openapi: 3.0.2
info:
description: '
CropPAL2020 [Home Page](https://croppal.org/)
* Attributes with format `array[integer]` or `array[number]` allow range queries. e.g.
`9,` translates to `attr >= 9`, `9,12` translates to `attr >= 9 and attr <= 12`. More
than 1 comma translates to an `in` query. No comma is an equality query.
* `$iso 86001 time interval` is explained [here](https://en.wikipedia.org/wiki/ISO_8601#Durations).
* `$string like` format will interpret any string with a `%` character as an SQL
"like" query.
* `$ordering columns` is a comma separated list of column names prefixed or postfixed
by `>` or `<` so that `col>` or `
col` is
descending.
* A `per_page` of 0 means return *all* data.
* The X-Fields header attribute `$mask` allows column filtering and its format
is explained [here](https://flask-restplus.readthedocs.io/en/stable/mask.html#syntax).
All times are in timezone Australia/Perth UTC+08:00.'
license:
name: Creative Commons Attribution 4.0 International License
url: http://creativecommons.org/licenses/by/4.0/
title: CropPAL2020
version: '0.3'
tags:
- description: CropPAL2020
name: CropPAL2020
- description: SUBAlang based queries
name: suba
paths:
/Affiliation:
get:
operationId: get_Affiliation
parameters:
- explode: false
in: query
name: id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: lat
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: lng
schema:
format: number interval
items:
type: number
type: array
style: form
- in: query
name: pmid
schema:
type: string
- in: query
name: affiliation
schema:
type: string
- in: query
name: country_code
schema:
enum:
- AR
- AT
- AU
- BE
- BR
- CA
- CH
- CL
- CN
- CZ
- DE
- DK
- ES
- FI
- FR
- GB
- GR
- HK
- HR
- HU
- ID
- IE
- IL
- IN
- IR
- IT
- JP
- KR
- LT
- LU
- MX
- NL
- 'NO'
- NP
- PE
- PH
- PK
- PL
- PT
- RU
- SA
- SE
- SG
- SI
- SK
- TH
- TN
- TR
- TW
- US
- VN
- ZA
type: string
- in: query
name: country
schema:
type: string
- in: query
name: timestamp
schema:
format: iso 86001 date-time interval
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: &id002
- 0
- 2
- 5
- 10
- 20
- 50
- 100
type: integer
responses:
'200':
content:
application/json: &id001
schema:
$ref: '#/components/schemas/A%20page%20of%20Affiliations'
text/csv: *id001
description: A page of Affiliations
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Affiliation
tags:
- CropPAL2020
/Blast:
get:
operationId: get_Blast
parameters:
- explode: false
in: query
name: id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: locus
schema:
type: string
- explode: false
in: query
name: slen
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: db
schema:
type: string
- in: query
name: accession
schema:
type: string
- explode: false
in: query
name: tlen
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: expect
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: score
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: query_start
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: query_end
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: target_start
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: target_end
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: accession_taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id003
schema:
$ref: '#/components/schemas/A%20page%20of%20Blasts'
text/csv: *id003
description: A page of Blasts
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Blast
tags:
- CropPAL2020
/Exp:
get:
operationId: get_Exp
parameters:
- explode: false
in: query
name: id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: source
schema:
enum:
- gfp
- msms
type: string
- in: query
name: locus
schema:
type: string
- in: query
name: taxaid
schema:
enum:
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
format: integer interval
items:
type: integer
type: array
- in: query
name: paper
schema:
type: string
- in: query
name: location
schema:
enum:
- cytoskeleton
- cytosol
- endoplasmic reticulum
- extracellular
- golgi
- mitochondrion
- nucleus
- peroxisome
- plasma membrane
- plastid
- unclear
- vacuole
type: string
- in: query
name: source_id
schema:
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id004
schema:
$ref: '#/components/schemas/A%20page%20of%20Exps'
text/csv: *id004
description: A page of Exps
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Experimental Data
tags:
- CropPAL2020
/Homology:
get:
operationId: get_Homology
parameters:
- in: query
name: locus
schema:
type: string
- in: query
name: species
schema:
enum:
- arabidopsis_thaliana
- brassica_napus
- brassica_rapa
- glycine_max
- hordeum_vulgare
- musa_acuminata
- oryza_sativa
- solanum_lycopersicum
- solanum_tuberosum
- sorghum_bicolor
- triticum_aestivum
- vitis_vinifera
- zea_mays
type: string
- in: query
name: taxaid
schema:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
format: integer interval
items:
type: integer
type: array
- explode: false
in: query
name: identity
schema:
format: number interval
items:
type: number
type: array
style: form
- in: query
name: homology_type
schema:
enum:
- gene_split
- homoeolog_many2many
- homoeolog_one2many
- homoeolog_one2one
- ortholog_many2many
- ortholog_one2many
- ortholog_one2one
- within_species_paralog
type: string
- in: query
name: homology_locus
schema:
type: string
- in: query
name: homology_species
schema:
type: string
- explode: false
in: query
name: homology_taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: homology_identity
schema:
format: number interval
items:
type: number
type: array
style: form
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id005
