openapi: 3.0.3
info:
description: "This is an API for iPTMNet providing information about post-translational modifications (PTMs) combined from multiple sources and tools."
version: 1.0.0
title: iPTMNet
contact:
email: apiteam@swagger.io
license:
name: CC BY-NC-ND 4.0
url: https://creativecommons.org/licenses/by-nc-nd/4.0/
tags:
- name: default
paths:
/search:
get:
summary: "Search for proteins in the iPTMnet database"
description: "Search for proteins in the iPTMnet database"
operationId: "search"
parameters:
- name: search_term
description: "The term you would like to search for"
in: query
required: true
schema:
type: string
- name: term_type
description: "The type of search term"
in: query
required: true
schema:
type: string
- name: ptm_type
description: "The type of PTM to search for. Possible values are Acetylation, C-Glycosylation, Myristoylation, Ubiquitination, N-Glycosylation, S-Glycosylation, Phosphorylation, S-Nitrosylation, O-Glycosylation, Methylation, Sumoylation"
in: query
required: false
schema:
type: array
items:
type: integer
- name: role
description: ""
in: query
required: true
schema:
type: string
- name: organism
description: "The type of organism to search. The organism is represented by it's taxon ID."
in: query
required: false
schema:
type: array
items:
type: string
- name: paginate
description: "A flag that controls if the API should return paginated results. Possible values are 'true' or 'false'"
in: query
required: false
schema:
type: string
- name: start_index
description: "The start index for results to return. The indexing is zero based, hence the first index starts from zero."
in: query
required: false
schema:
type: integer
- name: end_index
description: "The end index for results to return. The indexing is zero based, hence the end index will be one less than the total count."
in: query
required: false
schema:
type: integer
tags:
- default
responses:
'200':
description: "A list of result items."
headers:
count:
schema:
type: integer
description: "The total number of items present in the result."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/search_result_item"
'400':
description: "bad input parameter"
/browse:
get:
summary: "Browse for proteins in the iPTMnet database"
description: "Browse for proteins in the iPTMnet database that are relevant to the given search term."
operationId: "browse"
parameters:
- name: term_type
description: "The type of search term"
in: query
required: true
schema:
type: string
- name: ptm_type
description: "The type of PTM to search for. Possible values are Acetylation, C-Glycosylation, Myristoylation, Ubiquitination, N-Glycosylation, S-Glycosylation, Phosphorylation, S-Nitrosylation, O-Glycosylation, Methylation, Sumoylation"
in: query
required: false
schema:
type: array
items:
type: integer
- name: role
description: ""
in: query
required: true
schema:
type: string
- name: organism
description: "The type of organism to search. The organism is represented by it's taxon ID."
in: query
required: false
schema:
type: array
items:
type: string
- name: start_index
description: "The start index for results to return. The indexing is zero based, hence the first index starts from zero."
in: query
required: false
schema:
type: integer
- name: end_index
description: "The end index for results to return. The indexing is zero based, hence the end index will be one less than the total count."
in: query
required: false
schema:
type: integer
tags:
- default
responses:
'200':
description: "A list of result items."
headers:
count:
schema:
type: integer
description: "The total number of items present in the result."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/search_result_item"
'400':
description: "bad input parameter"
/statistics:
get:
summary: "Retrieve the statistics for the database"
description: "Retrieve the statistics for the database"
operationId: statistics
tags:
- default
responses:
'200':
description: "A list of result items."
headers:
count:
schema:
type: integer
description: "The total number of items present in the result."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/inline_response_200_1"
'400':
description: "bad input parameter"
/{id}/info:
get:
summary: "Retrieve top level info about a iPTMNet entry."
description: "By passing a IPTMNet identifier, you can retrieve top level info about that protein entry in iPTMNet."
operationId: getIdInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "an info object."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/protein_info"
'400':
description: "bad input parameter"
/{id}/msa:
get:
summary: "Retrieve the annotated MSA for the iPTMNet Entry"
description: "By passing a IPTMNet identifier, you can retrieve the default annotated Multiple Sequence Alignment for the entry"
operationId: getMsaInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "an array of sequences."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/alignment"
'400':
description: "bad input parameter"
'501':
description: "Not yet implemented. Need to find format."
/{id}/substrate:
get:
summary: "Retrieve the list of PTM sites and annotations with that given substrate"
description: "By passing a IPTMNet identifier, you can retrieve the list of PTM sites and annotations with that given substrate"
operationId: getSubstrateInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "Set of tables for the PTM sites for each proteoform of the given protein"
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/inline_response_200"
'501':
description: "Not yet implemented. Need to find format."
