Brassica Information Portal API
General introduction
BIP provides a HTTP RESTful API which uses JSON to represent resources. Resources represent
database model elements (tables) which constitute BIP Schema. Full access to the API is allowed for all registered users.
In order to authenticate your request, pass the X-BIP-Api-Key
header in
each call to the API.
The API exposes several resources for which fetching and submission of new entries is supported [1]. These include:
- LinkageGroup
- LinkageMap
- MapLocusHit
- MapPosition
- MarkerAssay
- PlantAccession
- PlantLine
- PlantPopulation
- PlantPopulationList
- PlantScoringUnit
- PlantTrial
- PlantVariety
- TraitDescriptor
- TraitScore
- DesignFactor
- PopulationLocus
- Primer
- Probe
- Qtl
- QtlJob
All attributes are expressed as basic data types such as int
,
string
, date
or arrays of these. Most of the related
objects are not directly included in the response - instead they are represented by identifiers (or arrays
of identifiers); for instance taxonomy_term_id
or qtl_ids
.
Use these identifiers to retrieve the relevant resources with further API calls.
Those related objects which are not available through a dedicated API read call are
always embedded in the parent data structure - for example, population_type
.
They are usually represented by the object
format in the attribute tables.
Example
HTTP/1.1 200 OK
Content-Type: application/json; charset=utf-8
{
"plant_population": {
"id": 1,
"name": "BnaWAIT_01",
"population_type": {
"population_type": "Integrated",
"population_class": "Mapping",
...
},
...
"linkage_map_ids": [8]
}
}
Several resources support fetching data only:
- Country
- PlantPart
- PopulationType
- TaxonomyTerm
- Trait
Fetching data
Any resource can be fetched by passing its id
.
Multiple resources can be fetched with or without additional parameters
to filter results. These parameters are specific for each
resource and will be described in detail later on.
If a resource is owned by another BIP user, and is set as not published, you will not be able to fetch it.
Fetching multiple resources always yields paginated results.
page | int | Page number (default: 1) | |
per_page | int | Page size (default: 50, max: 200) |
meta[page] | int | Current page number | |
meta[per_page] | int | Page size | |
meta[total_count] | int | Total number of existing records |
Example
GET /api/v1/plant_lines?page=2&per_page=100 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
HTTP/1.1 200 OK
Content-Type: application/json
{
"plant_lines": [
{
"id": 6,
...
},
...
],
"meta": {
"page": 2,
"per_page": 100,
"total_count": 1291
}
}
Remember to replace X-BIP-Api-Key
with your own API key.
Filtering data
Most resources can be filtered by selected attributes. The attribute tables (listed below for each resource type) indicate when a specific attribute may be subject to filtering - look for the `Q` marker. The usage pattern is as follows:
resource_name[query][attribute_name] | depends on the attribute format | Should return only those resources which declare a certain value for attribute_name. |
Examples
-
Plant Line filtering by
plant_line_name
GET /api/v1/plant_lines?plant_line[query][plant_line_name]=WINFRED HTTP/1.1 Content-Type: application/json Accept: application/json X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Sign in to try it in your browser! -
Multiple filtering attributes can be applied in a single query - here we filter Plant Varieties by
owner
andregistration_year
GET /api/v1/plant_varieties?plant_variety[query][owner]=Limagrain&plant_variety[query][reqistration_year]=1998 HTTP/1.1 Content-Type: application/json Accept: application/json X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Sign in to try it in your browser!
One additional special filter, called only_mine
may be used to fetch
only the resources which you own (that is, which were created by you). This is how
you use this special filter:
GET /api/v1/plant_varieties?only_mine=true HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Searching for data
It is also possible to search for a given resource by passing a term and matching it against multiple attributes at once. This resembles the search capability available on the BIP front page. Such queries need to be scoped by resource type.
What exactly is being sought? The resource attributes that are checked for the presence of the search term
are basically all those marked with the `Q` tag in the attribute tables.
Additionally, some related resource attributes are checked - the rule of thumb is that if an attribute
value is visible as a column in the
browse data
tables, it should be searchable via the fetch
API parameter.
resource_name[fetch] | string | Given a term, it should return all resources of a given type whose attribute values match (at least partially) the search term. |
Examples
-
Plant Lines search
GET /api/v1/plant_lines?plant_line[fetch]=WINFRED HTTP/1.1 Content-Type: application/json Accept: application/json X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Sign in to try it in your browser! -
The result includes metadata showing how many records were found - see the
total_count
value in themeta
result document element. It is therefore possible to combine filtering and pagination in a single request, e.g. to retrieve further data.GET /api/v1/plant_lines?plant_line[fetch]=WINFRED&per_page=2&page=2 HTTP/1.1 Content-Type: application/json Accept: application/json X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Sign in to try it in your browser! -
Searching by related object attribute - the
name
of a Taxonomy TermGET /api/v1/plant_populations?plant_population[fetch]=oleracea&per_page=5 HTTP/1.1 Content-Type: application/json Accept: application/json X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Sign in to try it in your browser!
