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 | URL | Type | Focus | Collection | |
|---|---|---|---|---|---|
| List of Prokaryotic names with Standing in Nomenclature | http://www.bacterio.cict.fr/ | 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 | http://www.itis.gov/ | Taxonomy | All life | Taxon names, current status, source information. | |
| NCBI Taxonomy | http://www.ncbi.nlm.nih.gov/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 | http://www.bucknell.edu/msw3/ | Taxonomy | Mammals | Reasonably authoritative for mammals, does not have full references online. | |
| Interim Register of Marine and Nonmarine Genera | http://www.cmar.csiro.au/datacentre/irmng/ | 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 | http://www.iucnredlist.org/search/link/507358c3-ac245141 | Names (taxonomy?) | Eukaryotes? | Widely used outside of biology (in law, etc.) | |
| AmphibiaWeb | http://amphibiaweb.org/ | Taxonomy | Amphibians | Has lists of families and lists of species available for direct download. | |
| AntWeb | http://www.antweb.org/ | Taxonomy | Ants | List of species | |
| Hymenoptera Online | http://hol.osu.edu/ | Taxonomy | Hymenoptera | Incorporates data from AntWeb; in turn incorporated by ITIS, which is incorporated by CoL. | |
| World Register of Marine Species | http://www.marinespecies.org/ | Taxonomy? | Marine species | Available on EOL. Supported by dwca-hunter, which downloads it from EOL. | |
| Catalogue of Life | http://www.catalogueoflife.org/ | 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 | http://researcharchive.calacademy.org/research/diatoms/names/about.html | Taxonomy? | Diatoms (Bacillariophyceae) | ? | |
| Index Nominum Algarum | http://ucjeps.berkeley.edu/INA.html | Taxonomy? | Algae | ? | |
| AlgaeBase | http://www.algaebase.org/ | ? | Algae | ? | |
| Taxonomicon | http://taxonomicon.taxonomy.nl/Default.aspx | ? | ? | Has some interesting association data, e.g. Panthera tigris with Influenza H5N1 | |
| Stromboidea | http://www.stromboidea.de/ | ? | ? | ? | |
| The AOU Check-list of North American Birds | http://www.aou.org/checklist/north/print.php | ? | ? | ? |
Other databases available for download
- USDA GRIN Taxonomy
- Checklists on Project Gutenberg
- 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
- IOC World Bird List
-
- Does not appear to contain synonyms: http://www.worldbirdnames.org/ioc-lists/master-list/
- USDA PLANTS checklist
- Sponge barcoding project
- 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.