/{id}/proteoforms:
get:
summary: "Retrieve the list of proteoforms for this entry"
description: "By passing a IPTMNet identifier, you can retrieve the list of proteoforms for this entry"
operationId: getProteoformInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "A list of proteoforms"
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/proteoform"
'400':
description: "bad input parameter"
/{id}/ptmppi:
get:
summary: "Retrieve the list of PTM dependent ppi for the iPTMNet Entry"
description: "By passing an IPTMNet identifier, you can retrieve the list of PTM dependent ppi for the iPTMNet Entry"
operationId: getPtmppiInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "A list of post translational modification dependent protein protein interactions"
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/ptm_ppi"
'400':
description: "bad input parameter"
/{id}/proteoformppi:
get:
summary: "Retrieve the list of PPI among the proteoforms for the iPTMNet Entry"
description: "By passing a IPTMNet identifier, you can retrieve the list of PPI among the proteoforms for the iPTMNet Entry"
operationId: getProteoformPpiInfo
tags:
- default
parameters:
- name: id
in: path
required: true
schema:
type: string
description: "The iPTMNet ID. Usually reuse UniProt Accession numbers."
responses:
'200':
description: "A list of proteoform protein protein interactions"
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/proteoform_ppi"
'400':
description: "bad input parameter"
/batch_ptm_enzymes:
post:
description: "Retrieve PTM enzymes information for a given list items"
summary: "Retrieve PTM enzymes information for a given list items"
operationId: batchPtmEnzymes
tags:
- default
requestBody:
description: "The list of items for which to retrieve information."
required: true
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/batch_param"
responses:
'200':
description: "A list of result items."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/batch_result_ptm_enzymes"
'400':
description: "bad input parameter"
/batch_ptm_ppi:
post:
description: "Retrieve PTM dependent PPI information for a given list items"
summary: "Retrieve PTM dependent PPI information for a given list items"
operationId: batchPtmPpi
tags:
- default
requestBody:
description: "The list of items for which to retrieve information."
required: true
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/batch_param"
responses:
'200':
description: "A list of result items."
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/batch_result_ptm_ppi"
'400':
description: "bad input parameter"
servers:
- url: https://research.bioinformatics.udel.edu/iptmnet/api
components:
schemas:
source_stats_source:
type: object
properties:
name:
type: string
url:
type: string
organism_stats_organism:
type: object
properties:
taxon_id:
type: integer
format: int64
taxon_name:
type: string
common_name:
type: string
batch_result_ptm_enzymes_ptm_enzyme:
type: object
properties:
uniprot_id:
type: string
name:
type: string
batch_result_ptm_enzymes_substrate:
type: object
properties:
uniprot_id:
type: string
name:
type: string
batch_result_ptm_enzymes:
type: object
properties:
ptm_type:
type: string
substrate:
$ref: "#/components/schemas/batch_result_ptm_enzymes_substrate"
site:
type: string
site_position:
type: string
ptm_enzyme:
$ref: "#/components/schemas/batch_result_ptm_enzymes_ptm_enzyme"
score:
type: integer
source:
type: array
items:
$ref: "#/components/schemas/source"
pmids:
type: integer
batch_result_ptm_ppi:
type: object
properties:
ptm_type:
type: string
substrate:
$ref: "#/components/schemas/batch_result_ptm_enzymes_substrate"
site:
type: string
site_position:
type: string
interactant:
$ref: "#/components/schemas/batch_result_ptm_enzymes_ptm_enzyme"
association_type:
type: string
source:
type: array
items:
$ref: "#/components/schemas/source"
pmids:
type: integer
proteoform_ppi_protein_1:
type: object
properties:
pro_id:
type: string
label:
type: string
proteoform_ppi_protein_2:
type: object
properties:
pro_id:
type: string
label:
type: string
ptm_ppi_substrate:
type: object
properties:
uniprot_id:
type: string
name:
type: string
proteoform_ptm_enzyme:
type: object
properties:
pro_id:
type: string
label:
type: string
substrate_table_inner_enzyme:
type: object
properties:
id:
type: string
type:
type: string
enum:
- 'pro_id'
- 'uniprot_ac'
name:
type: string
substrate_table_inner:
type: object
properties:
site:
type: string
'PTM Type':
$ref: "#/components/schemas/substrate_table_inner_enzyme"
