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AMBIT REST API: Bundle resource

bundle: a collection of things, or a quantity of material, tied or wrapped up together.

A Bundle resource provides means to define collections of Substance, Compounds and Endpoints. API documentation

Bundle

  1. Bundle summary [api-docs]
  2. List compounds in a bundle [api-docs]
  3. List substances in a bundle [api-docs]
  4. List endpoints in a bundle [api-docs]
  5. List studies defined by a bundle [api-docs]
  6. Compound role (bundle_uri parameter added to compound queries) [api-docs] [example]
  7. Substance role (bundle_uri parameter added to substance queries) [api-docs] [example]
  8. Endpoint role (bundle_uri parameter added to endpoint queries) [api-docs] [example]
  9. Filter endpoints by endpoints, defined in a bundle (filterbybundle parameter ) [api-docs] [examples]
  10. Filter endpoints by substances, defined in a bundle (filterbybundle parameter ) [api-docs] [examples]
  11. Filter substances by a bundle (filterbybundle parameter ) [api-docs] [examples]
  12. Create an empty bundle [api-docs]
  13. Update a bundle [api-docs]
  14. Get all bundles [api-docs] The result is a Dataset metadata.
  15. Delete a bundle [api-docs]
  16. Dataset of substances, defined by the bundle [api-docs] The format is the same as for Substance dataset. The substances and the endpoints can be added and removed to / from the bundle.
  17. Add or delete substance to / from a bundle [api-docs]
  18. Add or delete compound to / from a bundle [api-docs]
  19. Add or delete endpoint categories to / from a bundle [api-docs]
  20. Copy selected study entries (determined by selected substances and endpoint) into local copy in a bundle /bundle/{idbundle}/matrix [api-docs]
  21. Delete local study copy in a bundle /bundle/{idbundle}/matrix [api-docs]
  22. Read the local copy of studies (same format as /bundle/{idbundle}/dataset ) [api-docs]
  23. Mark values in the local copy of studues as deleted PUT /bundle/{idbundle}/matrix/deleted. JSON format expected
  24. Update local copy of studies /bundle/{idbundle}/matrix . Does not add substances! Content-type should be either application/json or multipart/form-data with *.json file attached json schema. The study.owner.substance.uuid should be an existing Substance UUID. [api-docs]. study JSON example :

Example 1

{
    "study": [
        {
            "owner": {
                "substance": {
                    "uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734"
                }
            },
            "protocol": {
                "topcategory": "TOX",
                "category": {
                    "code": "TO_ACUTE_ORAL_SECTION"
                },
                "endpoint": "Acute toxicity: oral.001",
                "guideline": [
                    "OECD Guideline 401 (Acute Oral Toxicity)"
                ]
            },
            "citation": {
                "title": "Study reference",
                "year": "2015",
                "owner": "My company"
            },
            "parameters": {
                "Species": "rat",
                "Sex": "male/female"
            },
            "interpretation": {
                "result": "not classified",
                "criteria": "EU"
            },
            "reliability": {
                "r_isRobustStudy": "false",
                "r_isUsedforClassification": "false",
                "r_isUsedforMSDS": "false",
                "r_purposeFlag": "",
                "r_studyResultType": "",
                "r_value": "3 (not reliable)"
            },
            "effects": [
                {
                    "endpoint": "LD50",
                    "conditions": {
                        "Sex": "male"
                    },
                    "result": {
                        "unit": "mg/kg bw",
                        "loQualifier": ">",
                        "loValue": 5000
                    }
                },
                {
                    "endpoint": "LD50",
                    "conditions": {
                        "Sex": "female"
                    },
                    "result": {
                        "unit": "mg/kg bw",
                        "loQualifier": ">",
                        "loValue": 2000,
                        "upQualifier": "<",
                        "upValue": 5000
                    }
                }
            ]
        },
        {
            "uuid": null,
            "owner": {
                "substance": {
                    "uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734"
                },
                "company": {
                    "uuid": "TEST-e535bebb-e59f-3906-f988-554478ad3734",
                    "name": "Morgoth"
                }
            },
            "citation": {
                "title": "Study reference 123",
                "year": "2014",
                "owner": "Your company"
            },
            "protocol": {
                "topcategory": "ENV FATE",
                "category": {
                    "code": "TO_BIODEG_WATER_SCREEN_SECTION"
                },
                "endpoint": "Biodegradation in water: screening tests.001",
                "guideline": [
                    "OECD Guideline 301 D (Ready Biodegradability: Closed Bottle Test)"
                ]
            },
            "parameters": {
                "TEST TYPE": "aerobic"
            },
            "reliability": {
                "r_isRobustStudy": "false",
                "r_isUsedforClassification": "false",
                "r_isUsedforMSDS": "false",
                "r_purposeFlag": "",
                "r_studyResultType": "",
                "r_value": "3 (not reliable)"
            },
            "interpretation": {
                "result": "readily biodegradable",
                "criteria": ""
            },
            "effects": [
                {
                    "endpoint": "% Degradation",
                    "conditions": {
                        "Time point": "3 h"
                    },
                    "result": {
                        "unit": "%",
                        "loQualifier": "",
                        "loValue": 0
                    }
                },
                {
                    "endpoint": "% Degradation",
                    "conditions": {
                        "Time point": "7 d"
                    },
                    "result": {
                        "unit": "%",
                        "loQualifier": "",
                        "loValue": 20
                    }
                },
                {
                    "endpoint": "% Degradation",
                    "conditions": {
                        "Time point": "14 d"
                    },
                    "result": {
                        "unit": "%",
                        "loQualifier": "",
                        "loValue": 50
                    }
                },
                {
                    "endpoint": "% Degradation",
                    "conditions": {
                        "Time point": "28 d"
                    },
                    "result": {
                        "unit": "%",
                        "loQualifier": "",
                        "loValue": 85
                    }
                }
            ]
        }
    ]
}

Example 2

{
    "study": [
        {
            "uuid": "IUC5-69f39568-46e4-45ba-94f6-f00765525422",
            "owner": {
                "substance": {
                    "uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734"
                },
                "company": {
                    "uuid": "TEST-e535bebb-e59f-3906-f988-554478ad3734",
                    "name": "Morgoth"
                }
            },
            "protocol": {
                "topcategory": "TOX",
                "category": {
                    "code": "TO_ACUTE_ORAL_SECTION"
                },
                "endpoint": "Acute toxicity: oral.001",
                "guidance": [
                    "OECD Guideline 401 (Acute Oral Toxicity)"
                ]
            },
            "parameters": {
                "Year": "1999",
                "Reference": "ano",
                "Species": "rat",
                "Sex": "male/female"
            },
            "reliability": {
                "r_isRobustStudy": "false",
                "r_isUsedforClassification": "false",
                "r_isUsedforMSDS": "false",
                "r_purposeFlag": "",
                "r_studyResultType": "",
                "r_value": "3 (not reliable)"
            },
            "interpretation": {
                "result": "not classified",
                "criteria": "EU"
            },
            "effects": [
                {
                    "endpoint": "LD50",
                    "conditions": {
                        "Sex": "male"
                    },
                    "result": {
                        "unit": "mg/kg bw",
                        "loQualifier": ">",
                        "loValue": 5000
                    }
                },
                {
                    "endpoint": "LD50",
                    "conditions": {
                        "Sex": "female"
                    },
                    "result": {
                        "unit": "mg/kg bw",
                        "loQualifier": ">",
                        "loValue": 2000,
                        "upQualifier": "<",
                        "upValue": 5000
                    }
                }
            ]
        }
    ]
}