In order to maintain consistency between successive searches, all search results are ordered
by their internal id
BIP identifier. This ensures the API will return the same results
in the same order in two subsequent calls - provided, of course, no new data is submitted
in the meantime. For this reason the results of `fetch` API calls might differ slightly from
what can be obtained via the web search form.
Traversing data model
Each record returned by described methods includes its BIP internal numerical identifier, id
.
Also, a list of related records is usually provided as an array of such numbers, for instance a Plant
Scoring Unit may have multiple related Trait Scores:
{
"plant_scoring_units": [
{
"id": :84208,
"trait_score_ids": [98413,98412],
...
}
]
}
Using these identifiers it is possible to query BIP for these related records:
GET /api/v1/trait_scores?trait_score[query][id]=98413 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Please note the plant_scoring_unit_id
field in the returned JSON response. Due to the
symmetry of relations, this should refer back to the original Plant Scoring Unit record (id
84208).
Submitting new data
The following resources can currently be submitted via API calls:
- LinkageGroup
- LinkageMap
- MapLocusHit
- MapPosition
- MarkerAssay
- PlantAccession
- PlantLine
- PlantPopulation
- PlantPopulationList
- PlantScoringUnit
- PlantTrial
- PlantVariety
- TraitDescriptor
- TraitScore
- DesignFactor
- PopulationLocus
- Primer
- Probe
- Qtl
- QtlJob
Data submission is based on the JSON format, i.e., the API POST
request should pass a JSON document whose root element matches the name of the
target resource type (e.g. plant_population
).
Each resource section below shows an example of such a POST
API call.
For each resource some attributes (described later) are required in create requests.
Skipping any of those will result in a
422
error response. Passing attributes which are not recognized by the API will also
produce 422
errors.
Examples
-
Missing value for required attribute
HTTP/1.1 422 Unprocessable Entity Content-Type: application/json { "errors": [ { "attribute": "name", "message": "Can't be blank" } ] }
-
Misspelled attribute name
HTTP/1.1 422 Unprocessable Entity Content-Type: application/json { "errors": [ { "attribute": "priner", "message": "Unrecognized attribute name" } ] }
Most of the resource attributes, as shown in the following attribute tables,
are textual (string
format) - these are simply pieces of text of
arbitrary length, enclosed in double quotation marks "
. Attributes
that are of int
format are passed without quotes.
Dates should be entered in a textual format - several different notations are
recognized and accepted, although we suggest sticking to a single, consistent
format - YYYY-MM-DD
. Examples are provided below:
Example
{
"plant_population": {
...
"description": "Example of text content",
"date_established": "2015-05-30",
"taxonomy_term_id": 5,
...
}
}
Two attributes are never entered by users, but are instead automatically set by the server:
entered_by_whom | string | Always set to the name of the user whose API Key was used to submit the data. | |
date_entered | date | Always set to the day the data was successfully submitted. |
Finally, attributes marked as readonly
in the attribute
tables cannot be directly set. These include single related resources
(one such example is the population_type
of a Plant Population).
In this case, one should provide the BIP identifier of a related object when submitting
new data. For instance, when submitting a new Plant Population:
Example
{
"plant_population": {
...
"population_type": "DH segregating", # WRONG
"population_type_id": 1, # RIGHT
...
}
}
If the provided identifier does not exist in the BIP database, the following error will be returned:
HTTP/1.1 422 Unprocessable Entity
Content-Type: application/json
{
"errors": [
{
"attribute": "plant_population_id",
"message": "DETAIL: Key (plant_population_id)=(1000000) is not present in table \"plant_populations\"."
}
]
}
Another case of a readonly
attribute involves multiple related
resources - for instance, plant_trials_ids
of a Plant Population.
In such cases the correct relationship is set while submitting the corresponding
resource (i.e., in a reverse fashion). For example, when submitting a new Plant Trial,
supplying a correct value of plant_population_id
will create the intended relationship.
If the submission is successful, you will get a JSON document in return. Since the document
describes the submitted record, it will mostly contain the data you have just submitted.
However, it also provides the internal BIP identifier assigned to the new
record - see the value of the id
attribute.
HTTP/1.1 201 Created
Content-Type: application/json
{
"plant_line": {
"plant_line_name": "Plant line by API",
...
"entered_by_whom": "Your User Name",
"date_entered": "2015-07-18"
"id": 25697
}
}
You may now utilize that identifier to relate your newly created object with other records you are about to submit (for instance, new Plant Populations).
Publishing submitted data
The basic data management policy of BIP is that after you submit your data it becomes public and can be cited as a public resource by other users. However, you can explicitly state that you wish your data to remain private.
Example
POST /api/v1/trait_scores HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"trait_score": {
"published": false,
...
}
}
Data submitted as private can be published at a later date. Resources which are to be published need to be updated one by one.
Example
PATCH /api/v1/trait_scores/:id/publish HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
The rule of thumb is that after publishing data you have exactly one week to revoke publication. Please use this time to check whether all information was correctly provided. After one week, the publication becomes permanent and cannot be revoked.