schema:
$ref: '#/components/schemas/A%20page%20of%20Homologys'
text/csv: *id005
description: A page of Homologys
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Homology
tags:
- CropPAL2020
/Location:
get:
operationId: get_Location
parameters:
- in: query
name: locus
schema:
type: string
- in: query
name: taxaid
schema:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
format: integer interval
items:
type: integer
type: array
- in: query
name: assembly
schema:
type: string
- in: query
name: description
schema:
type: string
- explode: false
in: query
name: residues
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: mwt
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: pi
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: gravy
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: location_consensus
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_all_predictors
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_bacello
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_chlorop
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_epiloc
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_ipsort
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_mitoprot
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_multiloc2
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_plantmploc
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_pprowler
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_predotar
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_pts1
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_targetp
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_wolfpsort
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: location_yloc
schema:
format: set
items:
type: string
type: array
style: form
- in: query
name: athaliana
schema:
type: string
- explode: false
in: query
name: blast_id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id006
schema:
$ref: '#/components/schemas/A%20page%20of%20Locations'
text/csv: *id006
description: A page of Locations
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: subcellular predictions for proteins
tags:
- CropPAL2020
/PPI:
get:
operationId: get_PPI
parameters:
- explode: false
in: query
name: id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: Ath_locusA
schema:
type: string
- in: query
name: Ath_locusB
schema:
type: string
- in: query
name: paper
schema:
type: string
- in: query
name: location
schema:
enum:
- null
- cytoskeleton
- cytosol
- endoplasmic reticulum
- extracellular
- golgi
- mitochondrion
- nucleus
- peroxisome
- plasma membrane
- plastid
- vacuole
type: string
- in: query
name: locusA
schema:
type: string
- explode: false
in: query
name: taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: locusB
schema:
type: string
- explode: false
in: query
name: taxaidB
schema:
format: integer interval
items:
type: integer
type: array
style: form
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id007
schema:
$ref: '#/components/schemas/A%20page%20of%20PPIs'
text/csv: *id007
description: A page of PPIs
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table PPI
tags:
- CropPAL2020
/Paper:
get:
operationId: get_Paper
parameters:
- in: query
name: abstract
schema:
type: string
- in: query
name: id
schema:
type: string
- in: query
name: repository
schema:
type: string
- in: query
name: author
schema:
type: string
- in: query
name: authors
schema:
type: string
- explode: false
in: query
name: year
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: title
schema:
type: string
- in: query
name: journal
schema:
type: string
- in: query
name: volume
schema:
type: string
- in: query
name: issue
schema:
type: string
- in: query
name: pages
schema:
type: string
- in: query
name: href
schema:
type: string
- explode: false
in: query
name: source
schema:
format: set
items:
type: string
type: array
style: form
- in: query
name: doi
schema:
type: string
- in: query
name: pmc
schema:
type: string
- explode: false
in: query
name: species
schema:
format: set
items:
type: string
type: array
style: form
- in: query
name: updated
schema:
format: iso 86001 date-time interval
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id008
schema:
$ref: '#/components/schemas/A%20page%20of%20Papers'
text/csv: *id008
description: A page of Papers
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Paper
tags:
- CropPAL2020
/Seq:
get:
operationId: get_Seq
parameters:
- in: query
name: seq
schema:
type: string
- in: query
name: locus
schema:
type: string
- in: query
name: taxaid
schema:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
format: integer interval
items:
type: integer
type: array
- in: query
name: assembly
schema:
type: string
- explode: false
in: query
name: start
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: end
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: strand
schema:
type: string
- in: query
name: locus_type
schema:
type: string
- in: query
name: gene
schema:
type: string
- in: query
name: transcript
schema:
type: string
- in: query
name: description
schema:
type: string
- in: query
name: description_trimmed
schema:
type: string
- in: query
name: md5
schema:
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id009
schema:
$ref: '#/components/schemas/A%20page%20of%20Seqs'
text/csv: *id009
description: A page of Seqs
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Seq
tags:
- CropPAL2020
/SubaCon:
get:
operationId: get_SubaCon
parameters:
- in: query
name: locus
schema:
type: string
- explode: false
in: query
