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Protocol(s) [GET]


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.
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.
projects Comma-separated list of project ids
Defaults to all available projects
Limits scope of query
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"
            }
        }
    ]
}