Example
PATCH /api/v1/trait_scores/:id/revoke HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
This operation will not delete your data, but BIP will no longer show it to other users. You can publish it again whenever you wish.
Deleting submitted data
Mistakes do happen and therefore we provide the ability to delete submitted resources. You can only delete private resources or published resources for which the revocation timer has not yet expired. Should you wish to delete any other data, please contact the BIP support team directly.
Example
DELETE /api/v1/plant_populations/5555 HTTP/1.1
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
This example shows how to delete the Plant Population with the internal
BIP id
equal 5555. This may result in several different responses:
Examples
-
Wrong, nonexistent Plant Population
HTTP/1.1 404 Not Found Content-Type: application/json { "reason": "Resource not found" }
-
API key owner and resource owner are not the same user
HTTP/1.1 401 Unauthorized Content-Type: application/json { "reason": "API key owner and resource owner mismatch" }
-
The requested resource is already past its revocation period and cannot be deleted anymore
HTTP/1.1 403 Forbidden Content-Type: application/json { "reason": "This resource is already published and irrevocable" }
-
The call was a success, the resource was deleted
HTTP/1.1 204 No Content
API client example
In order to demonstrate the capabilities of the API and to assist new programmers in preparing their own BIP client code, we provide a fairly complex example of a client program, written in Ruby (Ruby MRI interpreter version 2.2 is required to run it).
The sample client consists of two elements:
You will also need your API key. Please refer to the general introduction for instructions on how to obtain it. Additional information regarding the example is contained in the script file - the code is rather self-explanatory, and we provide embedded comments.
It should be noted that this script is not meant to be a generic, all-purpose client for the BIP API. Rather, its purpose is to provide an example of how to prepare your own scripts, matching specific user requirements. The sample data was generated on the basis of RIPR project data, with altered (fictional) values.
Detailed model introduction
Below, the resources (which mostly represent data base tables in the BIP data model) and their attributes (which correspond, to large extent, with individual columns in data base tables) that are exposed with the API are described in more detail. Use these attributes in your calls to the API. For each resource, a set of examples for various API calls is given below its attributes table.
Country
id | int | readonly, Q | Unique BIP database identifier |
country_code | string | Q | ISO 3166-1 alpha-3 code of this Country |
country_name | string | Q | Name of this Country in English |
plant_trial_ids | int[] | Zero or more BIP identifiers of Plant Trials which took place in this Country | |
originating_plant_variety_ids | int[] | Zero or more BIP identifiers of Plant Varieties originating in this Country | |
registered_plant_variety_ids | int[] | Zero or more BIP identifiers of Plant Varieties registered in this Country |
Example
GET /api/v1/countries?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/countries/2 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
DesignFactor
id | int | readonly, Q | Unique BIP database identifier |
design_factor_name | string | An optional name assigned to this design factor | |
institute_id | string | Name of the institute in case which designed the experiment | |
trial_location_name | string | Optional name of the location where this design was used | |
design_unit_counter | string | required | The ordinal number of a unique design factor for a given plant trial; it is safe to set it to the number of the smallest design factors (e.g. "354") |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
design_factors | string[] | required | List of values for subsequent design factors, which go from the biggest factor to the smallest one, structures as factor_number (e.g. "block_2", "row_V", "plot_354") |
plant_scoring_unit_ids | int[] | readonly | Zero or more BIP identifiers of Plant Scoring Units which have this Design Factor in a Plant Trial |
Example
GET /api/v1/design_factors?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/design_factors/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/design_factors HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"design_factor": {
"design_factor_name": "New design of our institute",
"design_factors": ["block_2", "row_V", "plot_354"],
"design_unit_counter": "354"
}
}
LinkageGroup
id | int | readonly, Q | Unique BIP database identifier |
linkage_group_label | string | required, Q | The label given to this linkage group by the database curator |
linkage_group_name | string | required, Q | Unique name of this linkage group |
total_length | string | Q | Total length of this linkage group in centimorgan (cM) |
lod_threshold | string | Q | The threshold of LOD score of similarity for this linkage group |
consensus_group_assignment | string | required, Q | Consensus group identification (e.g. A01, C09) in accordance with community naming standards |
consensus_group_orientation | string | Q | Consensus orientation of the linkage group on the target chromosome |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
linkage_map_id | int | BIP identifier of the Linkage Maps this group belongs to | |
map_position_ids | int[] | readonly | Zero or more BIP identifiers of Map Positions related to this group |
map_locus_hit_ids | int[] | readonly | Zero or more BIP identifiers of Map Locus Hits related to this group |
qtl_ids | int[] | readonly | Zero or more BIP identifiers of Quantitative Trait Loci related to this group |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/linkage_groups?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/linkage_groups/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/linkage_groups HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"linkage_group": {
"linkage_group_label": "2015_group1",
"linkage_group_name": "NG2",
"consensus_group_assignment": "C02"
}
}
LinkageMap
id | int | readonly, Q | Unique BIP database identifier |
linkage_map_label | string | required, Q | Label assigned to this linkage map by the database curator |
linkage_map_name | string | required, Q | Unique name of this linkage map |
map_version_no | string | required, Q | Descriptive number of this linkage map's version |
map_version_date | date | Q | Date on which this linkage map was prepared |