name: taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: suba_location
schema:
format: set
items:
type: string
type: array
style: form
- explode: false
in: query
name: exp_data
schema:
format: integer interval
items:
type: integer
type: array
style: form
- explode: false
in: query
name: cell plate
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: cytoskeleton
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: cytosol
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: endoplasmic reticulum
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: extracellular
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: golgi
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: mitochondrion
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: nucleus
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: peroxisome
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: plasma membrane
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: plastid
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: unclear
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: vacuole
schema:
format: number interval
items:
type: number
type: array
style: form
- explode: false
in: query
name: endosome
schema:
format: number interval
items:
type: number
type: array
style: form
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id010
schema:
$ref: '#/components/schemas/A%20page%20of%20SubaCons'
text/csv: *id010
description: A page of SubaCons
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table SubaCon
tags:
- CropPAL2020
/Taxa:
get:
operationId: get_Taxa
parameters:
- explode: false
in: query
name: taxaid
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: species_name
schema:
type: string
- in: query
name: species_name2
schema:
type: string
- in: query
name: species_name3
schema:
type: string
- in: query
name: species
schema:
type: string
- in: query
name: common_name
schema:
type: string
- in: query
name: comments
schema:
type: string
- in: query
name: species_name_paper
schema:
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id011
schema:
$ref: '#/components/schemas/A%20page%20of%20Taxas'
text/csv: *id011
description: A page of Taxas
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table Taxa
tags:
- CropPAL2020
/XRefs:
get:
operationId: get_XRefs
parameters:
- explode: false
in: query
name: id
schema:
format: integer interval
items:
type: integer
type: array
style: form
- in: query
name: locus
schema:
type: string
- in: query
name: db
schema:
type: string
- in: query
name: xrefid
schema:
type: string
- in: query
name: comment
schema:
type: string
- in: query
name: species
schema:
type: string
- in: query
name: taxa
schema:
type: string
- description: Order results
explode: false
in: query
name: ordering
schema:
format: ordering columns
items:
format: column ordering
type: string
type: array
style: form
- description: Select fields
explode: false
in: query
name: select
schema:
format: mask
items:
format: column select
type: string
type: array
style: form
- description: Page number
in: query
name: page
schema:
default: 1
type: integer
- description: Results per page (0 means *all* results)
in: query
name: per_page
schema:
default: 10
enum: *id002
type: integer
responses:
'200':
content:
application/json: &id012
schema:
$ref: '#/components/schemas/A%20page%20of%20XRefs'
text/csv: *id012
description: A page of XRefs
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query table XRefs
tags:
- CropPAL2020
/suba/entity_properties:
get:
description: Query metadata about Entity columns and relationships.
operationId: get_columns_resource
parameters:
- in: query
name: entity_name
required: true
schema:
enum:
- Affiliation
- Blast
- Exp
- Homology
- Location
- PPI
- Paper
- Seq
- SubaCon
- Taxa
- XRefs
type: string
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/Entity%20Properties'
description: Entity properties
'404':
content:
application/json:
schema:
$ref: '#/components/schemas/BaseException'
description: no such entity
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Entity properties including columns and relationships
tags:
- suba
/suba/paginate/{path}:
get:
description: This target should be used with the `next_url` and `prev_url` attributes
returned by a previous search `/oas3/suba/query`. It returns the next or previous
page of the current result.
operationId: get_paginate_resource
parameters:
- description: encoded url of previous or next page of current query (json|compress|btoa|quote)
in: query
name: path
required: true
schema:
type: string
responses:
'200':
content:
application/json:
schema:
discriminator:
propertyName: entity_name
oneOf:
- $ref: '#/components/schemas/A%20suba%20page%20of%20Locations'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Papers'
- $ref: '#/components/schemas/A%20suba%20page%20of%20XRefs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Blasts'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Seqs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Exps'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Homologys'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Affiliations'
- $ref: '#/components/schemas/A%20suba%20page%20of%20SubaCons'
- $ref: '#/components/schemas/A%20suba%20page%20of%20PPIs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Taxas'
description: Success
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Target for prev/next urls
tags:
- suba
parameters:
- in: path
name: path
required: true
schema:
type: string
/suba/query:
post:
description: Probably better to use [this page](https://croppal.org/oas3/search.html).
