I am searching for an un-encoded data file with common and scientific names for example of a few hundred species or tens of thousands, where I can search the common and scientific labels of organisms.
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2$\begingroup$ English common names or from different countries/languages? $\endgroup$– fileunderwaterOct 31, 2016 at 8:35
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$\begingroup$ I suggest using Wikidata, although extracting the information may not be straightforward. $\endgroup$– PereOct 31, 2016 at 9:34
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1$\begingroup$ English common names would be fine for myself, if you have various related resources it's always good to know. $\endgroup$– bandybabboonOct 31, 2016 at 10:54
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4 Answers
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Uniprot has a list of the controlled vocabulary for common and scientific names of species listed here.
An example entry:
ACAER E 111511: N=Acanthodactylus erythrurus
C=Spanish fringe-toed lizard
S=Lacerta erythrura
In the example the N is the scientific binomial name (Canthodactylus erythrurus), C is the common name (Spanish fringe-toed lizard).
ACAER is the id code, 111511 is the code for the taxonomic node, E means it is a eukaryote, and S is a synonym of either name.
The list contains 25336 scientific names currently, which falls short of the ~2.5m species in GBIF, or the 10s, or 100s of millions that are estimated to exist. The Uniprot list does, however, represent every organism included in Uniprot, which is widely regarded as being among the most comprehensive protein databases that exist today.
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$\begingroup$ That's a fairy short species list though, if it is meant for general-purpose use (i.e. not specifically in relation to Uniprot data). $\endgroup$ Oct 31, 2016 at 9:04
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$\begingroup$ This is a worthwhile point. Uniprot hold additional lists for different strains that may account for some of the difference (i.e GBIF count each strain as a separate name, Uniprot packs many strains under 1 species name-not negligible for bacteria). I cannot verify any redundancy measures taken by GBIF and I cannot find any peer reviewed article of GBIF. This would explain a lot of over-estimation since both Uniprot and GBIF are pulling species names from many of the same external databases. $\endgroup$– JamesOct 31, 2016 at 10:06
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1$\begingroup$ Just a note here, this list includes many viral strains, which may or may not be something you want. $\endgroup$– AmoryOct 31, 2016 at 13:06
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Maybe not a direct answer to your question, depending on what you mean with "unencoded data file", but the Global Biodiversity Information Facility (GBIF) has an API where you extract data for species names. Their database includes common names (aka vernacular names) when they have that, and often common names from different languages. Using this API, you can extract data and construct a name file for a particular taxa that you are interested in.
As an example, this is the list of the first 20 vernacular names found for Passer domesticus (House sparrow):
{
"endOfRecords" : false,
"results" : [
{
"language" : "",
"sourceTaxonKey" : 100220560,
"source" : "Global Invasive Species Database",
"vernacularName" : "English sparrow"
},
{
"language" : "",
"sourceTaxonKey" : 100220560,
"vernacularName" : "Europese huismuis",
"source" : "Global Invasive Species Database"
},
{
"vernacularName" : "Gorrion domestico",
"source" : "Global Invasive Species Database",
"language" : "",
"sourceTaxonKey" : 100220560
},
{
"source" : "Integrated Taxonomic Information System (ITIS)",
"vernacularName" : "Gorrión casero",
"language" : "spa",
"sourceTaxonKey" : 102101640
},
{
"vernacularName" : "Gorrión Común",
"sourceTaxonKey" : 123213203,
"language" : "spa"
},
{
"language" : "spa",
"sourceTaxonKey" : 101186844,
"source" : "The European Nature Information System (EUNIS)",
"vernacularName" : "Gorrión Común"
},
{
"language" : "spa",
"sourceTaxonKey" : 114130266,
"source" : "Colaboraciones Americanas Sobre Aves",
"vernacularName" : "Gorrión casero"
},
{
"vernacularName" : "Gorrión casero",