mapping_software | string | Description of the software package used to create this linkage map | |
mapping_function | string | Description of the algorithm used to create this linkage map | |
map_author | string | Person who created this linkage map | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
pubmed_id | string | PubMed identifier of the publication where this linkage map was published | |
plant_population_id | int | BIP identifier of the Plant Population for which this linkage map was created | |
linkage_group_ids | int[] | readonly | Zero or more BIP identifiers of Linkage Groups belonging to this map |
map_locus_hit_ids | int[] | readonly | Zero or more BIP identifiers of Map Locus Hits related to this map |
qtl_job_ids | int[] | readonly | Zero or more BIP identifiers of Qtl Jobs that computed elements of this map |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/linkage_maps?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/linkage_maps/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/linkage_maps HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"linkage_map": {
"linkage_map_label": "2015_group1",
"linkage_map_name": "B rapa map 2015",
"map_version_no": "2"
}
}
MapLocusHit
id | int | readonly, Q | Unique BIP database identifier |
consensus_group_assignment | string | required, Q | Consensus group identification (e.g. A01, C09) in accordance with community naming standards |
canonical_marker_name | string | required, Q | Marker assay related to this map locus hit |
associated_sequence_id | string | required, Q | Identifier of the nucleotide sequence related to this hit in external database |
sequence_source_acronym | string | required, Q | Name of the external database where to look for the associated nucleotide sequence |
atg_hit_seq_id | string | Q | Associated identifier in the e!ensembl portal |
atg_hit_seq_source | string | Q | Indication about the source of the sequence (usually the e!ensembl portal) |
bac_hit_seq_id | string | Q | Identification of sequence obtained with bacterial artificial chromosome (BAC) method |
bac_hit_seq_source | string | Q | Indication about the source of the BAC sequence (usually NCBI services) |
bac_hit_name | string | Q | Brassica BAC clone identifier as used in the linked external database |
linkage_map_id | int | BIP identifier of the Linkage Map related to this locus hit | |
linkage_group_id | int | BIP identifier of the Linkage Group related to this locus hit | |
population_locus_id | int | BIP identifier of the Population Locus related to this locus hit | |
map_position_id | int | BIP identifier of the Map Position of this locus hit | |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/map_locus_hits?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/map_locus_hits/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/map_locus_hits HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"map_locus_hit": {
"consensus_group_assignment": "C02",
"canonical_marker_name": "PW177",
"associated_sequence_id": "1",
"sequence_source_acronym": "NCBI_GSS"
}
}
MapPosition
id | int | readonly, Q | Unique BIP database identifier |
map_position | string | required, Q | Position identifier |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
marker_assay_id | int | BIP identifier of the associated Marker Assay | |
linkage_group_id | int | BIP identifier of the Linkage Group this map position is listed in | |
population_locus_id | int | BIP identifier of the Population Locus for this map position | |
map_locus_hit_ids | int[] | readonly | Zero or more BIP identifiers of Map Locus Hits related to this position |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/map_positions?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/map_positions/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/map_positions HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"map_position": {
"map_position": "102.5"
}
}
MarkerAssay
id | int | readonly, Q | Unique BIP database identifier |
marker_assay_name | string | required, Q | Unique name assigned to this marker assay by the data contributor or database curator |
canonical_marker_name | string | required, Q | Canonical name for this assay as assigned by the database curator |
marker_type | string | Q | The type of marker represented by this data |
separation_system | string | Q | Separation system applied in this marker assay |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
probe_id | int | BIP identifier of the associated Probe | |
primer_a_id | int | BIP identifier of the Primer associated with this marker assay (5` end) | |
primer_b_id | int | BIP identifier of the Primer associated with this marker assay (3` end) | |
population_locus_ids | int[] | readonly | Zero or more BIP identifiers of Population Locus related to this marker assay |
map_position_ids | int[] | readonly | Zero or more BIP identifiers of Map Positions related to this marker assay |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/marker_assays?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/marker_assays/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/marker_assays HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"marker_assay": {
"marker_assay_name": "My marker assay name",
"canonical_marker_name": "Mma"
}
}
PlantAccession
id | int | readonly, Q | Unique BIP database identifier |
plant_accession | string | required, Q | Unique name given to this accession |
plant_accession_derivation | string | Q | What is the source of plant accession information (for instance, an experiment) |
accession_originator | string | Q | Person who maintains this accession |
originating_organisation | string | required, Q | Name of the legal entity that maintains this accession |
year_produced | string | Q | Year the plant was produced in |
date_harvested | date | Q | Day the plant was harvested on |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
plant_line_id | int | required (if no plant_variety_id) | BIP identifier of the associated Plant Line |
plant_variety_id | int | required (if no plant_line_id) | BIP identifier of the associated Plant Variety |
plant_scoring_unit_ids | int[] | readonly | Zero or more BIP identifiers of Plant Scoring Units performed for this plant |
published_on | datetime | readonly | The day and time the data was published |
plant_line_id
and plant_variety_id
attributes should be provided (but never both). Also note that the combination of (plant_accession
, originating_organisation
and year_produced
must uniquely identify the accession, i.e. no two records with identical values in all three fields may exist in the database.