score:
type: integer
format: int64
minimum: 0
maximum: 4
sources:
type: string
format: url
PMIDs:
type: array
items:
type: string
organism:
type: object
properties:
taxon_code:
type: string
species:
type: string
common_name:
type: string
source_stats:
type: object
properties:
source:
$ref: "#/components/schemas/source_stats_source"
substrates_protein:
type: integer
substrate_proteoforms:
type: integer
sites:
type: integer
enzymes:
type: integer
enzyme_substrate_pairs:
type: integer
enzyme_substrate_sites:
type: integer
ptm_dependent_ppi:
type: integer
pmids:
type: integer
organism_stats:
type: object
properties:
organism:
$ref: "#/components/schemas/organism_stats_organism"
substrates_protein:
type: integer
substrate_proteoforms:
type: integer
sites:
type: integer
enzymes:
type: integer
enzyme_substrate_pairs:
type: integer
enzyme_substrate_sites:
type: integer
ptm_dependent_ppi:
type: integer
pmids:
type: integer
event_stats:
type: object
properties:
event_name:
type: string
substrates_protein:
type: integer
substrate_proteoforms:
type: integer
sites:
type: integer
enzymes:
type: integer
enzyme_substrate_pairs:
type: integer
enzyme_substrate_sites:
type: integer
ptm_dependent_ppi:
type: integer
pmids:
type: integer
general_stats:
type: object
properties:
substrates_protein:
type: integer
substrate_proteoforms:
type: integer
sites:
type: integer
enzymes:
type: integer
enzyme_substrate_pairs:
type: integer
enzyme_substrate_sites:
type: integer
ptm_dependent_ppi:
type: integer
pmids:
type: integer
batch_param:
type: object
properties:
substrate_ac:
type: string
site_residue:
type: string
site_position:
type: string
search_result_item:
type: object
properties:
iptm_id:
type: string
protein_name:
type: string
gene_name:
type: string
synonyms:
type: array
items:
type: string
organism:
$ref: "#/components/schemas/organism"
substrate_role:
type: boolean
substrate_num:
type: integer
enzyme_role:
type: boolean
enzyme_num:
type: integer
ptm_dependent_ppi_role:
type: boolean
ptm_dependent_ppi_num:
type: integer
sites:
type: integer
isoforms:
type: integer
source:
type: object
properties:
name:
type: string
url:
type: string
format: url
proteoform_ppi:
type: object
properties:
protein_1:
$ref: "#/components/schemas/proteoform_ppi_protein_1"
relation:
type: string
protein_2:
$ref: "#/components/schemas/proteoform_ppi_protein_2"
source:
$ref: "#/components/schemas/source"
pmid:
type: integer
ptm_ppi:
type: object
properties:
ptm_type:
type: string
substrate:
$ref: "#/components/schemas/ptm_ppi_substrate"
site:
type: string
interactant:
$ref: "#/components/schemas/ptm_ppi_substrate"
association_type:
type: string
source:
$ref: "#/components/schemas/source"
pmid:
type: integer
proteoform:
type: object
properties:
pro_id:
type: string
label:
type: string
sites:
type: array
items:
type: string
ptm_enzyme:
$ref: "#/components/schemas/proteoform_ptm_enzyme"
source:
$ref: "#/components/schemas/source"
substrate_table:
type: array
items:
$ref: "#/components/schemas/substrate_table_inner"
pro_info:
type: object
properties:
id:
type: string
name:
type: string
definition:
type: string
short_label:
type: string
category:
type: string
enum:
- external
- family
- gene
- sequence
- modification, complex
- organism-family
- organism-gene
- organism-sequence
- organism-modification
- organism-complex
- union
- organism-seqgroup
protein_info:
type: object
properties:
uniprot_ac:
type: string
uniprot_id:
type: string
protein_name:
type: string
gene_name:
type: string
synonyms:
type: array
items:
type: string
organism:
$ref: "#/components/schemas/organism"
pro:
$ref: "#/components/schemas/pro_info"
decoration:
type: object
properties:
ptm_type:
type: string
source:
$ref: "#/components/schemas/source"
pmids:
type: array
items:
type: string
alignment_item:
type: object
properties:
site:
type: string
source:
type: array
items:
$ref: "#/components/schemas/decoration"
alignment:
type: object
properties:
id:
type: string
sequence:
type: array
items:
$ref: "#/components/schemas/alignment_item"
inline_response_200:
type: object
properties:
form:
type: string
table:
$ref: "#/components/schemas/substrate_table"
inline_response_200_1:
type: object
properties:
general_info:
$ref: "#/components/schemas/general_stats"
event_type:
type: array
items:
$ref: "#/components/schemas/event_stats"
top_organisms:
type: array
items:
$ref: "#/components/schemas/organism_stats"
source:
type: array
items:
$ref: "#/components/schemas/source_stats"