POST /api/v1/pept2taxa
Returns the set of taxa extracted from the UniProt entries containing a given tryptic peptide.
This method returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface.
Request
The pept2taxa method can be used by doing a HTTP POST-request (preferred) or GET-request to http://api.unipept.ugent.be/api/v1/pept2taxa
. 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 tryptic peptides.
input
input[]
is a required parameter that takes one or more tryptic peptides. Unipept will return the set of organisms associated with the UniProt entries that contain any of the input[]
peptides in their protein sequence. To pass multiple peptides at once, simply add multiple input[]
parameters (see example).
Input size
Unipept puts no restrictions on the number of peptides passed to the input[]
parameter. Keep in mind that searching for lots of peptides at once may cause the request to timeout or, in the case of a GET-request, exceed the maximum URL length. When performing bulk searches, we suggest splitting the input set over requests of 100 peptides each.
equate_il
equate_il
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
, isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt entries. This setting is similar to checking the Equate I and L? checkbox when performing a search with the Tryptic Peptide Analysis in the web interface.
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 of each organism. 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 matching UniProt entries 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:
peptide
: the peptide that matched this recordtaxon_id
: the NCBI taxon id of the organism associated with the matching recordtaxon_name
: the name of the organism associated with the matching recordtaxon_rank
: the taxonomic rank of the organism associated with the matching record
When the extra
parameter is set to true
, objects contain additional information about the lineages of the organism 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 |
Tryptic peptide to search for. Add multiple parameters to search for multiple peptides. Value: String |
equate_il optional |
Equate isoleucine (I) and leucine (L). Value: Must betrue or false (default)
|
extra optional |
Return additional lineage information if true or false (default)
|
names optional |
Return names of ranks in the lineage if true or false (default)
|
Examples
Example Retrieve all organisms associated with the UniProt entries containing a given tryptic peptide
This example retrieves all organisms associated with the UniProt entries containing the peptide AIPQLEVARPADAYETAEAYR. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2taxa \ -d 'input[]=AIPQLEVARPADAYETAEAYR'GET
http://api.unipept.ugent.be/api/v1/pept2taxa.json?input[]=AIPQLEVARPADAYETAEAYR
Response
[
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 367928,
taxon_name: 'Bifidobacterium adolescentis ATCC 15703',
taxon_rank: 'no rank'
},
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 411481,
taxon_name: 'Bifidobacterium adolescentis L2-32',
taxon_rank: 'no rank'
}
]
Example Retrieve all organisms associated with the UniProt entries containing any of multiple tryptic peptides
This example retrieves all organisms associated with the UniProt entries containing the peptide AIPQLEVARPADAYETAEAYR or APVLSDSSCK. The result is the same as the combination of this search and this search with the Tryptic Peptide Analysis in the web interface.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2taxa \ -d 'input[]=AIPQLEVARPADAYETAEAYR' \ -d 'input[]=APVLSDSSCK'GET
http://api.unipept.ugent.be/api/v1/pept2taxa.json?input[]=AIPQLEVARPADAYETAEAYR&input[]=APVLSDSSCK
Response
[
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 367928,
taxon_name: 'Bifidobacterium adolescentis ATCC 15703',
taxon_rank: 'no rank'
},
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 411481,
taxon_name: 'Bifidobacterium adolescentis L2-32',
taxon_rank: 'no rank'
},
{
peptide: 'APVLSDSSCK',
taxon_id: 9823,
taxon_name: 'Sus scrofa',
taxon_rank: 'species'
}
]
Example Retrieve all organisms associated with the UniProt entries containing a single tryptic peptide, while equating I and L
This example retrieves all organisms associated with the UniProt entries containing the peptide APVISDSSCK. In searching, isoleucine (I) and leucine (L) are considered equal. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2taxa \ -d 'input[]=APVISDSSCK' \ -d 'equate_il=true'GET
http://api.unipept.ugent.be/api/v1/pept2taxa.json?input[]=APVISDSSCK&equate_il=true
Response
[
{
peptide: 'APVISDSSCK',
taxon_id: 9823,
taxon_name: 'Sus scrofa',
taxon_rank: 'species'
}
]
Example Retrieve all organisms and lineage associated with the UniProt entries containing a single tryptic peptide
This example retrieves all organisms associated with the UniProt entries containing the peptide AIPQLEVARPADAYETAEAYR including the complete lineage of these organisms. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2taxa \ -d 'input[]=AIPQLEVARPADAYETAEAYR' \ -d 'extra=true'GET
http://api.unipept.ugent.be/api/v1/pept2taxa.json?input[]=AIPQLEVARPADAYETAEAYR&extra=true
Response
[
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 367928,
taxon_name: 'Bifidobacterium adolescentis ATCC 15703',
taxon_rank: 'no rank',
superkingdom_id: 2,
kingdom_id: null,
subkingdom_id: null,
superphylum_id: null,
phylum_id: 201174,
subphylum_id: null,
superclass_id: null,
class_id: 1760,
subclass_id: 85003,
infraclass_id: null,
superorder_id: null,
order_id: 85004,
suborder_id: null,
infraorder_id: null,
parvorder_id: null,
superfamily_id: null,
family_id: 31953,
subfamily_id: null,
tribe_id: null,
subtribe_id: null,
genus_id: 1678,
subgenus_id: null,
species_group_id: null,
species_subgroup_id: null,
species_id: 1680,
subspecies_id: null,
varietas_id: null,
forma_id: null
},
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 411481,
taxon_name: 'Bifidobacterium adolescentis L2-32',
taxon_rank: 'no rank',
superkingdom_id: 2,
kingdom_id: null,
subkingdom_id: null,
superphylum_id: null,
phylum_id: 201174,
subphylum_id: null,
superclass_id: null,
class_id: 1760,
subclass_id: 85003,
infraclass_id: null,
superorder_id: null,
order_id: 85004,
suborder_id: null,
infraorder_id: null,
parvorder_id: null,
superfamily_id: null,
family_id: 31953,
subfamily_id: null,
tribe_id: null,
subtribe_id: null,
genus_id: 1678,
subgenus_id: null,
species_group_id: null,
species_subgroup_id: null,
species_id: 1680,
subspecies_id: null,
varietas_id: null,
forma_id: null
}
]
Example Retrieve all organisms and lineage names associated with the UniProt entries containing a single tryptic peptide
This example retrieves all organisms associated with the UniProt entries containing the peptide AIPQLEVARPADAYETAEAYR, including the complete lineage of these organisms with the names of all ranks. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.