operationId: post_builder_resource
requestBody:
content:
application/x-www-form-urlencoded:
schema: &id013
properties:
entity_name:
enum:
- Affiliation
- Blast
- Exp
- Homology
- Location
- PPI
- Paper
- Seq
- SubaCon
- Taxa
- XRefs
type: string
ordering:
description: Order results
format: ordering columns
items:
format: column ordering
type: string
type: array
page:
default: 1
description: Page number
type: integer
per_page:
default: 10
description: Results per page (0 means *all* results)
enum: *id002
type: integer
query:
description: SUBA query
format: SUBA query string
type: string
select:
description: Select fields
format: mask
items:
format: column select
type: string
type: array
type: object
multipart/form-data:
schema: *id013
required: true
responses:
'200':
content:
application/json: &id014
schema:
discriminator:
propertyName: entity_name
oneOf:
- $ref: '#/components/schemas/A%20suba%20page%20of%20Locations'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Papers'
- $ref: '#/components/schemas/A%20suba%20page%20of%20XRefs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Blasts'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Seqs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Exps'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Homologys'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Affiliations'
- $ref: '#/components/schemas/A%20suba%20page%20of%20SubaCons'
- $ref: '#/components/schemas/A%20suba%20page%20of%20PPIs'
- $ref: '#/components/schemas/A%20suba%20page%20of%20Taxas'
text/csv: *id014
description: A page of SUBA results
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
'400':
content:
application/json: &id015
schema:
$ref: '#/components/schemas/LanguageException'
text/csv: *id015
description: SUBA Language Exception
headers:
Access-Control-Allow-Origin:
description: permitted cross-site locations
schema:
default: '*'
type: string
summary: Query Entities with SUBA query language
tags:
- suba
components:
responses:
LanguageException:
content:
application/json:
schema:
$ref: '#/components/schemas/LanguageException'
description: SUBA language syntax error
MaskError:
description: When any error occurs on mask
NoResultFound:
content:
application/json:
schema:
$ref: '#/components/schemas/BaseException'
description: No such element in database
OperationalError:
content:
application/json:
schema:
$ref: '#/components/schemas/BaseException'
description: Database language SQL error
ParseError:
description: When a mask can't be parsed
ProgrammingError:
content:
application/json:
schema:
$ref: '#/components/schemas/BaseException'
description: Database language programming error
schemas:
A SUBA page of results:
discriminator:
propertyName: entity_name
properties:
entity_name:
description: entity or table queried
enum:
- Affiliation
- Blast
- Exp
- Homology
- Location
- PPI
- Paper
- Seq
- SubaCon
- Taxa
- XRefs
example: Affiliation
type: string
next_url:
type: string
page:
description: Page number for this page of results
type: integer
pages:
description: Total number of pages for this query
type: integer
per_page:
default: 10
description: Number of items per page of results
enum: *id002
example: 10
format: one of a set of integers
type: integer
prev_url:
type: string
total:
description: Total number of results
type: integer
required:
- entity_name
- page
- per_page
type: object
A page of Affiliations:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Affiliation'
type: array
type: object
A page of Blasts:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Blast'
type: array
type: object
A page of Exps:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Exp'
type: array
type: object
A page of Homologys:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Homology'
type: array
type: object
A page of Locations:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Location'
type: array
type: object
A page of PPIs:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/PPI'
type: array
type: object
A page of Papers:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Paper'
type: array
type: object
A page of Seqs:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Seq'
type: array
type: object
A page of SubaCons:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/SubaCon'
type: array
type: object
A page of Taxas:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Taxa'
type: array
type: object
A page of XRefs:
allOf:
- $ref: '#/components/schemas/A%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/XRefs'
type: array
type: object
A page of results:
discriminator:
propertyName: entity_name
properties:
entity_name:
description: entity or table queried
enum:
- Location
- Paper
- XRefs
- Blast
- Seq
- Exp
- Homology
- Affiliation
- SubaCon
- PPI
- Taxa
example: Location
type: string
page:
description: Page number for this page of results
type: integer
pages:
description: Total number of pages for this query
type: integer
per_page:
default: 10
description: Number of items per page of results
enum: *id002
example: 0
format: one of a set of integers
type: integer
total:
description: Total number of results
type: integer
required:
- entity_name
- page
- per_page
type: object
A suba page of Affiliations:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Affiliation'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of Blasts:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Blast'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of Exps:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Exp'
type: array
type: object
x-mask: '{*,items{id,source,locus,taxaid,paper,location,match_type,source_id}}'
A suba page of Homologys:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Homology'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of Locations:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Location'
type: array
type: object
x-mask: '{*,items{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id,exp,papers,seq,homology}}'
A suba page of PPIs:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/PPI'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of Papers:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Paper'
type: array
type: object
x-mask: '{*,items{abstract,comment,contributed,contributor,id,repository,author,authors,year,title,journal,volume,issue,pages,href,source,doi,pmc,species,updated,exp,affiliations,prediction}}'
A suba page of Seqs:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Seq'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of SubaCons:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/SubaCon'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of Taxas:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/Taxa'
type: array
type: object
x-mask: '{*,items{*}}'
A suba page of XRefs:
allOf:
- $ref: '#/components/schemas/A%20SUBA%20page%20of%20results'
- properties:
items:
items:
$ref: '#/components/schemas/XRefs'
type: array
type: object
x-mask: '{*,items{*}}'
Affiliation:
properties:
affiliation:
example: Department of Plant and Microbial Biology, University of California,
Berkeley, CA 94720-3102, USA.
