The phenoclinic query allows the user to search individuals or biosamples filtering by their phonoclinic information.
This information is structured as specified in the Beacon schemas: Individuals and Biosamples.
For the purpose of simplicity, the "simple" fileds (i.e. the ones only nested with the terms "id" and "label") can be used without specifying these terms. For example, ethnicity=NCIT:C16352 instead of ethnicity.id=NCIT:C16352 or ethnicity=England instead of ethnicity.label=England
Some of the available fields and how to use them are specified in the tables below.
In multiple filters queries, the key-value pairs need to be comma-separated. Also, remember the possibility of using Filtering Terms.
Individuals
| field | how to use | example |
|---|---|---|
| id | id=<id value> | id=HG02315 |
| ethnicity.id | ethnicity=<ethnicity.id value> | ethnicity=NCIT:C16352 |
| ethnicity.label | ethnicity=<ethnicity.label value> | ethnicity=Black or Black British |
| geographicOrigin.id | geographicOrigin=<geographicOrigin.id value> | geographicOrigin=GAZ:00002641 |
| geographicOrigin.label | geographicOrigin=<geographicOrigin.label value> | geographicOrigin=England |
| sex.id | sex=<sex.id value> | sex=NCIT:C16576 |
| sex.label | sex=<sex.label value> | sex=female |
| measurements.assayCode with measurements.measurementValue | <measurements.assayCode value> ><= <measurements.measurementValue value> | Weight>90 |
| diseases.diseaseCode.label | diseases.diseaseCode.label=<diseases.diseaseCode.label value> | diseases.diseaseCode.label=asthma |
| diseases.diseaseCode.id | diseases.diseaseCode.id=<diseases.diseaseCode.id value> | diseases.diseaseCode.id=ICD10:J45 |
| interventionsOrProcedures.procedureCode.label | interventionsOrProcedures.procedureCode.label=<interventionsOrProcedures.procedureCode.label value> | interventionsOrProcedures.procedureCode.label=OPCS(v4-0.0):Radiocarpal joint |
| interventionsOrProcedures.procedureCode.id | interventionsOrProcedures.procedureCode.id=<interventionsOrProcedures.procedureCode.label value> | interventionsOrProcedures.procedureCode.id=OPCS4:Z82.1 |
Biosamples
| field | how to use | example |
|---|---|---|
| id | id=<id value> | id=synthetic_sample_4 |
| individualId | individualId=<individualId value> | individualId=HG00100 |
| collectionDate | collectionDate=<collectionDate value> | collectionDate=2020-09-11 |
| collectionMoment | collectionMoment=<collectionMoment value> | collectionMoment=P40Y1M1D |
| biosampleStatus.id | biosampleStatus=<biosampleStatus.id value> | biosampleStatus=EFO:0009654 |
| biosampleStatus.label | biosampleStatus=<biosampleStatus.label value> | biosampleStatus=reference sample |
