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

[Ramiro Magno]

Hi Brandon,

Terrific explanation, thanks!

All the best, RM

On Thu, 18 Jul 2019 at 16:41, Brandon Walts <bwalts at ebi.ac.uk> wrote:

> Hi Ramiro
>
> It's safest to use the "name" value for the validation you describe. That
> said, the REST endpoints should accept any of the aliases as well.
>
> Regarding the meanings of "name", "scientific name", "display name", and
> "common name": "name" is the internal name used to uniquely identify a
> particular database. "Scientific name" is the name of the species,
> formatted with capitalisation and spacing for the website, and without a
> strain identifier (if any). Display names, likewise, are the names used for
> display on the website. Scientific, display, and common names are not
> suitable as species parameters because some of them contain characters that
> will not work in URLs (e.g. Mouse C57BL/6NJ), and they may not uniquely
> identify a database (e.g. species with multiple strains). "Human" works
> because there is an alias "human", and the lookup is case insensitive.
>
> Aliases are assigned to each species by hand. Although some patterns are
> commonly seen, for example first letter of genus and first three letters of
> species ("ggor"), there is no systematic rule for creating aliases. This is
> partly due to the requirement that each alias be unique - having unique
> aliases that conform to a scheme simply can't scale. Because of those
> scaling issues, we are also no longer assigning aliases for new species
> (such as goat), although existing aliases will stay.
>
> Best regards
> -Brandon
> On 18/07/2019 15:01, Ramiro Magno wrote:
>
> 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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