type: string
country:
example: United States
maxLength: 24
type: string
country_code:
enum:
- AR
- AT
- AU
- BE
- BR
- CA
- CH
- CL
- CN
- CZ
- DE
- DK
- ES
- FI
- FR
- GB
- GR
- HK
- HR
- HU
- ID
- IE
- IL
- IN
- IR
- IT
- JP
- KR
- LT
- LU
- MX
- NL
- 'NO'
- NP
- PE
- PH
- PK
- PL
- PT
- RU
- SA
- SE
- SG
- SI
- SK
- TH
- TN
- TR
- TW
- US
- VN
- ZA
example: US
maxLength: 24
type: string
id:
example: 1
readOnly: true
type: integer
lat:
example: 37.8739
type: number
lng:
example: -122.265
type: number
pmid:
example: '9465122'
maxLength: 24
type: string
timestamp:
example: '2019-09-02T08:32:56'
format: date-time
type: string
required:
- id
type: object
x-mask: '{*}'
BaseException:
properties:
message:
title: Error Message
type: string
required:
- message
type: object
Blast:
properties:
accession:
example: ATCG00020.1
maxLength: 32
type: string
accession_taxaid:
example: 3702
type: integer
blast_protein:
$ref: '#/components/schemas/blast_protein.Location'
db:
example: athaliana
maxLength: 32
type: string
expect:
example: 0.0
type: number
id:
example: 1
readOnly: true
type: integer
locus:
example: AGP50735
maxLength: 32
type: string
protein:
$ref: '#/components/schemas/protein.Location'
query_end:
example: 353
type: integer
query_start:
example: 1
type: integer
score:
example: 1824.0
type: number
slen:
example: 353
type: integer
target_end:
example: 352
type: integer
target_start:
example: 0
type: integer
taxaid:
example: 4513
type: integer
tlen:
example: 353
type: integer
required:
- id
type: object
x-mask: '{*}'
Entity Properties:
discriminator:
propertyName: entity_name
properties:
columns:
allOf:
- $ref: '#/components/schemas/FieldMetaData'
description: field meta data of model
entity_name:
description: Name of Entity
enum:
- Affiliation
- Blast
- Exp
- Homology
- Location
- PPI
- Paper
- Seq
- SubaCon
- Taxa
- XRefs
example: Affiliation
type: string
masked:
description: Columns or Relationships available but not sent by default.
items:
type: string
type: array
relationships:
allOf:
- $ref: '#/components/schemas/FieldMetaData'
description: field meta data of model
required:
- entity_name
type: object
Exp:
description: Experimental Data
properties:
id:
example: 1
readOnly: true
type: integer
location:
enum:
- cytoskeleton
- cytosol
- endoplasmic reticulum
- extracellular
- golgi
- mitochondrion
- nucleus
- peroxisome
- plasma membrane
- plastid
- unclear
- vacuole
example: mitochondrion
maxLength: 21
type: string
locus:
example: Zm00001d022169_P022
maxLength: 32
type: string
paper:
example: '10330475'
maxLength: 32
type: string
prediction:
$ref: '#/components/schemas/prediction.Location'
source:
enum:
- gfp
- msms
example: gfp
maxLength: 4
type: string
source_id:
example: '1343'
type: string
taxaid:
enum:
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 4577
format: one of a set of integers
type: integer
required:
- id
type: object
x-mask: '{id,source,locus,taxaid,paper,location,match_type,source_id}'
FieldMetaData:
properties:
description:
type: string
name:
type: string
type:
type: string
type: object
Homology:
properties:
homology_identity:
example: 83.0097
type: number
homology_locus:
example: HORVU0Hr1G024720.1
maxLength: 32
readOnly: true
type: string
homology_protein:
$ref: '#/components/schemas/homology_protein.Location'
homology_species:
example: hordeum_vulgare
maxLength: 255
type: string
homology_taxaid:
example: 4513
type: integer
homology_type:
enum:
- gene_split
- homoeolog_many2many
- homoeolog_one2many
- homoeolog_one2one
- ortholog_many2many
- ortholog_one2many
- ortholog_one2one
- within_species_paralog
example: within_species_paralog
maxLength: 255
type: string
identity:
example: 48.4419
type: number
locus:
example: AGP50735
maxLength: 32
readOnly: true
type: string
protein:
$ref: '#/components/schemas/protein.Location'
species:
enum:
- arabidopsis_thaliana
- brassica_napus
- brassica_rapa
- glycine_max
- hordeum_vulgare
- musa_acuminata
- oryza_sativa
- solanum_lycopersicum
- solanum_tuberosum
- sorghum_bicolor
- triticum_aestivum
- vitis_vinifera
- zea_mays
