User:Gaurav/Biodiversity databases

Here is some information on biodiversity databases I collected once. Someday I (or someone else) will hopefully move them into List of biodiversity databases.

Name	Type	Focus	Collection
List of Prokaryotic names with Standing in Nomenclature	Taxonomy	Prokaryotes (bacteria and archaea)	Taxon names, current status, changes over time. Includes new descriptions, subspecific splits, and those published outside the International Journal of Systematic and Evolutionary Microbiology.
Integrated Taxonomic Information System	Taxonomy	All life	Taxon names, current status, source information.
NCBI Taxonomy	Taxonomy	All life, some non-living things	Widely used in the Semantic Web community because of the taxonomy ontology.
Mammal Species of the World, 3rd edition	Taxonomy	Mammals	Reasonably authoritative for mammals, does not have full references online.
Interim Register of Marine and Nonmarine Genera	Names (taxonomy?)	All life?	Big dataset, should be pretty clean, should be pretty independent of other sources, maybe.	Available on GBIF as DwC-A.
IUCN Red List	Names (taxonomy?)	Eukaryotes?	Widely used outside of biology (in law, etc.)
AmphibiaWeb	Taxonomy	Amphibians	Has lists of families and lists of species available for direct download.
AntWeb	Taxonomy	Ants	List of species
Hymenoptera Online	Taxonomy	Hymenoptera	Incorporates data from AntWeb; in turn incorporated by ITIS, which is incorporated by CoL.
World Register of Marine Species	Taxonomy?	Marine species	Available on EOL. Supported by dwca-hunter, which downloads it from EOL.
Catalogue of Life	Taxonomy?	All life?	Downloads are Windows only, but consist largely of MySQL dumps, so it should be possible to get them working whenever. Annual downloads available for 2000 and 2002-2011. Available on EOL.
Catalogue of Diatom Names	Taxonomy?	Diatoms (Bacillariophyceae)	?
Index Nominum Algarum	Taxonomy?	Algae	?
AlgaeBase	?	Algae	?
Taxonomicon	?	?	Has some interesting association data, e.g. Panthera tigris with Influenza H5N1
Stromboidea	?	?	?
The AOU Check-list of North American Birds	?	?	?

Other databases available for download

USDA GRIN Taxonomy

• http://www.ars-grin.gov/
• http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?view=downl&language=en

Checklists on Project Gutenberg

• Animals: http://www.gutenberg.org/ebooks/bookshelf/150

GBIF

• A source of verbatim names (although presumably some of those names have been corrected): http://data.gbif.org/species/4969819/

Freebase

Wikispecies

ENA (EMBL-EBI) taxonomy data

• Identical to NCBI Taxonomy, including using the same identifiers: http://www.ebi.ac.uk/ena/about/taxonomy_download

Cephaloleia beetles

• Most other LifeDesks don't have a one-click classification-as-DwC-A download option like this one does: http://cephaloleia.lifedesks.org/

Metalmark Moths

• http://choreutidae.lifedesks.org/

IOC World Bird List

• Does not appear to contain synonyms: http://www.worldbirdnames.org/ioc-lists/master-list/

USDA PLANTS checklist

• http://plants.usda.gov/dl_all.html

Sponge barcoding project

• http://www.palaeontologie.geo.uni-muenchen.de/sbd/list.php

MycoBank

• http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&Page=200&ViewMode=Basic

AntWeb

• Has a bunch of separately available resources.
• The Bolton catalog -- including publications -- can be bought on CD: http://www.amazon.com/Boltons-Catalogue-Ants-World-1758-2005/dp/0674021517
• They also have http://www.antcat.org/ (the Bolton catalogue) and http://www.antwiki.org/ (which does have a download, see above!)
• Links to publications, which are are identified by page and PDFs included for some.
• See http://www.antwiki.org/Category:Species for all the species (nicely formatted!) on AntWiki

VegBank

http://vegbank.org/vegbank/general/faq.html#whatconcept (has taxon concepts!)

iNaturalist

http://www.inaturalist.org/taxon_changes (has taxon concepts!)

Databases NOT available for download

• WoRMS: Need permission.
• PaleoDB
• TROPICOS
• The Plant List
• AlgaTerra (microalgae)
• http://apps.kew.org/wcsp/about.do
• Amphibian Species of the World: http://research.amnh.org/vz/herpetology/amphibia/
• The Global Lepidoptera Names Index: http://www.nhm.ac.uk/research-curation/research/projects/lepindex/
• Fishbase: http://www.fishbase.org/ (available on EOL)
• Index to Organism Names (ION): http://www.organismnames.com/
• Index Fungorum: http://www.indexfungorum.org/
• Angiosperm Phylogeny Website: http://www.mobot.org/MOBOT/research/APWeb/welcome.html
• Reptile Database: http://reptile-database.reptarium.cz/advanced_search?submit=Search -- Available on EOL.
• Wikispecies -- http://species.wikimedia.org/ (but dwca-hunter can download it)
• A Checklist of Mosses. M.R. Crosby et. al. 1999 http://www.mobot.org/mobot/tropicos/most/checklist.shtml
• AviBase (birds): http://avibase.bsc-eoc.org/
• Species Fungorum's Family Names Database: searching for '%' appears to provide every family name (2,172 records returned): http://www.speciesfungorum.org/Names/families.asp
• AlgaTerra Diatom Names: http://www.algaterra.org/L-B-Names.htm
• http://www.isth.info/biodiversity/index.php
• World Porifera Database: http://www.marinespecies.org/porifera/porifera.php?p=taxlist&pid=558&rComp=%3E%3D&tRank=220
• Glomeromycota SPECIES LIST: http://www.lrz.de/~schuessler/amphylo/
• UNH HGGS Nematode Database: http://nematol.unh.edu/browse.php
• Checklist of the beetles of Canada and Alaska: http://www.canacoll.org/Coleo/Checklist/checklist.htm
• In 1936, 1947 and 1949, the AAAS published a list of higher zoological names: http://www.biodiversitylibrary.org/bibliography/6792

Regional databases

Australia

• Australia's Virtual Herbarium: http://avh.ala.org.au/sp/help.html#downloads
• Australia Plant Name Index: http://www.cpbr.gov.au/apni/apni.html

Lists of other databases

• CoL’s databases: http://www.catalogueoflife.org/col/info/databases
• http://www.theplantlist.org/about/#collaborators
• http://bgbm3.bgbm.fu-berlin.de/IOPI/GPC/datasets.asp

Others

Databases to add to one of the lists above after more research.

• http://www.sel.barc.usda.gov/diptera/biosys.htm