. 2017, Nature</a> - Mammal-virus database with <a
href="https://www.nature.com/articles/nature22975?sf90794030">analysis</a>.</li>
<li><a href="http://pearl.berkeley.edu/">PEARL</a> - Conservation
assessments of macroparasitic invertebrates.</li>
<li><a href="http://www.phi-base.org/index.jsp">PHI-base</a> - A
database with information on specific genes of fungal, Oomycete and
bacterial pathogens that affect pathogenicity. Focused on agricultural
and medical pathogens of importance.</li>
<li><a href="http://data.predict.global/">PREDICT</a> - 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.</li>
<li><a
href="https://figshare.com/articles/The_phylogenetic_range_of_bacterial_and_viral_pathogens_of_vertebrates_dataset_and_supplementary_material/8262779">Shaw
et al. 2020</a> - 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. <a
href="https://onlinelibrary.wiley.com/doi/10.1111/mec.15463">Analysis</a>
published in Molecular Ecology.</li>
<li><a href="http://www.genome.jp/virushostdb/view/">Virus-Host DB</a> -
A synthesis of host-virus associations from genomes posted in
NCBI/RefSeq and GenBank.</li>
<li><a href="https://www.web-of-life.es/">Web of Life</a> - An
aggregated resource and graphical user interface for easily visualizing
and downloading data on ecological networks, including host-parasite
interactions. As of January 2024, the host-parasite communities are
exclusively gleaned from <a
href="https://www.journals.uchicago.edu/doi/full/10.1086/674445">Hadfield
et al. 2013</a> whose original data files are provided on <a
href="https://datadryad.org/stash/dataset/doi:10.5061/dryad.jf3tj">Dryad</a>.</li>
<li><a href="http://www.mgc.ac.cn/cgi-bin/ZOVER/main.cgi">Zover</a> - A
conglomeration of the previous bat (<a
href="www.mgc.ac.cn/DBatVir">DBatVir</a>) and rodent virus (<a
href="http://www.mgc.ac.cn/DRodVir/">DRodVir</a>) databases with the
addition of mosquito- and tick- borne viruses. Database is described <a
href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab862/6389491?login=true">here</a>.</li>
</ul>
<h2 id="museums-collections">Museums &amp; Collections</h2>
<ul>
<li><a
href="https://portal.fiocruz.br/en/biological-collections">Biological
Collections of Oswaldo Cruz Institute in Rio de Janeiro, Brazil</a> -
scientific institution with the largest <a
href="http://chioc.fiocruz.br/catalogue">helminth collection</a> in
Latin America with nearly 40,000 specimens. The institute also houses
several other open-access catalogues of <a
href="http://colprot.fiocruz.br/index?catalogue">protozoa</a> and <a
href="http://cavaisc.fiocruz.br/catalogue">medically important vector
species</a>.</li>
<li><a
href="https://science.dmns.org/integrative-collections/dmns-zoology-collections/">Denver
Museum of Nature and Science</a> - Collection of mammalian ecto- and
endo- parasites primarily focused on the Rocky Mountain and Great Plains
regions of the United States. Accessible through <a
href="http://arctos.database.museum/SpecimenSearch.cfm">Arctos</a>.</li>
<li><a href="http://hwml.unl.edu/resources/database-68">Harold W. Manter
Laboratory of Parasitology Collection</a> - Specimen collection focused
“on the helminth parasites of mammals of the Nearctic and Neotropical
regions stressing studies of the phylogeny and diversity of parasites of
Rodentia, Marsupialia, Xenarthra, and Chiroptera.” The archive site for
the <a href="https://www.amsocparasit.org/">American Society of
Parasitologists</a>. Accessible through <a
href="http://arctos.database.museum/SpecimenSearch.cfm">Arctos</a>.</li>
<li><a
href="https://www.nrm.se/english/researchandcollections/zoology/collections/invertebrates.305_en.html">Invertebrates
Collection of the Swedish Museum of Natural History</a> - Swedish Museum
with collection of &gt;10,000 flatworms, &gt;2,000 nematodes, and select
other parasite groups. Accessible through <a
href="https://www.gbif.org/dataset/56aa0680-0c60-11dd-84cd-b8a03c50a862">GBIF</a>.</li>
<li><a
href="https://www.depts.ttu.edu/nsrl/collections/Invertebrate_Zoology/index.php">Invertebrate
Zoology collection of the Museum of Texas Tech University</a> -
Previously the Medical Zoology Collection, a portion of this collection
includs endo- and ecto-parasites of medical and veterinary importance.
Accessible through <a
href="https://www.gbif.org/dataset/13fdfab7-e281-428d-8c1f-e72eb7398e97">GBIF</a>.</li>
<li><a href="https://www.kiseichu.org/e-top">Meguro Parasite Museum</a>
- Museum in Tokyo, Japan focused on human parasites with over 60,000
specimens. Data is not digitized, though the museum’s founder, Dr. S.
