GET /api/v1/vaults/<vault_id>/protocols/<id>
Returns a single protocol
GET /api/v1/vaults/<vault_id>/protocols
Returns a list of protocols based on criteria as specified by parameters:
Query Parameters (all optional):
protocols |
Comma-separated list of protocol ids Cannot be used with other parameters |
names |
Comma separated list of protocol names Cannot be used with other parameters |
async |
Boolean If true, do an asynchronous export (see Async Export) Use for large data sets. This is recommended any time you want to download more than page_size results. Note: any page_size parameter used in an API GET call that also uses the async=true parameter will be ignored. The GET call will return all valid data for the given GET call. |
only_ids |
Boolean If true, only the Protocol IDs are returned, allowing for a smaller and faster response. (Async should still be used when many IDs are expected.)
Note: any Default: false |
created_before |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
created_after |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
modified_before |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
modified_after |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
runs_modified_before |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
runs_modified_after |
Date (YYYY-MM-DDThh:mm:ss±hh:mm) |
plates |
Comma-separated list of plate ids |
molecules |
Comma-separated list of molecule ids |
offset |
The index of the first object actually returned. Defaults to 0. |
page_size |
The maximum number of objects to return in this call. Default is 50, maximum is 1000. If the response exceeds the page_size, we strongly recommend using the async option instead of downloading multiple chunks. Note: any page_size parameter used in an API GET call that also uses the async=true parameter will be ignored. The GET call will return all valid data for the given GET call. |
data_sets |
Comma-separated list of public dataset ids Defaults to no data sets Limits scope of query |
slurp |
Specify the slurp_id of an import operation. Once an import has been committed, you can return additional JSON results that will expose the Protocol and Run(s) of data that were imported. |
Notes on Date/Time
The CDD Vault API accepts ISO 8601 date/time formats in any API call that allows a date-type parameter. For example, the full date and timestamp may be used in GET calls that support a date parameter. You may still simply provide a date-only parameter, like "created_after=2020-05-20".
You may also specify a date + timestamp, like "created_after= 2020-05-20 14:53:12", to indicate "20 May 2020 14:53:12 PDT" (PDT is based on the user's time zone setting). The timestamp portion can also include a UTC (Coordinated Universal Time) offset, like "created_after= 2020-05-27T14:48:40-07:00" which indicates that the time specified is -7 hours from the UTC time.
Examples
curl -H "X-CDD-Token: $TOKEN" https://app.collaborativedrug.com/api/v1/vaults/489978881/protocols/54803
Returns:
{
"id": 64079,
"class": "protocol",
"created_at": "2021-12-17T22:49:32.000Z",
"modified_at": "2021-12-17T23:06:27.000Z",
"name": "Primary Inhibition",
"data_set": {
"name": "CDD AgCo",
"id": 5481
},
"readout_definitions": [
{
"id": 761997,
"class": "readout definition",
"created_at": "2021-12-17T23:04:17.000Z",
"modified_at": "2021-12-17T23:04:47.000Z",
"name": "Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"description": "Percent Inhibition",
"protocol_condition": false
},
{
"id": 761998,
"class": "readout definition",
"created_at": "2021-12-17T23:04:38.000Z",
"modified_at": "2021-12-17T23:04:38.000Z",
"name": "Cell Line",
"data_type": "Text",
"description": "Cell Line",
"protocol_condition": true
},
{
"id": 761999,
"class": "readout definition",
"created_at": "2021-12-17T23:05:16.000Z",
"modified_at": "2021-12-17T23:05:16.000Z",
"name": "Avg Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"aggregation": "batch",
