General Nature API

Nature Talk
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Hey Everybody,

I have been looking for ages for a database of animal data. I want to make a request - English or Latin and get back all the information regarding an animal.

For example if I query lion I should get all the interesting information about lions:
Latin Panthera leo
German Löwe
Weight 200 kg
Height 1.2 m
Length
Number of offspring 2 (range 1-4)
lifespan 15
average lifespan 6

I just made up these numbers off the top of my head so don’t use them anywhere. However I am looking for something for building a website and want the numbers to be accurate.

UMichigan have a great website - Animaldiversity.org with lots of this data but I was looking for something more accessible and more precisely organised along the lines of an API.

Anybody know of anything?

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Wikidata often has this information for common species: https://www.wikidata.org/wiki/Q140

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Wikidata is general and has an API. here’s all the stuff in Wikidata connected to Panthera leo: https://www.wikidata.org/wiki/Q140.

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(jinx)

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! :speak_no_evil:

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Thanks for the quick replies. Wikidata isn’t quite what I want as there is a lot missing for some quite common (well known and well researched) species.

It is a very useful resource but I was hoping for something more trustworthy. The data in the data boxes on wikipedia is sometimes quite inaccurate and as far as I know this is the same data.

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if you don’t like Wikidata, you could try EOL, which is another generic resource that offers an API, too. here’s the data on EOL for Panthera Leo: https://eol.org/pages/328672/data.

if EOL doesn’t satisfy you either, then maybe just scrape the AnimalDiversity.org pages? you could also look at the More Info box in the About section of the iNat taxon page to see if any of those sources might offer an API or other data delivery method that will satisfy your needs.

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I can’t think of any examples where those various infoboxes on Wikipedia species pages (e.g. taxoboxes or mycomorphboxes) are pulling information from Wikidata but I could be wrong. Wikidata also has the benefit of being able to immediately revise any incorrect information and provide a source for the correction. But yeah, it’s definitely patchy in its coverage.

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Wikidata is the repository for all structured data in the Wikipedia family. One would imagine that the info boxes come from structured data. But maybe not.

I have been looking at the IUCN api (and will use some features) but they are sort of specialised in the conservation direction rather than the basic stuff that I want.

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Of the two common examples I linked above (e.g. a taxobox is present on every English Wikipedia taxon article), neither are associated with Wikidata.

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I don’t know if this is what you want, but take a look at: https://genomics.senescence.info/species/index.html

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That is interesting. I must look into what they use the data for then.

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Thanks Dan. Not quite what I want but it is a part of it.

I guess it might be hard to find something that has everything that I need in one place. :smile:

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not sure if it’s worth repeating, but Wikidata has most of the data from your example in one place, and EOL has all of it, though its API is probably harder to access / use that Wikidata’s.

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My example was just that, an example.

Wikidata is unfortunately missing most of the data I want for almost all animals. It has very basic information.

I have not been able to every find any information on EOL except for taxonomy data. Is there more? I wouldn’t worry about the difficulty of the API. While I am not an expert I can get around these problems more easily than finding the data.

Ideally what I would like is an api access to AnimalDivesisty web from the university of Michigan. They have the data but not in an accessible form.

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i haven’t tried myself, but the documents indicate that the EOL v3 API allows you to get structured data, including organism traits, etc. here are some of the sample cypher queries they provide to query for different kinds of information: https://github.com/EOL/eol_website/blob/master/doc/query-examples.md

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I think one of the keywords to use is “traits”. This is a list of open traits databases https://opentraits.org/datasets.html, although it is sometimes a bit specific and it is not a single API from which to access everything. I know there are quite a few large trait databases for plants, but I’m not aware of any for the whole animal kingdom.

Also, if you are familiar with R, there is an rOpenSci package called traits that allows access to the EOL API https://docs.ropensci.org/traits/ I never used it though.

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Thanks guys. I will have a look at ‘traits’ though the EOL

Unfortunately I don’t know any R. Only Python.

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if you don’t know R, i’m not sure what you necessarily gain by using that particular R package. it looks like it would be straightforward enough in Python to use something like requests to hit /services/cypher. (the only parameters are the query and output format.) the hoops that you have to jump through either way are getting the power user access to EOL, getting an API token, and learning the Cypher syntax and traits database schema (at least well enough to adapt some of the sample queries).

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