Yamaguti, described many of the specimens in 10 volumes of <a
href="https://www.worldcat.org/title/systema-helminthum/oclc/427905372/editions?editionsView=true&amp;referer=br">Systema
Helminthum</a>. Collections primarily from Japan, Indonesia and
Hawaii.</li>
<li><a
href="https://www.mnhn.fr/en/collections/collection-groups/marine-invertebrates/parasitic-worms-helminths">Muséum
National d’Histoire Naturelle (MNHN - Paris)</a> - Helminth collection
with more than 30,000 occurences of helminths with particular focus in
tropical regions. Accessible through <a
href="https://www.gbif.org/dataset/e0ebf2a1-3656-468a-b0b6-1aa93ff43fef#description">GBIF</a>.</li>
<li><a href="https://msb.unm.edu/divisions/parasites/index.html">Museum
of Southwestern Biology, Division of Parasites</a> - Specimen collection
of parasites amphibians, reptiles, birds, and mammals. Particular focus
on parasites of small mammals in high altidude locations and Sevilleta
Long Term Ecological Research Station in New Mexico, and parasites of
seabirds in the artic and Antartica. Accessible through <a
href="http://arctos.database.museum/SpecimenSearch.cfm">Arctos</a>.</li>
<li><a href="https://acarology.osu.edu/database">Ohio State University
Acarology Collection</a> - Nearly 70,000 vouchered specimens of mites
from around the globe starting from 1864. Information includes host
species, collection gps points, collection location (e.g. ear), and
collection method. Can also be accessed through <a
href="https://www.gbif.org/dataset/96b54e8c-f762-11e1-a439-00145eb45e9a">GBIF</a>.</li>
<li><a
href="http://www.samuseum.sa.gov.au/collections/biological-sciences/parasites/the-australian-helminthological-collection-database">South
Australian Museum’s Australian Helminthological Collection</a> -
Downloadable excel document of nearly 50,000 specimens of helminths
primarily from Australian vertebrates. Most specimens are
Platyhelminths, Acanthocephala, or Nematoda from mammals, birds, or
Elasmobranchii. Some specimens are included in the <a
href="http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/">LNHM
database</a> and accessible through <a
href="https://github.com/ropensci/helminthR">helminthR</a>.</li>
<li><a href="http://www.outbreakmuseum.com">The International Outbreak
Museum</a> - Museum focused on human food-borne outbreaks, with each <a
href="http://www.outbreakmuseum.com/exhibits/">exhibit</a> being a
different historical outbreak. Part of <a
href="https://health.oregonstate.edu/fomes">The Northwest Center for
Foodborne Outbreak Management, Epidemiology, and Surveillance</a>.</li>
<li><a
href="https://www.nal.usda.gov/exhibits/speccoll/exhibits/show/parasitic-diseases-with-econom/u-s--national-animal-parasite-">U.S.
National Parasite Collection</a> - Specimen collection maintained by
USDA that focuses on agriculturally important helminths and protozoans
from North America. Accessible through <a
href="http://arctos.database.museum/SpecimenSearch.cfm">Arctos</a>.</li>
</ul>
<h2 id="citizen-science-projects">Citizen Science Projects</h2>
<ul>
<li><a href="https://www.gardenwildlifehealth.org">Garden Wildlife
Health</a> - 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.</li>
<li><a href="https://www.monarchparasites.org/">Project Monarch
Health</a> - A citizen science project running since 2006 to test adult
monarch butterflies from the U.S. and Canada for the protozoan parasite
<em>Ophryocystis elektroscirrha</em>. Participants submit spore samples
collected from adult abdomems with tape for laboratory assessment at
University of Georgia.</li>
</ul>
<h2 id="reporting-systems">Reporting Systems</h2>
<ul>
<li><a href="https://empres-i.apps.fao.org/">EMPRES-i+ Global Animal
Disease Information System</a> - A web platform maintained by FAO that
provides geolocated data on animal diseases such as rabies,
foot-and-mouth disease, or MERS coronavirus. This is a tracking service
in which countries and veterinarians can opt-in to reporting.<br />
</li>
<li><a href="https://www.healthmap.org/en/">Healthmap</a> - A web
platform that provides infectious disease outbreak alerts for humans and
animals.</li>
<li><a href="https://wwwn.cdc.gov/norsdashboard/">NORS</a> - A web
platform that provides human foodborne, waterborne, and other enteric
infectious disease outbreaks for the United States. Available from
1971.</li>
<li><a href="http://www.promedmail.org/">Program for Monitoring Emerging
Diseases (ProMed)</a> - 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. <a
href="https://eidr-connect.eha.io/events/auto">EIDR-Connect</a> parses
ProMed reports into disease outbreak events, curated by disease
experts.</li>
<li><a href="https://www.contagionlive.com/outbreak-monitor">The