"description": "Average Inhibition for Batches",
"protocol_condition": false,
"calculation": 41938
}
],
"calculations": [
{
"id": 41938,
"class": "custom calculation",
"created_at": "2021-12-17T23:05:16.000Z",
"modified_at": "2021-12-17T23:05:16.000Z",
"inputs": {
"input_readout_definitions": [
761997
]
},
"outputs": {
"output_readout_definition": 761999
},
"formula": "average([761997])",
"aggregate_readouts_by": "batch and run"
}
],
"runs": [
{
"id": 614703,
"class": "run",
"created_at": "2021-12-17T23:05:42.000Z",
"modified_at": "2021-12-17T23:06:27.000Z",
"run_date": "2021-12-17",
"person": "Elvis Presley",
"place": "Graceland",
"conditions": "Taking Care of Business",
"source_files": [],
"attached_files": [],
"project": {
"name": "test",
"id": 11871
}
}
],
"projects": [
{
"name": "Inhibition CRO",
"id": 11871
}
],
"owner": "Charlie Weatherall",
"protocol_statistics": [
{
"protocol": {
"id": 64079,
"name": "Primary Inhibition"
},
"readout_definition": {
"id": 761997,
"name": "Inhibition"
},
"statistics": [
{
"name": "z_prime_factor",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "positive_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "negative_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "reference_molecule",
"count": 0,
"average": null,
"standard_deviation": null
}
]
}
],
"category": "In vivo",
"description": "Activity assayed with 4T1-luc cells.",
"protocol_fields": {
"Category": "In vivo",
"Description": "Activity assayed with 4T1-luc cells.",
"Instrument": "SpectraMax L microplate reader",
"Detection Method": "Biolunimescence",
"SOP Version": "1.1"
}
}
To retrieve protocol details with IDs 1 and 537677966:
curl -H "X-CDD-Token: $TOKEN" https://app.collaborativedrug.com/api/v1/vaults/489978881/protocols?protocols=1,537677966
Returns:
{
"count": 2,
"offset": 0,
"page_size": 50,
"objects": [
{
"id": 64079,
"class": "protocol",
"created_at": "2021-12-17T22:49:32.000Z",
"modified_at": "2021-12-17T23:06:27.000Z",
"name": "Test",
"data_set": {
"name": "CWTest",
"id": 5481
},
"readout_definitions": [
{
"id": 761997,
"class": "readout definition",
"created_at": "2021-12-17T23:04:17.000Z",
"modified_at": "2021-12-17T23:04:47.000Z",
"name": "Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"description": "Percent Inhibition",
"protocol_condition": false
},
{
"id": 761998,
"class": "readout definition",
"created_at": "2021-12-17T23:04:38.000Z",
"modified_at": "2021-12-17T23:04:38.000Z",
"name": "Cell Line",
"data_type": "Text",
"description": "Cell Line",
"protocol_condition": true
},
{
"id": 761999,
"class": "readout definition",
"created_at": "2021-12-17T23:05:16.000Z",
"modified_at": "2021-12-17T23:05:16.000Z",
"name": "Avg Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"aggregation": "batch",
"description": "Average Inhibition for Batches",
"protocol_condition": false,
"calculation": 41938
}
],
"calculations": [
{
"id": 41938,
"class": "custom calculation",
"created_at": "2021-12-17T23:05:16.000Z",
"modified_at": "2021-12-17T23:05:16.000Z",
"inputs": {
"input_readout_definitions": [
761997
]
},
"outputs": {
"output_readout_definition": 761999
},
"formula": "average([761997])",
"aggregate_readouts_by": "batch and run"
}
],
"runs": [
{
"id": 614703,
"class": "run",
"created_at": "2021-12-17T23:05:42.000Z",
"modified_at": "2021-12-17T23:06:27.000Z",
"run_date": "2021-12-17",
"person": "Elvis Presley",
"place": "Graceland",
"conditions": "Taking Care of Business",
"source_files": [],
"attached_files": [],
"project": {
"name": "test",
"id": 11871
}
}
],
"projects": [
{
"name": "test",
"id": 11871
}
],
"owner": "Charlie Weatherall",
"protocol_statistics": [
{
"protocol": {
"id": 64079,
"name": "Test"
},
"readout_definition": {
"id": 761997,
"name": "Inhibition"
},
"statistics": [
{
"name": "z_prime_factor",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "positive_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "negative_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "reference_molecule",