Example
GET /api/v1/plant_accessions?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_accessions/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_accessions HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_accession": {
"plant_accession": "Accession1",
"originating_organisation": "EI",
"plant_line_id": 15523
}
}
PlantLine
id | int | readonly, Q | Unique BIP database identifier |
plant_line_name | string | required, Q | Unique name of this Plant Line provided by the person who submitted the data |
common_name | string | Q | Common name of this Plant Line that is widely recognized by the breeder community |
named_by_whom | string | Individual or legal entity which gave the line its name | |
organisation | string | Q | Legal entity which owns this Plant Line |
genetic_status | string | Q | Design method used to obtain this population line (i.e. open pollinated, inbred, substitution lines) |
sequence_identifier | string | Q | Identifier of the line sequence, in an external database, like NCBI SRA. Identifiers starting with SR will be automatically recognized as SRA submissions. |
previous_line_name | string | Q | Old name of the Plant Line, if changed |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_provenance | string | Additional information regarding the origin of this data | |
data_owned_by | string | Name of the legal entity which published this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
taxonomy_term_id | int | BIP identifier of a Taxonomy Term entry related to this record | |
plant_variety_id | int | BIP identifier of the Plant Variety which this Plant Line is classified as | |
plant_variety_name | string | readonly | Legacy Plant Variety name (pending curation) |
fathered_descendant_ids | int[] | readonly | Zero or more BIP identifiers of Plant Populations descending from this entry in the male line |
mothered_descendant_ids | int[] | readonly | Zero or more BIP identifiers of Plant Populations descending from this entry in the female line |
plant_accession_ids | int[] | readonly | Zero or more BIP identifiers of related Plant Accessions |
plant_population_ids | int[] | readonly | Zero or more BIP identifiers of Plant Populations bred in this Plant Line |
plant_population_list_ids | int[] | readonly | Zero or more BIP identifiers of Plant Population Lists, which serve as a join table between Plant Lines and Plant Populations |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_lines?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_lines/9189 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_lines HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_line": {
"plant_line_name": "My new line"
}
}
PlantPart
id | int | readonly, Q | Unique BIP database identifier |
plant_part | string | Name of the part of a plant | |
description | string | Longer text explaining what part of plant this record represents | |
label | string | Plant Ontology identifier, if available | |
canonical | boolean | Set to true if the term is defined in Plant Ontology; false otherwise | |
described_by_whom | string | The person or organization who described this dictionary entry | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
trait_descriptor_ids | int[] | Zero or more BIP identifiers of Trait Descriptors that describe traits scored using this Plant Part |
Example
GET /api/v1/plant_parts?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_parts/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
PlantPopulation
id | int | readonly, Q | Unique BIP database identifier |
name | string | required, Q | Unique name of this Plant Population provided when submitting data |
data_owned_by | string | Name of the legal entity which published this data | |
population_type | object | readonly | Additional information about the type of this population |
description | string | Q | Textual description of the population,provided by the data publisher |
date_established | date | Year of population introduction | |
established_by_whom | string | The person, if known, who introduced this population | |
establishing_organisation | string | required, Q | Legal entity that introduced this population |
population_owned_by | string | Name of the legal entity which owns this population | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
taxonomy_term_id | int | BIP identifier of a Taxonomy Term entry related to this record | |
population_type_id | int | BIP identifier of the Population Type assigned to this population | |
male_parent_line_id | int | BIP identifier of the Plant Line which this population descends from in the male line | |
female_parent_line_id | int | BIP identifier of the Plant Line which this population descends from in the female line | |
linkage_map_ids | int[] | readonly | Zero or more BIP identifiers of Linkage Maps defined for this population |
population_locus_ids | int[] | readonly | Zero or more BIP identifiers of Population Loci published for this population up until the present date |
plant_trial_ids | int[] | readonly | Zero or more BIP identifiers of trait Plant Trials performed for this population until the present date |
plant_line_ids | int[] | readonly | Zero or more BIP identifiers of Plant Lines that this population is associated with |
plant_population_list_ids | int[] | readonly | Zero or more BIP identifiers of Plant Population Lists, which serve as a join table between Plant Lines and Plant Populations |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_populations?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_populations/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_populations HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_population": {
"name": "My new population"
}
}
PlantPopulationList
sort_order | string | - | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
plant_population_id | int | required | BIP identifier of the Plant Population related to this list |
plant_line_id | int | required | BIP identifier of the Plant Line related to this list |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_population_lists?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_population_lists/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_population_lists HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_population_list": {
"plant_population_id": 5,
"plant_line_id": 78
}
}
PlantScoringUnit
id | int | readonly, Q | Unique BIP database identifier |
scoring_unit_name | string | required, Q | Unique name assigned to this scoring unit by the person who submitted the data |