example: hordeum_vulgare
maxLength: 255
type: string
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 4513
format: one of a set of integers
type: integer
required:
- homology_locus
- locus
type: object
x-mask: '{*}'
LanguageException:
allOf:
- $ref: '#/components/schemas/BaseException'
- properties:
html:
title: html of error
type: string
lexdata:
title: query string being parsed
type: string
paths:
items:
type: string
title: attribute locations
type: array
pos:
title: position of lexical error
type: integer
type: object
Location:
description: subcellular predictions for proteins
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id,exp,papers,seq,homology}'
PPI:
properties:
Ath_locusA:
example: AT1G01010.1
maxLength: 11
type: string
Ath_locusB:
example: AT1G10030.1
maxLength: 11
type: string
id:
example: 1
readOnly: true
type: integer
location:
enum:
- null
- cytoskeleton
- cytosol
- endoplasmic reticulum
- extracellular
- golgi
- mitochondrion
- nucleus
- peroxisome
- plasma membrane
- plastid
- vacuole
maxLength: 21
type: string
locusA:
example: Bra033296.1-P
maxLength: 32
type: string
locusB:
example: Bra018466.1-P
maxLength: 32
type: string
paper:
example: '21798944'
maxLength: 11
type: string
ppi_protein:
$ref: '#/components/schemas/ppi_protein.Location'
protein:
$ref: '#/components/schemas/protein.Location'
taxaid:
example: 3711
type: integer
taxaidB:
example: 3711
type: integer
required:
- id
type: object
x-mask: '{*}'
Paper:
properties:
abstract:
example: Plants constantly monitor their light environment in order to grow
and develop optimally, in part through use of the phytochromes, which
sense red/far-red light. A phytochrome binding protein, PKS1 (phytochrome
kinase substrate 1), was identified that is a substrate for light-regulated
phytochrome kinase activity in vitro. In vivo experiments suggest that
PKS1 is phosphorylated in a phytochrome-dependent manner and negatively
regulates phytochrome signaling. The data suggest that phytochromes signal
by serine-threonine phosphorylation.
type: string
affiliations:
items:
$ref: '#/components/schemas/affiliations.Affiliation'
type: array
author:
example: Fankhauser C et al.
type: string
authors:
example: C:C:Fankhauser,K C:KC:Yeh,J C:JC:Lagarias,H:H:Zhang,T D:TD:Elich,J:J:Chory
type: string
doi:
example: 10.1126/science.284.5419.1539
maxLength: 128
type: string
exp:
items:
$ref: '#/components/schemas/exp.Exp'
type: array
href:
example: http://www.ncbi.nlm.nih.gov/pubmed/10348744
type: string
id:
example: '10348744'
maxLength: 19
readOnly: true
type: string
issue:
example: '5419'
type: string
journal:
example: Science
type: string
pages:
example: 1539-41
type: string
pmc:
maxLength: 19
type: string
prediction:
items:
$ref: '#/components/schemas/prediction.Location'
type: array
repository:
example: pubmed
maxLength: 7
type: string
source:
items:
type: string
type: array
species:
items:
type: string
type: array
title:
example: PKS1, a substrate phosphorylated by phytochrome that modulates
light signaling in Arabidopsis.
type: string
updated:
example: '2019-08-28T06:48:18'
format: date-time
type: string
volume:
example: '284'
type: string
year:
example: 1999
type: integer
required:
- id
type: object
x-mask: '{abstract,comment,contributed,contributor,id,repository,author,authors,year,title,journal,volume,issue,pages,href,source,doi,pmc,species,updated,exp,affiliations,prediction}'
Seq:
properties:
assembly:
example: '3'
maxLength: 32
type: string
description:
example: gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:LON3
description:Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
description_trimmed:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
end:
example: 1719608
type: integer
gene:
example: AT3G05780
maxLength: 32
type: string
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
locus_type:
example: chromosome
maxLength: 11
type: string
md5:
example: 470387ca090d261145cd85497351e4af
format: byte
type: string
prediction:
$ref: '#/components/schemas/prediction.Location'
seq:
example: MMPKRFNTSGFDTTLRLPSYYGFLHLTQSL...