"count": 0,
"average": null,
"standard_deviation": null
}
]
}
],
"category": "In vivo",
"description": "Total luciferase activity was assayed from lungs harvested from BALB/c mice injected i.v. with 4T1-luc cells. Lungs were homogenized in cell lysis buffer (Promega, Madison, WI, USA). Protein concentration was determined using a Thermo Scientific Pierce bicinchoninic acid protein assay kit (Pierce Biotechnology, Rockford, IL, USA). The Dual-Luciferase Reporter Assay System (Promega) was used to detect luciferase activity. In these experiments, 20 μl of sample supernatant was mixed with 50 μl of luciferase assay reagent, and luciferase activity was quantified using a SpectraMax L microplate reader (Molecular Devices, Sunnyvale, CA, USA). The results are reported as relative light units.",
"protocol_fields": {
"Category": "In vivo",
"Description": "Total luciferase activity was assayed from lungs harvested from BALB/c mice injected i.v. with 4T1-luc cells. Lungs were homogenized in cell lysis buffer (Promega, Madison, WI, USA). Protein concentration was determined using a Thermo Scientific Pierce bicinchoninic acid protein assay kit (Pierce Biotechnology, Rockford, IL, USA). The Dual-Luciferase Reporter Assay System (Promega) was used to detect luciferase activity. In these experiments, 20 μl of sample supernatant was mixed with 50 μl of luciferase assay reagent, and luciferase activity was quantified using a SpectraMax L microplate reader (Molecular Devices, Sunnyvale, CA, USA). The results are reported as relative light units.",
"Instrument": "SpectraMax L microplate reader",
"Detection Method": "Biolunimescence",
"SOP Version": "1.1"
}
},
{
"id": 64080,
"class": "protocol",
"created_at": "2021-12-17T23:15:58.000Z",
"modified_at": "2021-12-17T23:16:26.000Z",
"name": "Follow-Up Inhibition",
"data_set": {
"name": "CWTest",
"id": 5481
},
"readout_definitions": [
{
"id": 762000,
"class": "readout definition",
"created_at": "2021-12-17T23:15:58.000Z",
"modified_at": "2021-12-17T23:15:58.000Z",
"name": "Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"description": "Percent Inhibition",
"protocol_condition": false
},
{
"id": 762001,
"class": "readout definition",
"created_at": "2021-12-17T23:15:58.000Z",
"modified_at": "2021-12-17T23:15:58.000Z",
"name": "Cell Line",
"data_type": "Text",
"description": "Cell Line",
"protocol_condition": true
},
{
"id": 762002,
"class": "readout definition",
"created_at": "2021-12-17T23:15:58.000Z",
"modified_at": "2021-12-17T23:15:58.000Z",
"name": "Avg Inhibition",
"unit_label": "%",
"data_type": "Number",
"precision_type": "significant figure",
"precision_number": 3,
"aggregation": "batch",
"description": "Average Inhibition for Batches",
"protocol_condition": false,
"calculation": 41939
}
],
"calculations": [
{
"id": 41939,
"class": "custom calculation",
"created_at": "2021-12-17T23:15:58.000Z",
"modified_at": "2021-12-17T23:15:58.000Z",
"inputs": {
"input_readout_definitions": [
762000
]
},
"outputs": {
"output_readout_definition": 762002
},
"formula": "average([762000])",
"aggregate_readouts_by": "batch and run"
}
],
"projects": [
{
"name": "test",
"id": 11871
}
],
"owner": "Charlie Weatherall",
"protocol_statistics": [
{
"protocol": {
"id": 64080,
"name": "Follow-Up Inhibition"
},
"readout_definition": {
"id": 762000,
"name": "Inhibition"
},
"statistics": [
{
"name": "z_prime_factor",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "positive_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "negative_control",
"count": 0,
"average": null,
"standard_deviation": null
},
{
"name": "reference_molecule",
"count": 0,
"average": null,
"standard_deviation": null
}
]
}
],
"category": "In vivo",
"description": "Activity assayed with 4T1-luc cells.",
"protocol_fields": {
"Category": "In vivo",
"Description": "Activity assayed with 4T1-luc cells.",
"Instrument": "SpectraMax L microplate reader",
"Detection Method": "Biolunimescence",
"SOP Version": "1.1"
}
}
]
}