number_units_scored | string | Q | Number of units scored for this particual scoring scenario |
scoring_unit_sample_size | string | Q | The size of the scored unit |
scoring_unit_frame_size | string | Q | The size of the scored unit |
date_planted | date | Q | Day on which the population scored in this unit was planted |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
design_factor_id | int | BIP identifier of the Design Factor object, which stores additional information concerning the design of this experiment | |
plant_accession_id | int | required | BIP identifier of the associated database Plant Accession |
plant_trial_id | int | required | BIP identifier of the Plant Trial in the scope of which this plant scoring took place |
trait_score_ids | int[] | readonly | Zero or more BIP identifiers of Trait Scores recorded in this scoring unit |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_scoring_units?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_scoring_units/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_scoring_units HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_scoring_unit": {
"scoring_unit_name": "plant_2/2016",
"plant_accession_id": 755,
"plant_trial_id": 1
}
}
PlantTrial
id | int | readonly, Q | Unique BIP database identifier |
plant_trial_name | string | required, Q | Unique name assigned to this scoring trial by the person who submitted the data |
project_descriptor | string | required, Q | Name of the project that undertook the trial |
plant_trial_description | string | required, Q | Additional descriptive information concerning the trial |
trial_year | string | required, Q | Year (or years) the trial took place |
institute_id | string | required, Q | Name of the legal entity that performed this plant trial |
trial_location_site_name | string | Q | Site where the plant trial was performed |
place_name | string | required | Place where the plant trial was performed |
country | object | Country where the plant trial took place | |
latitude | string | Geographical latitude of the exact location where this trial took place | |
longitude | string | Geographical longitude of the exact location where this trial took place | |
altitude | string | Altitude of the exact location where this trial took place | |
terrain | string | Description of the environment of the cultivation process (e.g. what type of glasshouse was used) | |
soil_type | string | Type of soil was used in the cultivation process | |
contact_person | string | Contact information for this trial | |
design_type | string | How the cultivation and the trial were designed | |
statistical_factors | string | Factors which influenced statistical analysis of the trial's outcome | |
design_factors | string | Additional information about the design factors involved in the plant trial | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
pubmed_id | string | PubMed identifier of the publication where this plant trial was published | |
plant_population_id | int | BIP identifier of the plant population that was the subject of this trial | |
country_id | int | BIP identifier of the country where this trial took place | |
plant_scoring_unit_ids | int[] | readonly | Zero or more BIP identifiers of Plant Scoring Units recorded during this trial |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_trials?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_trials/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_trials HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_trial": {
"plant_trial_name": "BIPrassica Trial Spring 2016",
"project_descriptor": "BIPrassica Project",
"trial_year": "2016",
"place_name": "Norwich",
"country_id": 107
}
}
PlantVariety
id | int | readonly, Q | Unique BIP database identifier |
plant_variety_name | string | required, Q | The name of this variety provided either by the person submitting the data or the database curator |
crop_type | string | Q | Crop type of this variety (e.g. kale, swede, rape etc.) |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_provenance | string | Additional information regarding the origin of this data | |
data_attribution | string | Q | Additional information about the data attribution for this variety |
year_registered | string | Q | Year (or years) when this variety was officially registered |
breeders_variety_code | string | Q | Code assigned to this variety by plant breeders |
owner | string | Q | Name of the legal organization which introduced this variety |
quoted_parentage | string | Q | Parentage information for this variety as given in literature or provided by the database curator |
female_parent | string | Q | Female parent of this variety, if identified |
male_parent | string | Q | Male parent of this variety, if identified |
countries_of_origin | object[] | readonly | Zero or more JSON documents listing countries that this variety originates from |
countries_of_origin_ids | int[] | writeonly | Zero or more BIP identifiers of countries that this variety originates from |
countries_registered | object[] | readonly | Zero or more JSON documents listing countries that this variety is registered in |
countries_registered_ids | int[] | writeonly | Zero or more BIP identifiers of countries that this variety is registered in |
plant_accession_ids | int[] | readonly | Zero or more BIP identifiers of related Plant Accessions |
plant_line_ids | int[] | readonly | Zero or more BIP identifiers of Plant Lines classified under this plant variety |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/plant_varieties?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/plant_varieties/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/plant_varieties HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"plant_variety": {
"plant_variety_name": "BIPrassica"
}
}
PopulationLocus
id | int | readonly, Q | Unique BIP database identifier |
mapping_locus | string | required, Q | Unique name assigned to this population locus by the person submitting the data |
defined_by_whom | string | Q | Name of the person who defined and described this population locus |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
plant_population_id | int | BIP identifier of the plant population for which the locus was identified | |
marker_assay_id | int | BIP identifier of the marker assay associated with this locus | |
map_position_ids | int[] | readonly | Zero or more BIP identifiers of map positions associated with this locus |
