/
proteins.yaml
339 lines (327 loc) · 8.38 KB
/
proteins.yaml
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precise_abundance:
get:
parameters:
- in: query
name: uniprot_id
schema:
type: array
items:
type: string
example: [Q54JE4]
required: true
- in: query
name: target_species
schema:
type: string
required: false
example: homo sapiens
- in: query
name: taxon_distance
schema:
type: boolean
required: false
example: false
tags:
- Proteins
summary: Get abundance values for proteins
description: "If abundance value for the protein is not found, one can search for proximity proteins\n
using proximity_abundance"
responses:
"200":
description: OK
content:
application/json:
schema:
$ref: "#/components/schemas/ProteinAbundance"
proximity_abundance:
get:
parameters:
- in: query
name: uniprot_id
schema:
type: string
required: true
- in: query
name: distance
schema:
type: integer
required: true
- in: query
name: depth
schema:
type: integer
required: true
tags:
- Proteins
summary: Get abundance values for proteins along the taxonomic tree
description: Search for analog proteins by traversing the taxonomic tree
responses:
"200":
description: OK
content:
application/json:
schema:
$ref: "#/components/schemas/ProximityProteinAbundance"
proximity_abundance_kegg:
get:
parameters:
- in: query
name: kegg_id
schema:
type: string
required: true
- in: query
name: anchor
schema:
type: string
default: homo sapiens
required: false
description: anchor organism
- in: query
name: distance
schema:
type: integer
required: true
tags:
- Proteins
summary: Get abundance values for proteins along the taxonomic tree
description: Search for analog proteins by traversing the taxonomic tree
responses:
"200":
description: OK
content:
application/json:
schema:
$ref: "#/components/schemas/ProximityProteinAbundance"
meta:
meta_single:
get:
parameters:
- in: query
name: ncbi_taxon_id
schema:
type: integer
required: false
- in: query
name: name
schema:
type: string
required: false
- in: query
name: ko
schema:
type: string
required: false
tags:
- Proteins
summary: Get meta information for proteins with one input
description: "Get meta information for proteins,\n
input only the taxon_id or name (either kegg orthology\n
name or protein name)."
responses:
"200":
description: OK
content:
application/json:
schema:
$ref: "#/components/schemas/ProteinMetaSingle"
meta_combo:
get:
parameters:
- in: query
name: uniprot_id
schema:
type: array
items:
type: string
required: false
- in: query
name: ncbi_taxon_id
schema:
type: integer
required: false
- in: query
name: species_name
schema:
type: string
required: false
- in: query
name: name
schema:
type: string
required: false
tags:
- Proteins
summary: Get meta information for proteins
description: "Get meta information for proteins,\n
uniprot_id overrides all other input options.\n
Combination of protein_name + taxon_id yields\n
all uniprot_id that has abundance information in\n
that particular organism. species_name overrides\n
ncbi_taxon_id. Users should try different combinations\n
to get a feel of what each combination returns."
responses:
"200":
description: OK
content:
application/json:
schema:
$ref: "#/components/schemas/ProteinMetaCombo"
summary:
num_protein:
get:
tags:
- Proteins
- Count
summary: Get number of unique proteins.
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
num_organism:
get:
tags:
- Proteins
- Organism
summary: Get number of unique organisms in protein collection.
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
num_abundances:
get:
tags:
- Proteins
summary: Get number of proteins with abundance values
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
num_obs_abundances:
get:
tags:
- Proteins
summary: Get number of observed abundance values
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
num_obs_modifications:
get:
tags:
- Proteins
summary: Get number of observed protein modifications
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
num_publications:
get:
tags:
- Proteins
summary: Get number of publications used to get protein abundances.
description: For about page
responses:
"200":
description: OK
content:
application/json:
schema:
type: integer
similar_protein:
refseq:
get:
parameters:
- in: query
name: uniprot_id
schema:
type: string
required: true
- in: query
name: identity
schema:
type: integer
enum: [100, 90, 50]
default: 90
required: false
tags:
- Proteins
summary: Get similar proteins based on refseq
description: This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters.
responses:
"200":
description: OK
content:
application/json:
schema:
type: array
items:
type: string
nullable: true
related:
related_reactions_by_kegg:
get:
parameters:
- in: query
name: ko
schema:
type: string
required: true
example: K00426
tags:
- Proteins
summary: Get related reactions based on kegg ortholog groups
description: Finds all reactions catalyzed by proteins belonging to one kegg group
responses:
"200":
description: OK
content:
application/json:
schema:
type: array
items:
type: object
nullable: true
related_reactions_by_uniprot:
get:
parameters:
- in: query
name: uniprot_id
schema:
type: string
required: true
example: Q55804
tags:
- Proteins
summary: Get related reactions based on protein's uniprot_id
description: Finds all reactions catalyzed by protein or the subunit of the enzyme contains protein
responses:
"200":
description: OK
content:
application/json:
schema:
type: array
items:
type: object
nullable: true