POST$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2taxa \ -d 'input[]=AIPQLEVARPADAYETAEAYR' \ -d 'extra=true' \ -d 'names=true'GET
http://api.unipept.ugent.be/api/v1/pept2taxa.json?input[]=AIPQLEVARPADAYETAEAYR&extra=true&names=true
Response
[
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 367928,
taxon_name: 'Bifidobacterium adolescentis ATCC 15703',
taxon_rank: 'no rank',
superkingdom_id: 2,
superkingdom_name: 'Bacteria',
kingdom_id: null,
kingdom_name: '',
subkingdom_id: null,
subkingdom_name: '',
superphylum_id: null,
superphylum_name: '',
phylum_id: 201174,
phylum_name: 'Actinobacteria',
subphylum_id: null,
subphylum_name: '',
superclass_id: null,
superclass_name: '',
class_id: 1760,
class_name: 'Actinobacteria',
subclass_id: 85003,
subclass_name: 'Actinobacteridae',
infraclass_id: null,
infraclass_name: '',
superorder_id: null,
superorder_name: '',
order_id: 85004,
order_name: 'Bifidobacteriales',
suborder_id: null,
suborder_name: '',
infraorder_id: null,
infraorder_name: '',
parvorder_id: null,
parvorder_name: '',
superfamily_id: null,
superfamily_name: '',
family_id: 31953,
family_name: 'Bifidobacteriaceae',
subfamily_id: null,
subfamily_name: '',
tribe_id: null,
tribe_name: '',
subtribe_id: null,
subtribe_name: '',
genus_id: 1678,
genus_name: 'Bifidobacterium',
subgenus_id: null,
subgenus_name: '',
species_group_id: null,
species_group_name: '',
species_subgroup_id: null,
species_subgroup_name: '',
species_id: 1680,
species_name: 'Bifidobacterium adolescentis',
subspecies_id: null,
subspecies_name: '',
varietas_id: null,
varietas_name: '',
forma_id: null,
forma_name: ''
},
{
peptide: 'AIPQLEVARPADAYETAEAYR',
taxon_id: 411481,
taxon_name: 'Bifidobacterium adolescentis L2-32',
taxon_rank: 'no rank',
superkingdom_id: 2,
superkingdom_name: 'Bacteria',
kingdom_id: null,
kingdom_name: '',
subkingdom_id: null,
subkingdom_name: '',
superphylum_id: null,
superphylum_name: '',
phylum_id: 201174,
phylum_name: 'Actinobacteria',
subphylum_id: null,
subphylum_name: '',
superclass_id: null,
superclass_name: '',
class_id: 1760,
class_name: 'Actinobacteria',
subclass_id: 85003,
subclass_name: 'Actinobacteridae',
infraclass_id: null,
infraclass_name: '',
superorder_id: null,
superorder_name: '',
order_id: 85004,
order_name: 'Bifidobacteriales',
suborder_id: null,
suborder_name: '',
infraorder_id: null,
infraorder_name: '',
parvorder_id: null,
parvorder_name: '',
superfamily_id: null,
superfamily_name: '',
family_id: 31953,
family_name: 'Bifidobacteriaceae',
subfamily_id: null,
subfamily_name: '',
tribe_id: null,
tribe_name: '',
subtribe_id: null,
subtribe_name: '',
genus_id: 1678,
genus_name: 'Bifidobacterium',
subgenus_id: null,
subgenus_name: '',
species_group_id: null,
species_group_name: '',
species_subgroup_id: null,
species_subgroup_name: '',
species_id: 1680,
species_name: 'Bifidobacterium adolescentis',
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 pept2taxa method on live data and see the response.
Request
Response