type: string
start:
example: 1714941
type: integer
strand:
example: '-'
maxLength: 1
type: string
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
transcript:
example: AT3G05780.1
maxLength: 32
type: string
required:
- locus
type: object
x-mask: '{*}'
SubaCon:
properties:
cell plate:
example: 0.0
type: number
cytoskeleton:
example: 0.0
type: number
cytosol:
example: 0.0
type: number
endoplasmic reticulum:
example: 0.0
type: number
endosome:
example: 0.0
type: number
exp_data:
example: 0
type: integer
extracellular:
example: 0.25
type: number
golgi:
example: 0.0
type: number
locus:
example: AGP50735
maxLength: 32
readOnly: true
type: string
mitochondrion:
example: 0.25
type: number
nucleus:
example: 0.0
type: number
peroxisome:
example: 0.0
type: number
plasma membrane:
example: 0.25
type: number
plastid:
example: 0.0
type: number
prediction:
$ref: '#/components/schemas/prediction.Location'
suba_location:
items:
type: string
type: array
taxaid:
example: 4513
type: integer
unclear:
example: 0.0
type: number
vacuole:
example: 0.25
type: number
required:
- locus
type: object
x-mask: '{*}'
Taxa:
properties:
comments:
example: dicot
type: string
common_name:
example: thale cress
maxLength: 255
type: string
species:
example: arabidopsis thaliana
maxLength: 255
type: string
species_name:
example: arabidopsis_thaliana
maxLength: 255
type: string
species_name2:
example: athaliana
maxLength: 255
type: string
species_name3:
example: a_thaliana
maxLength: 255
type: string
species_name_paper:
example: a. thaliana
maxLength: 255
type: string
taxaid:
example: 3702
readOnly: true
type: integer
required:
- taxaid
type: object
x-mask: '{*}'
XRefs:
properties:
comment:
maxLength: 255
type: string
db:
example: ENA
maxLength: 17
type: string
id:
example: 1
readOnly: true
type: integer
locus:
example: AGP50735
maxLength: 128
type: string
prediction:
$ref: '#/components/schemas/prediction.Location'
species:
example: hvulgare
maxLength: 13
type: string
taxa:
example: '4513'
maxLength: 5
type: string
xrefid:
example: KC912687.1:CDS:complement(82..1143)
maxLength: 512
type: string
required:
- id
type: object
x-mask: '{*}'
affiliations.Affiliation:
properties:
affiliation:
example: Department of Plant and Microbial Biology, University of California,
Berkeley, CA 94720-3102, USA.
type: string
country:
example: United States
maxLength: 24
type: string
country_code:
enum:
- AR
- AT
- AU
- BE
- BR
- CA
- CH
- CL
- CN
- CZ
- DE
- DK
- ES
- FI
- FR
- GB
- GR
- HK
- HR
- HU
- ID
- IE
- IL
- IN
- IR
- IT
- JP
- KR
- LT
- LU
- MX
- NL
- 'NO'
- NP
- PE
- PH
- PK
- PL
- PT
- RU
- SA
- SE
- SG
- SI
- SK
- TH
- TN
- TR
- TW
- US
- VN
- ZA
example: US
maxLength: 24
type: string
id:
example: 1
readOnly: true
type: integer
lat:
example: 37.8739
type: number
lng:
example: -122.265
type: number
pmid:
example: '9465122'
maxLength: 24
type: string
timestamp:
example: '2019-09-02T08:32:56'
format: date-time
type: string
required:
- id
type: object
x-mask: '{*}'
blast_protein.Location:
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id}'
exp.Exp:
properties:
id:
example: 1
readOnly: true
type: integer
location:
enum:
- cytoskeleton
- cytosol
- endoplasmic reticulum
- extracellular
- golgi
- mitochondrion
- nucleus
- peroxisome
- plasma membrane
- plastid
- unclear
- vacuole
example: mitochondrion
maxLength: 21
type: string
locus:
example: Zm00001d022169_P022
maxLength: 32
type: string
paper:
example: '10330475'
maxLength: 32
type: string
source:
enum:
- gfp
- msms
example: gfp
maxLength: 4
type: string
source_id:
example: '1343'
type: string
taxaid:
enum:
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 4577
format: one of a set of integers
type: integer
required:
- id
type: object
x-mask: '{id,source,locus,taxaid,paper,location,match_type,source_id}'
homology.Homology:
properties:
homology_identity:
example: 83.0097
type: number
homology_locus:
example: HORVU0Hr1G024720.1
maxLength: 32
readOnly: true
type: string
homology_species:
example: hordeum_vulgare
maxLength: 255
type: string
homology_taxaid:
example: 4513
type: integer
homology_type:
enum:
- gene_split
- homoeolog_many2many
- homoeolog_one2many
- homoeolog_one2one
- ortholog_many2many
- ortholog_one2many
- ortholog_one2one
- within_species_paralog
example: within_species_paralog
maxLength: 255
type: string
identity:
example: 48.4419
type: number
locus:
example: AGP50735
maxLength: 32
readOnly: true
type: string
species:
enum:
- arabidopsis_thaliana
- brassica_napus
- brassica_rapa
- glycine_max
- hordeum_vulgare
- musa_acuminata
- oryza_sativa
- solanum_lycopersicum
- solanum_tuberosum
- sorghum_bicolor
- triticum_aestivum
- vitis_vinifera
- zea_mays
example: hordeum_vulgare
maxLength: 255
type: string
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 4513
format: one of a set of integers
type: integer
required:
- homology_locus
- locus
type: object
x-mask: '{locus,species,taxaid,identity,homology_type,homology_locus,homology_species,homology_taxaid,homology_identity}'
homology_protein.Location:
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id}'
papers.Paper:
properties:
abstract:
example: Plants constantly monitor their light environment in order to grow
and develop optimally, in part through use of the phytochromes, which
sense red/far-red light. A phytochrome binding protein, PKS1 (phytochrome
kinase substrate 1), was identified that is a substrate for light-regulated
phytochrome kinase activity in vitro. In vivo experiments suggest that
PKS1 is phosphorylated in a phytochrome-dependent manner and negatively
regulates phytochrome signaling. The data suggest that phytochromes signal
by serine-threonine phosphorylation.