map_locus_hit_ids | int[] | readonly | Zero or more BIP identifiers of Map Locus Hits associated with this locus |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/population_loci?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/population_loci/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/population_loci HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"population_locus": {
"mapping_locus": "A07.790"
}
}
PopulationType
id | int | readonly, Q | Unique BIP database identifier |
population_type | string | Textual description of the population type | |
population_class | string | Class of populations this type belongs to | |
assigned_by_whom | string | Assignee of this population type | |
plant_population_ids | int[] | Zero or more BIP identifiers of Plant Populations that are of this population type |
Example
GET /api/v1/population_types?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/population_types/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Primer
id | int | readonly, Q | Unique BIP database identifier |
primer | string | required, Q | Unique name that identifies this primer |
sequence | string | required, Q | Exact sequence of the primer |
sequence_id | string | Q | Identifier of the primer sequence, in a source database |
sequence_source_acronym | string | Q | Name of the source database where the probe sequence can be obtained |
description | string | Q | Additional description of the primer provided by the person who submitted the data |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
marker_assays_a_ids | int[] | readonly | Zero or more BIP identifiers of marker assays related to that primer (5` end) |
marker_assays_b_ids | int[] | readonly | Zero or more BIP identifiers of marker assays related to that primer (3` end) |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/primers?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/primers/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/primers HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"primer": {
"primer": "pr3_ENA3",
"sequence": "GTCAAGTTTCTCTCCACACC"
}
}
Probe
id | int | readonly, Q | Unique BIP database identifier |
probe_name | string | required, Q | Unique name that identifies this probe |
clone_name | string | required, Q | Clone type (e.g. genomic survey sequence GSS, expressed sequence tag EST, or similar) |
sequence_id | string | required, Q | Identifier of the probe sequence |
sequence_source_acronym | string | required, Q | Name of the source database where the probe sequence can be obtained |
date_described | date | Q | Day on which this probe was described |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
taxonomy_term_id | int | BIP identifier of the Taxonomy Term this probe is related to | |
marker_assay_ids | int[] | readonly | Zero or more BIP identifiers of marker assays related to this probe |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/probes?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/probes/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/probes HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"probe": {
"probe_name": "pR60",
"clone_name": "pR60",
"sequence_id": "70814396",
"sequence_source_acronym": "NCBI_GSS"
}
}
Qtl
id | int | readonly, Q | Unique BIP database identifier |
qtl_rank | string | required, Q | Order of QTL on an associated linkage group |
map_qtl_label | string | required, Q | Label assigned to this QTL |
outer_interval_start | string | Q | Start location of the mapped outer QTL interval (interpretation depends on the used interval mapping method) |
outer_interval_end | string | Q | End location of the mapped outer QTL interval (interpretation depends on the used interval mapping method) |
inner_interval_start | string | Q | Start location of the mapped inner QTL interval (interpretation depends on the used interval mapping method) |
inner_interval_end | string | Q | End location of the mapped inner QTL interval (interpretation depends on the used interval mapping method) |
qtl_mid_position | string | required, Q | Position used for mapping this QTL |
peak_value | string | Q | Peak probability value for the QTL intervals represented by this record (QTL curve peak value) |
peak_p_value | string | Q | - |
regression_p | string | Q | - |
residual_p | string | Q | - |
additive_effect | string | Q | - |
genetic_variance_explained | string | Q | - |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
pubmed_id | string | PubMed identifier of the publication where this QTL was published | |
qtl_job_id | int | BIP identifier of the QTL Job that describes the method used to obtain this QTL | |
linkage_group_id | int | BIP identifier of the Linkage Group that this QTL is associated with | |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/qtls?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/qtls/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/qtls HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"qtl": {
"qtl_rank": "7",
"map_qtl_label": "Mg-f-mr",
"qtl_mid_position": "52.96"
}
}
QtlJob
id | int | readonly, Q | Unique BIP database identifier |
qtl_job_name | string | required, Q | Name assigned to this QTL job by the database curator |
qtl_software | string | required, Q | Software used to obtain the associated QTLs in this QTL job |
qtl_method | string | required, Q | Algorithm used to map QTL intervals |
threshold_specification_method | string | Q | How the likelihood score threshold was specified for interval mapping |
interval_type | string | Q | Type of interval(s) measured in this QTL job |
inner_confidence_threshold | string | Q | Confidence level for the QTL inner interval |
outer_confidence_threshold | string | Q | Confidence level for the QTL outer interval |
qtl_statistic_type | string | Q | Statistical method used for computing QTL interval boundaries |
described_by_whom | string | Person who executed this QTL job | |
date_run | date | Q | Day on which the QTL job was executed |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
linkage_map_id | int | BIP identifier of the Linkage Map computed using this algorithm execution | |
qtl_ids | int[] | readonly | Zero or more BIP identifiers of QTLs that were defined as a result of this QTL job execution |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/qtl_jobs?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/qtl_jobs/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/qtl_jobs HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"qtl_job": {
"qtl_job_name": "My first QTL run",
"qtl_software": "QTL Cafe",
"qtl_method": "Marker regression"
}
}
TaxonomyTerm