"source" : "Yanayacu Natural History Research Group",
"sourceTaxonKey" : 119245200,
"language" : "spa"
},
{
"vernacularName" : "Gorrión casero",
"source" : "Catalogue of Life",
"sourceTaxonKey" : 119950016,
"language" : "spa"
},
{
"language" : "swe",
"sourceTaxonKey" : 101186844,
"vernacularName" : "Gråsparv",
"source" : "The European Nature Information System (EUNIS)"
},
{
"vernacularName" : "Gråspurv",
"language" : "dan",
"sourceTaxonKey" : 123213203
},
{
"vernacularName" : "Gråspurv",
"language" : "nob",
"sourceTaxonKey" : 123213203
},
{
"language" : "deu",
"sourceTaxonKey" : 116795880,
"vernacularName" : "Haussperling",
"source" : "Taxon list of animals with German names (worldwide) compiled at the SMNS",
"country" : "DE"
},
{
"language" : "deu",
"sourceTaxonKey" : 100483595,
"source" : "Belgian Species List",
"country" : "BE",
"vernacularName" : "Haussperling"
},
{
"language" : "deu",
"sourceTaxonKey" : 123213203,
"vernacularName" : "Haussperling"
},
{
"sourceTaxonKey" : 101186844,
"language" : "deu",
"source" : "The European Nature Information System (EUNIS)",
"vernacularName" : "Haussperling"
},
{
"source" : "The Clements Checklist",
"vernacularName" : "House Sparrow",
"language" : "eng",
"sourceTaxonKey" : 113987294
},
{
"vernacularName" : "House Sparrow",
"source" : "Taxonomy in Flux Checklist",
"language" : "eng",
"sourceTaxonKey" : 100159046
},
{
"source" : "Colaboraciones Americanas Sobre Aves",
"vernacularName" : "House Sparrow",
"language" : "eng",
"sourceTaxonKey" : 114130266
},
{
"sourceTaxonKey" : 102101640,
"language" : "eng",
"vernacularName" : "House Sparrow",
"source" : "Integrated Taxonomic Information System (ITIS)"
}
],
"limit" : 20,
"offset" : 0
}
Using this type of search: api.gbif.org/v1/species?name=Passer%20domesticus, you can look for all info for a particular species, starting from either a scientific name or a common name (in example, Passer domesticus).
GBIF includes information in 1,643,948 species (and counting), but I don't know for what proportion they have common names (or where there are common names).
answered Oct 31, 2016 at 8:45
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$\begingroup$ species names in many languages. Awesome thankyou. $\endgroup$ Oct 31, 2016 at 12:35
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2$\begingroup$ They seem to have some Unicode encoding issues, though. Not only does the API not specifically indicate via HTTP headers that the text it's returning is UTF-8 encoded, but some of the vernacular names (like
"Gorrión casero"above) actually appear to have UTF-8 encoding applied twice. $\endgroup$ Oct 31, 2016 at 18:38 -
$\begingroup$ @IlmariKaronen True. And thanks for the reformatting. $\endgroup$ Oct 31, 2016 at 19:46
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$\begingroup$ A lot of this data is also downloadable from GBIF: for example, if the Global Invasive Species Database seems to have the names you want, you can search for it at gbif.org/dataset -- many (most? all?) of the datasets can be downloaded as a "Darwin Core Archive" (a ZIP file containing CSV files) from the dataset page (gbif.org/dataset/b351a324-77c4-41c9-a909-f30f77268bc4). $\endgroup$– GauravNov 4, 2016 at 20:52
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If you're looking for marine species, the World Register of Marine Species is probably the best place to find this information.
The Ocean Biogeographic Information System also contains a tremendous amount of marine species.
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1$\begingroup$ Thanks alot. I was looking at flying fish today, the Uniprot list has at least 11 flying squid and flyingfish. thanks for the resource. $\endgroup$ Nov 2, 2016 at 20:00
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A late answer, but I think the mentioned sources are limited and the awesome download page of Observado.org offers a much better alternative.
The website of Observado, an initiative to collect species observations worldwide, has global species lists in csv format that are as complete as possible. The plant list currently has 381.473 records! You can download local species names in more languages you might have heard from, from English to Russian and from Frysk to Dzongkha.
Note that these lists are meant for observations in the field, and hence also contain multispecies, hybrids and synonyms. But these can be filtered out easily.
