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
- Takes additional parameters as query string:
genotype
– The colony name, e.gBL2274
pipeline
– The pipeline key, e.gUCD_001
viabilityComplete
– If viability complete istrue
orfalse
fertilityComplete
– If fertility complete istrue
orfalse
ignoreForCompleteness
– If the flag for ignored colony for completeness istrue
orfalse
- Example: https://api.mousephenotype.org/completeness/fertilityAndViability/UCD?fertilityComplete=false
/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.gBL2274
pipeline
– The pipeline key, e.gUCD_001
procedure
– The procedure, e.gIMPC_BLK_001
isComplete
– If the data is complete or not value astrue
orfalse
ignoreForCompleteness
– If the flag for ignored colony for completeness istrue
orfalse
insufficientNumbersHasValue
– If insufficientNumbers is not null astrue
orfalse
statusCodesOnly
– If status codes istrue
orfalse
earliestDobBefore
– Data bfore entered earliest Dob, eg2013-12-30
latestDateOfExperimentBefore
– Data bfore entered Latest date of experiment, eg2017-06-28
- 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.gBL2274
pipeline
– The pipeline key, e.gUCD_001
procedure
– The procedure, e.gIMPC_EVO_001
ignoreForCompleteness
– If the flag for ignored colony for completeness istrue
orfalse
- 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.gBL2274
originalGenotype
– The original genotype, e.gH-Grm6-G06-TM1B
geneSymbol
– The gene symbol, e.gGrm6
geneId
– The gene id, e.gMGI:1351343
method
– The method, e.gESCell
latestDateOfExperimentLt
– The latest date of experiment is less than given value in the format ofyyyy-MM-dd
latestDateOfExperimentGt
– The latest date of experiment is greater than given value in the format ofyyyy-MM-dd
lethalErrorMessagePresent
– If lethal error message is presentsubviableErrorMessagePresent
– 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
- Takes additional parameters as a query string:
genotype
– The colony name, e.gBL2274
- Example: https://api.mousephenotype.org/completeness/completenssQc/UCD
Data Structures
Datatype : lineqc[]
Datatype : lineqc[]
- Example Link: https://api.mousephenotype.org/completeness/lineqc/UCD
- Example Structure :
"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[]
Datatype : fertilityAndViability[]
- Example Link: https://api.mousephenotype.org/completeness/fertilityAndViability/UCD
- Example Structure :
"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[]
Datatype : colonyProcedureNumbers[]
- Example Link: https://api.mousephenotype.org/completeness/colonyProcedureNumbers/TCP
- Example Structure :
"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[]
Datatype : embryoCompleteness[]
- Example Link: https://api.mousephenotype.org/completeness/embryoCompleteness/H
- Example Structure :
"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[]
Datatype : completenssQc[]
- Example Link: https://api.mousephenotype.org/completeness/completenssQc/H
- Example Structure :
"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;"
}