id | int | readonly, Q | Unique BIP database identifier |
label | string | Gramene Taxonomy ontology identifier, if available | |
name | string | Regular taxonomical name | |
taxonomy_term_id | int | BIP identifier of the parent Taxonomy Term (not present for root terms) | |
canonical | boolean | Set to true if the term is defined in Gramene Taxonomy; false otherwise | |
plant_line_ids | int[] | Zero or more BIP identifiers of Plant Lines classified under this term | |
plant_population_ids | int[] | Zero or more BIP identifiers of Plant Populations classified under this term | |
probe_ids | int[] | Zero or more BIP identifiers of Probes classified under this term |
Example
GET /api/v1/taxonomy_terms?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/taxonomy_terms/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Trait
id | int | readonly, Q | Unique BIP database identifier |
name | string | Short textual definition of the trait | |
label | string | Trait Ontology term id, if available | |
description | string | Longer description of the trait, usually supplied by the ontology maintainers | |
canonical | string | Whether this trait is defined in Trait Ontology or not | |
data_provenance | string | Additional information regarding the origin of this data | |
trait_descriptor_ids | int[] | Zero or more BIP identifiers of Trait Descriptors related to this trait |
Example
GET /api/v1/traits?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/traits/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
TraitDescriptor
id | int | readonly, Q | Unique BIP database identifier |
descriptor_label | string | Q | Unique label assigned to this descriptor by the database curator |
category | string | Plant trait category described by this descriptor | |
units_of_measurements | string | required, Q | How the trait is measured |
trait_grades | object[] | Optional descriptive grades which can be applied to score this trait | |
where_to_score | string | Where the trait is measured | |
scoring_method | string | required, Q | Method used to obtain the trait measure |
when_to_score | string | When in the cultivation process the trait is measured | |
stage_scored | string | At what stage of plant growth the trait is scored | |
precautions | string | Special conditions taken into account when scoring the trait | |
materials | string | Q | Materials required for proper scoring |
instrumentation_required | string | Instruments required for proper scoring | |
controls | string | Control group (data) used in the scoring experiment | |
calibrated_against | string | How the instruments should be calibrated for the scoring experiment | |
likely_ambiguities | string | Ambiguities that may influence the trait measures taken | |
possible_interactions | string | Environmental interactions that should be taken into account when scoring | |
score_type | string | Nature of the final score (direct or otherwise, computation methods applied, etc.) | |
contact_person | string | Person to be contacted regarding further information about scoring this trait | |
authorities | string | Institutions or individuals who should be referred to regarding the method of scoring this trait | |
date_method_agreed | date | Day on which this scoring method was published | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
plant_part_id | int | BIP identifier of the plant part record that describes what part of plant was used for scoring this trait | |
trait_id | int | required | BIP identifier of the record in the Trait vocabulary that defines the scored trait |
trait | object | readonly | Entry in BIP traits vocabulary this Trait Descriptor refers to; describes the scored trait in detail |
trait_score_ids | int[] | readonly | Zero or more BIP identifiers of Trait Scores measured for this plant trait in various projects |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/trait_descriptors?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/trait_descriptors/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/trait_descriptors HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"trait_descriptor": {
"units_of_measurements": "percent total seed fatty acid (%)",
"category": "seed composition",
"scoring_method": "Gas Chromatography",
"trait_id": 1353
}
}
TraitScore
id | int | readonly, Q | Unique BIP database identifier |
score_value | string | required | Value measured and recorded in the trial |
value_type | string | Meaning of the score value | |
technical_replicate_number | string | Ordinal number of the technical replicate for which this score was measured | |
scoring_date | date | Day on which the scoring was performed | |
comments | string | Additional note from the person who published this data | |
entered_by_whom | string | The name of the person who published this data | |
date_entered | date | The day the data was published | |
data_owned_by | string | Name of the legal entity which published this data | |
data_provenance | string | Additional information regarding the origin of this data | |
confirmed_by_whom | string | The person who accepted this BIP database entry | |
plant_scoring_unit_id | int | required | BIP identifier of the Plant Scoring Unit that contains this trait score |
trait_descriptor_id | int | required | BIP identifier of the Trait Descriptor that provides more information about the scored trait |
published_on | datetime | readonly | The day and time the data was published |
Example
GET /api/v1/trait_scores?per_page=3 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
:id
Example
GET /api/v1/trait_scores/1 HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
Example
POST /api/v1/trait_scores HTTP/1.1
Content-Type: application/json
Accept: application/json
X-BIP-Api-Key: ba6d4625927ede0db8768782994d9276cfff9ba79e8df8c831aedc453e850836
{
"trait_score": {
"score_value": "1000",
"plant_scoring_unit_id": 56456,
"trait_descriptor_id": 2
}
}
CropStoreDB acknowledgement
As the BIP database Schema is based on the CropStoreDB schema, the definitions in the API documentation are heavily derived from those in CropStoreDB. We would like to acknowledge the CropStoreDB team managed by Graham King for the prior work this webpage draws from. Their database can be found on CropStoreDB and their resource is cited as Love et al. (2012).
Love, C. G., Andongabo, A. E., Wang, J., Carion, P. W. C., Rawlings, C. J. and King, G. J. (2012), InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data. Journal of Integrative Plant Biology, 54: 345–355. doi: 10.1111/j.1744-7909.2012.01120.x