type: string
author:
example: Fankhauser C et al.
type: string
authors:
example: C:C:Fankhauser,K C:KC:Yeh,J C:JC:Lagarias,H:H:Zhang,T D:TD:Elich,J:J:Chory
type: string
doi:
example: 10.1126/science.284.5419.1539
maxLength: 128
type: string
href:
example: http://www.ncbi.nlm.nih.gov/pubmed/10348744
type: string
id:
example: '10348744'
maxLength: 19
readOnly: true
type: string
issue:
example: '5419'
type: string
journal:
example: Science
type: string
pages:
example: 1539-41
type: string
pmc:
maxLength: 19
type: string
repository:
example: pubmed
maxLength: 7
type: string
source:
items:
type: string
type: array
species:
items:
type: string
type: array
title:
example: PKS1, a substrate phosphorylated by phytochrome that modulates
light signaling in Arabidopsis.
type: string
updated:
example: '2019-08-28T06:48:18'
format: date-time
type: string
volume:
example: '284'
type: string
year:
example: 1999
type: integer
required:
- id
type: object
x-mask: '{abstract,comment,contributed,contributor,id,repository,author,authors,year,title,journal,volume,issue,pages,href,source,doi,pmc,species,updated}'
ppi_protein.Location:
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id}'
prediction.Location:
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id}'
protein.Location:
properties:
assembly:
example: '3'
maxLength: 32
type: string
athaliana:
maxLength: 32
type: string
blast_id:
type: integer
description:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
exp:
description: papers describing localisation experiments
items:
$ref: '#/components/schemas/exp.Exp'
title: experiments
type: array
gravy:
example: -0.270887
type: number
homology:
items:
$ref: '#/components/schemas/homology.Homology'
type: array
location_all_predictors:
items:
type: string
type: array
location_bacello:
items:
type: string
type: array
location_chlorop:
items:
type: string
type: array
location_consensus:
items:
type: string
type: array
location_epiloc:
items:
type: string
type: array
location_ipsort:
items:
type: string
type: array
location_mitoprot:
items:
type: string
type: array
location_multiloc2:
items:
type: string
type: array
location_plantmploc:
items:
type: string
type: array
location_pprowler:
items:
type: string
type: array
location_predotar:
items:
type: string
type: array
location_pts1:
items:
type: string
type: array
location_targetp:
items:
type: string
type: array
location_wolfpsort:
items:
type: string
type: array
location_yloc:
items:
type: string
type: array
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
mwt:
example: 103482.0
type: number
papers:
items:
$ref: '#/components/schemas/papers.Paper'
type: array
pi:
example: 7.81999
type: number
residues:
example: 924
type: integer
seq:
allOf:
- $ref: '#/components/schemas/seq.Seq'
description: sequences from gramene release-40
title: sequences
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
required:
- locus
type: object
x-mask: '{locus,taxaid,assembly,description,residues,mwt,pi,gravy,location_consensus,location_all_predictors,location_bacello,location_chlorop,location_epiloc,location_ipsort,location_mitoprot,location_multiloc2,location_plantmploc,location_pprowler,location_predotar,location_pts1,location_targetp,location_wolfpsort,location_yloc,athaliana,blast_id}'
seq.Seq:
properties:
assembly:
example: '3'
maxLength: 32
type: string
description:
example: gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:LON3
description:Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
description_trimmed:
example: LON3Lon protease homolog 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M9L8]
type: string
end:
example: 1719608
type: integer
gene:
example: AT3G05780
maxLength: 32
type: string
locus:
example: AT3G05780.1
maxLength: 32
readOnly: true
type: string
locus_type:
example: chromosome
maxLength: 11
type: string
md5:
example: 470387ca090d261145cd85497351e4af
format: byte
type: string
start:
example: 1714941
type: integer
strand:
example: '-'
maxLength: 1
type: string
taxaid:
enum:
- 3702
- 3708
- 3711
- 3847
- 4081
- 4113
- 4513
- 4530
- 4558
- 4565
- 4577
- 4641
- 29760
example: 3702
format: one of a set of integers
type: integer
transcript:
example: AT3G05780.1
maxLength: 32
type: string
required:
- locus
type: object
x-mask: '{seq,locus,taxaid,assembly,start,end,strand,locus_type,gene,transcript,description,description_trimmed,md5}'
servers:
- url: https://croppal.org/oas3