Contagion Outbreak Monitor</a> - An interactive map of human bloodborne
or foodborne outbreaks in the past two years. Targeted to practitioners
and clinicians.</li>
<li><a href="https://whispers.usgs.gov/">WHISPers</a> - 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.</li>
<li><a
href="http://www.oie.int/wahis_2/public/wahid.php/Diseaseinformation/reportarchive">World
Animal Health Information System (WAHIS)</a> - The OIE archive of
country alerts and regular reports of certain pathogens. They also have
some nice interfaces to show disease distribution and timelines.</li>
</ul>
<h2 id="taxonomy">Taxonomy</h2>
<ul>
<li><a
href="https://www.gbif.org/en/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c">GBIF
Backbone Taxonomy</a> - Aggregation and synonymization of taxonomy for
animals, bacteria, protozoa, and viruses that synthesizes 56 taxonomy
sources.</li>
<li><a href="https://talk.ictvonline.org/taxonomy/">ICTV</a> - The viral
taxonomy authority with excellent archives and <a
href="https://talk.ictvonline.org/ictv-reports/">open reports</a>.</li>
<li><a href="http://www.iucnredlist.org/">IUCN Redlist</a> - Online
database that provides taxonomic information for wild hosts. You can use
the R package <code>rredlist</code> and the <a
href="http://apiv3.iucnredlist.org/api/v3/docs">API</a> to access the
data directly.</li>
<li><a href="https://www.mammaldiversity.org/">Mammal Diversity
Database</a> - Mammal taxonomic authority maintained by American Society
of Mammalogists. Versions are updated and recorded on Zenodo. Full
desrciption by <a
href="https://academic.oup.com/jmammal/article/99/1/1/4834091?login=false">Burgin
et al. (2018)</a>.</li>
<li><a href="https://www.ncbi.nlm.nih.gov/taxonomy">NCBI Taxonomy</a> -
The Taxonomy Database is a curated classification and nomenclature for
all of the organisms in the public sequence databases, both parasites
and hosts.</li>
</ul>
<h2 id="scientific-journals">Scientific Journals</h2>
<ul>
<li><a href="http://www.ajtmh.org/">American Journal of Tropical
Medicine and Hygiene</a> - AJTMH publishes a broad range of papers
covering topics in tropical medicine. Their archive is open-access after
a 12-month embargo.</li>
<li><a
href="https://annals-parasitology.eu/go.live.php/PL-H54/archive.html">Annals
of Parasitology</a> - Open-access scientific journal of the Polish
Parasitological Society, formerly <em>Wiadomości Parazytologiczne</em>,
that publishes issues quarterly. Open archives start from 2002.</li>
<li><a href="https://efsa.onlinelibrary.wiley.com/journal/18314732">EFSA
Journal</a> - Open-access journal of the European Food Safety Authority
with yearly reports of food-borne outbreaks and cases of zoonotic agents
and antibiotic resistance emergence in humans and animals.</li>
<li><a href="https://wwwnc.cdc.gov/eid/">Emerging Infectious
Diseases</a> - The CDC open-access journal.</li>
<li><a
href="https://content.sciendo.com/configurable/contentpage/journals$002fhelm$002fhelm-overview.xml">Helminthologia</a>
- Open-access scientific journal of the Slovak Academy of Sciences that
publishes quarterly since 1959. Open access from volume 43 (2006) -
present. Articles relate to human, veterinary and plant
helminthology.</li>
<li><a href="https://jesp.journals.ekb.eg/">Journal of the Egyptian
Society of Parasitology</a> - Open-access (2013 - present) scientific
journal of The Eyptian Society of Parasitology. Published since the
1970s, their archive is indexed in Pub-Med since 1972 (Index Medicus
ISSN: 0253-5890).</li>
<li><a href="http://www.jwildlifedis.org/loi/jwdi">Journal of Wildlife
Diseases</a> - JWD provides many open-access articles on new parasite
expansions or discoveries.</li>
<li><a
href="https://www.zobodat.at/publikation_series.php?id=1351">Mitteilungen
der Österreichischen Gesellschaft für Tropenmedizin und
Parasitologie</a> - 23 open access volumes (1971-2001) of the scientific
journal of the Austrian Society for Tropical Medicine and
Parasitology.</li>
<li><a href="https://www.parasite-journal.org/">Parasite</a> - Open
access journal associated with the Société Française de Parasitologie.
Focuses on both animal and human parasites.<br />
</li>
<li><a
href="http://publication.nhmus.hu/parasitologia/bannales.php?volume=1">Parasitologia
Hungarica</a> - 31 open-access volumes (1960-1998) of Parasitologia
Hungarica, a scientific journal hosted by the Hungarian Natural History
Museum.</li>
</ul>
<h1 id="license">License</h1>
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<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative
Commons Attribution-NonCommercial 4.0 International License</a>.</p>
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