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<p>Hi Ramiro</p>
<p>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. <br>
</p>
<p>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.</p>
<p>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.<br>
</p>
<p>Best regards<br>
-Brandon<br>
</p>
<div class="moz-cite-prefix">On 18/07/2019 15:01, Ramiro Magno
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20190718140328.C83B611AD1B_D307C30B@hh-mx4.ebi.ac.uk">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Anja,
<div><br>
</div>
<div>May I ask for you help this previous question of mine about
the 'species' name?</div>
<div><br>
</div>
<div>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...?</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Thank you again for your patience.</div>
<div><br>
</div>
<div>RM</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, 17 Jul 2019 at 14:25,
Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com"
moz-do-not-send="true">ramiro.magno@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi
<div><br>
</div>
<div>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 <a
href="http://rest.ensembl.org/documentation/info/analysis"
target="_blank" moz-do-not-send="true">http://rest.ensembl.org/documentation/info/analysis</a>.</div>
<div><br>
</div>
<div>My question is: what is the meaning of "Species name"
here? I am asking this because the endpoint <br>
<div><a
href="http://rest.ensembl.org/documentation/info/species"
target="_blank" moz-do-not-send="true">http://rest.ensembl.org/documentation/info/species</a> gives
me back a list of species. In this list there are
several fields related to the species name:</div>
<div><br>
</div>
<div> (i) name, e.g. 'gorilla_gorilla';</div>
<div> (ii) aliases, e.g., "gorilla gorilla", "9595",
"9593", "gorilla", "gorgor", "gorilla_gorilla_gorilla",
"ggor", "western gorilla", "gorilla gorilla
gorilla","ggorilla";</div>
</div>
<div> (iii) common_name, e.g. "Western Lowland Gorilla";</div>
<div> (iv) display_name, e.g. "Gorilla"</div>
<div><br>
</div>
<div>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)?</div>
<div><br>
</div>
<div>BTW: What is a good database key for species? The
'taxon_id' (returned by /info/species)?</div>
<div><br>
</div>
<div>Many thanks!</div>
<div><br>
</div>
<div>Ramiro Magno</div>
<div><br>
</div>
</div>
</blockquote>
</div>
<br>
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