POST /api/v1/taxonomy
Returns the taxonomic information for a given taxon identifier.
This method returns the taxonomic information from the Unipept Taxonomy, for a given NCBI taxon identifier.
Request
The taxonomy method can be used by doing a HTTP POST-request (preferred) or GET-request to http://api.unipept.ugent.be/api/v1/taxonomy
. Parameters can be included in the request body (POST) or in the query string (GET). The only required parameter is input[]
, which takes one or more taxon identifiers.
input
input[]
is a required parameter that takes one or more taxon identifiers. Unipept will return the taxonomic information for the given taxa. To pass multiple taxon identifiers, simply add multiple input[]
parameters (see example).
extra
extra
is an optional parameter and can either be true
or false
. When not set explicitly, the parameter defaults to false
. When the parameter is set to true
, Unipept will return the complete lineage for each taxon. See the response section for an overview of the information fields returned.
names
names
is an optional parameter and can either be true
or false
. When not set explicitly, the parameter defaults to false
. When both names
and extra
are set to true
, Unipept will return the names of all ranks in the lineage of each organism. Setting only names
to true
will not result in additional information fields being returned. . See the response section for an overview of the information fields returned.
Performance penalty
Setting names
to true
has a performance penalty inferred from additional database queries. Do not use this parameter unless the extra information fields are needed.
Response
The organisms associated with the given taxon identifiers are returned as a list of JSON objects. By default, each object contains the following information fields extracted from the UniProt entry and NCBI taxonomy:
taxon_id
: the NCBI taxon id of the organismtaxon_name
: the name of the organismtaxon_rank
: the taxonomic rank of the organism
When the extra
parameter is set to true
, objects contain additional information about the lineage of the organims extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields:
superkingdom_id
kingdom_id
subkingdom_id
superphylum_id
phylum_id
subphylum_id
superclass_id
class_id
subclass_id
infraclass_id
superorder_id
order_id
suborder_id
infraorder_id
parvorder_id
superfamily_id
family_id
subfamily_id
tribe_id
subtribe_id
genus_id
subgenus_id
species_group_id
species_subgroup_id
species_id
subspecies_id
varietas_id
forma_id
When both the names
and extra
parameters are set to true
, objects also contain the names for each rank in the lineage using the following information fields:
superkingdom_name
kingdom_name
subkingdom_name
superphylum_name
phylum_name
subphylum_name
superclass_name
class_name
subclass_name
infraclass_name
superorder_name
order_name
suborder_name
infraorder_name
parvorder_name
superfamily_name
family_name
subfamily_name
tribe_name
subtribe_name
genus_name
subgenus_name
species_group_name
species_subgroup_name
species_name
subspecies_name
varietas_name
forma_name
Parameters
Name | Description |
---|---|
input[] required |
Taxon identifier to search for. Add multiple parameters to search for multiple taxon identifiers. Value: String |
extra optional |
Return additional lineage information fields if true or false (default)
|
names optional |
Return names of ranks in the lineage if true or false (default)
|
Examples
Example Retrieve taxonomic information for a given taxon identifier
This example retrieves taxonomic information for the organism Bacteroides fragilis (taxon id 817).
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/taxonomy \ -d 'input[]=817'GET
http://api.unipept.ugent.be/api/v1/taxonomy.json?input[]=817
Response
[
{
taxon_id: 817,
taxon_name: 'Bacteroides fragilis',
taxon_rank: 'species'
}
]
Example Retrieve taxonomic information for a given list of taxon identifiers
This example retrieves taxonomic information for the organism Bacteroides fragilis (taxon id 817) and Bacteroides intestinalis (taxon id 329854).
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/taxonomy \ -d 'input[]=817' \ -d 'input[]=329854'GET
http://api.unipept.ugent.be/api/v1/taxonomy.json?input[]=817&input[]=329854
Response
[
{
taxon_id: 817,
taxon_name: 'Bacteroides fragilis',
taxon_rank: 'species'
},
{
taxon_id: 329854,
taxon_name: 'Bacteroides intestinalis',
taxon_rank: 'species'
}
]
Example Retrieve taxonomic information for a given taxon identifier including its complete lineage
This example retrieves taxonomic information for the organism Bacteroides fragilis (taxon id 817), including its complete lineage.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/taxonomy \ -d 'input[]=817' \ -d 'extra=true'GET
http://api.unipept.ugent.be/api/v1/taxonomy.json?input[]=817&extra=true
Response
[
{
taxon_id: 817,
taxon_name: 'Bacteroides fragilis',
taxon_rank: 'species',
superkingdom_id: 2,
kingdom_id: null,
subkingdom_id: null,
superphylum_id: 68336,
phylum_id: 976,
subphylum_id: null,
superclass_id: null,
class_id: 200643,
subclass_id: null,
infraclass_id: null,
superorder_id: null,
order_id: 171549,
suborder_id: null,
infraorder_id: null,
parvorder_id: null,
superfamily_id: null,
family_id: 815,
subfamily_id: null,
tribe_id: null,
subtribe_id: null,
genus_id: 816,
subgenus_id: null,
species_group_id: null,
species_subgroup_id: null,
species_id: 817,
subspecies_id: null,
varietas_id: null,
forma_id: null
}
]
Example Retrieve taxonomic information for a given taxon identifier including its complete lineage and names
This example retrieves taxonomic information or the organism Bacteroides fragilis (taxon id 817), including its complete lineage with names.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/taxonomy \ -d 'input[]=817' \ -d 'extra=true' \ -d 'names=true'GET
http://api.unipept.ugent.be/api/v1/taxonomy.json?input[]=817&extra=true&names=true
Response
[
{
taxon_id: 817,
taxon_name: 'Bacteroides fragilis',
taxon_rank: 'species',
superkingdom_id: 2,
superkingdom_name: 'Bacteria',
kingdom_id: null,
kingdom_name: '',
subkingdom_id: null,
subkingdom_name: '',
superphylum_id: 68336,
superphylum_name: 'Bacteroidetes/Chlorobi group',
phylum_id: 976,
phylum_name: 'Bacteroidetes',
subphylum_id: null,
subphylum_name: '',
superclass_id: null,
superclass_name: '',
class_id: 200643,
class_name: 'Bacteroidia',
subclass_id: null,
subclass_name: '',
infraclass_id: null,
infraclass_name: '',
superorder_id: null,
superorder_name: '',
order_id: 171549,
order_name: 'Bacteroidales',
suborder_id: null,
suborder_name: '',
infraorder_id: null,
infraorder_name: '',
parvorder_id: null,
parvorder_name: '',
superfamily_id: null,
superfamily_name: '',
family_id: 815,
family_name: 'Bacteroidaceae',
subfamily_id: null,
subfamily_name: '',
tribe_id: null,
tribe_name: '',
subtribe_id: null,
subtribe_name: '',
genus_id: 816,
genus_name: 'Bacteroides',
subgenus_id: null,
subgenus_name: '',
species_group_id: null,
species_group_name: '',
species_subgroup_id: null,
species_subgroup_name: '',
species_id: 817,
species_name: 'Bacteroides fragilis',
subspecies_id: null,
subspecies_name: '',
varietas_id: null,
varietas_name: '',
forma_id: null,
forma_name: ''
}
]
Try it
Use the API explorer form below to call the taxonomy method on live data and see the response.
Request
Response