[ensembl-dev] Ensembl REST API | exact meaning of 'Species name'

[Ramiro Magno]

Hi Anja,

May I ask for you help this previous question of mine about the 'species'
name?

I am implementing a function in R that will (hopefully) do input validation
on the species name before placing requests on the server. For that I need
to know what are bona fide species names. So I thought I'd get that info
from the /info/species endpoint but I am not entirely sure if I should use
the 'name' or whether to allow any of the other aliases...?

I noticed that for some endpoints I can use 'human' or 'homo_sapiens'
interchangeably but I am not sure if other aliases will work for all
endpoints too. For example, the display name for human is 'Human' (capital
H) does that work too? There are also aliases like 'homo' or 'hsap' will
that work? I am looking for a rule that is applicable to all species, not
just human.

Thank you again for your patience.

RM

On Wed, 17 Jul 2019 at 14:25, Ramiro Magno <ramiro.magno at gmail.com> wrote:

> Hi
>
> Several REST API endpoints use the parameter 'species' as a search
> parameter. Typically, the description of this parameter reads "Species
> name/alias", e.g., in http://rest.ensembl.org/documentation/info/analysis.
>
> My question is: what is the meaning of "Species name" here? I am asking
> this because the endpoint
> http://rest.ensembl.org/documentation/info/species gives me back a list
> of species. In this list there are several fields related to the species
> name:
>
>   (i) name, e.g. 'gorilla_gorilla';
>   (ii) aliases, e.g., "gorilla gorilla", "9595", "9593", "gorilla",
> "gorgor", "gorilla_gorilla_gorilla", "ggor", "western gorilla", "gorilla
> gorilla gorilla","ggorilla";
>   (iii) common_name, e.g. "Western Lowland Gorilla";
>   (iv) display_name, e.g. "Gorilla"
>
> I've seen also the concept "Scientific name" in the Ensembl website as
> well. Is this the same concept as 'name' aforementioned in (i) but without
> the underscore ('_') and capitalised (is this a fair assumption)?
>
> BTW: What is a good database key for species? The 'taxon_id' (returned by
> /info/species)?
>
> Many thanks!
>
> Ramiro Magno
>
>
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