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Completeness API Documentation

General

  • All requests are GET requests unless otherwise stated.

Requests

/fertilityAndViability/:centre

Returns a list of colonies with fertility and viability completion statuses and reasons

/colonyProcedureNumbers/:centre

Returns a list of procedures for each colony, with completion statuses based on numbers of procedures and status codes submitted, and a number of open QC issues

  • Takes additional parameters as query string:
    • genotype – The colony name, e.g BL2274
    • pipeline – The pipeline key, e.g UCD_001
    • procedure – The procedure, e.g IMPC_BLK_001
    • isComplete – If the data is complete or not value as true or false
    • ignoreForCompleteness – If the flag for ignored colony for completeness is true or false
    • insufficientNumbersHasValue – If insufficientNumbers is not null as true or false
    • statusCodesOnly – If status codes is true or false
    • earliestDobBefore – Data bfore entered earliest Dob, eg 2013-12-30
    • latestDateOfExperimentBefore – Data bfore entered Latest date of experiment, eg 2017-06-28
  • Example: https://api.mousephenotype.org/completeness/colonyProcedureNumbers/UCD

/lineqc/:centre

Returns a list of line procedure with QC errors if there are any

  • Takes additional parameters as query string:
    • genotype – The colony name, e.g BL2274
    • pipeline – The pipeline key, e.g UCD_001
    • procedure – The procedure, e.g IMPC_EVO_001
    • ignoreForCompleteness – If the flag for ignored colony for completeness is true or false
  • Example: https://api.mousephenotype.org/completeness/lineqc/UCD

/embryoCompleteness/:centre

Returns a list of embryo completeness

  • Takes additional parameters as query string:
    • genotype – The colony name, e.g BL2274
    • originalGenotype – The original genotype, e.g H-Grm6-G06-TM1B
    • geneSymbol – The gene symbol, e.g Grm6
    • geneId – The gene id, e.g MGI:1351343
    • method – The method, e.g ESCell
    • latestDateOfExperimentLt – The latest date of experiment is less than given value in the format of yyyy-MM-dd
    • latestDateOfExperimentGt – The latest date of experiment is greater than given value in the format of yyyy-MM-dd
    • lethalErrorMessagePresent – If lethal error message is present
    • subviableErrorMessagePresent – If subviable error message is present
  • Filtering will be performed if any of the subviableErrorMessagePresent or lethalErrorMessagePresent flags is set as true. If none of them is passed as an argument it will return everything. false values will not effect the result.
  • Example: https://api.mousephenotype.org/completeness/embryoCompleteness/UCD

/completenssQc/:centre

Returns a list of completeness qc

Data Structures

Datatype : lineqc[]

"lineqc": [
    {
        "genotype": "BL3798",
        "pipeline": "UCD_001",
        "procedure": "IMPC_EVL_001",
        "centre": "UCD",
        "sexChr": "",
        "breed": null,
        "outCome": "Homozygous - Lethal",
        "errors": [
            "total pups 28.0 are not equal to WTs 7.0 plus hets 20.0 plus homs 0.0,",
            "live pups 28.0 are not equal to live WTs 7.0 plus live hets 20.0 plus live homs 0.0 - NB if not submitted we have derived these numbers from live pups minus dead pups,"
        ]
    }
]

Datatype : fertilityAndViability[]

"fertilityAndViability": [
    {
        "genotypeId": 6,
        "genotype": "UCD-10243A-E8-2-1",
        "pipeline": "TCP_001",
        "centre": "TCP",
        "viabilityText": "",
        "fertilityText": "FER submission not found;",
        "viabilityComplete": true,
        "fertilityComplete": false,
        "ignoreForCompleteness": false
    }
]

Datatype : colonyProcedureNumbers[]

"colonyProcedureNumbers": [
    {
        "genotype": "UCD-10243A-E8-2-1",
        "pipeline": "TCP_001",
        "procedure": "IMPC_ABR_002",
        "centre": "TCP",
        "earliestDob": "2013-08-27",
        "latestDateOfExperiment": "2013-12-06",
        "femaleHet": 2,
        "maleHet": 2,
        "unsexedHet": 0,
        "femaleHom": 0,
        "maleHom": 0,
        "unsexedHom": 0,
        "maleHemi": 0,
        "femaleHetStatusCode": 0,
        "maleHetStatusCode": 0,
        "unsexedHetStatusCode": 0,
        "femaleHomStatusCode": 0,
        "maleHomStatusCode": 0,
        "unsexedHomStatusCode": 0,
        "maleHemisStatusCode": 0,
        "insufficientNumbers": null,
        "statusCodesOnly": false,
        "isComplete": true,
        "unresolvedQcIssues": 0,
        "ignoreForCompleteness": false
    }
]

Datatype : embryoCompleteness[]

"embryoCompleteness": [
    {
        "centre": "H",
        "pipeline": "HRWL_001",
        "project": "BaSH",
        "genotype": "H-Grm6-G06-TM1B",
        "geneSymbol": "Grm6",
        "geneId": "MGI:1351343",
        "alleleName": "Grm6<sup>tm1b(EUCOMM)Wtsi</sup>",
        "originalGenotype": "H-Grm6-G06-TM1B",
        "viaQc": "",
        "method": "ESCell",
        "latestDateOfExperiment": "2014-01-21",
        "gel": 0,
        "gpl": 0,
        "eol": 0,
        "eOLimages": 0,
        "eml": 0,
        "eMLimages": 0,
        "eVLoutcome": "None",
        "evlQc": "",
        "gem": 0,
        "gpm": 0,
        "elz": 2,
        "eLZimages": 1,
        "eVMoutcome": "None",
        "evmQc": "",
        "geo": 0,
        "gpo": 0,
        "emo": 0,
        "eMOimages": 0,
        "eVOoutcome": "None",
        "evoQc": "",
        "gep": 0,
        "gpp": 0,
        "ema": 0,
        "eMAimages": 0,
        "eVPoutcome": "None",
        "evpQc": "",
        "vIAoutcome": "Viable",
        "lethalErrorMessage": "",
        "subviableErrorMessage": ""
    }
]

Datatype : completenssQc[]

"completenssQc": [
     {
        "centre": "H",
        "procedure": "_VIA_/_FER_",
        "genotype": "H-Kdm8-A04-TM1B",
        "geneSymbol": "Kdm8",
        "geneId": "MGI:1924285",
        "alleleName": "Kdm8<sup>tm1b(EUCOMM)Wtsi</sup>",
        "error": "hom fertility data submitted for hom lethal line;"
    }