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Add hematology table min/max values #34

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merged 2 commits into from
May 10, 2024
Merged

Add hematology table min/max values #34

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66feba2
Update version of data model in code
amstilp May 10, 2024
d022400
Update hematology table with min/max values
amstilp May 10, 2024
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64 changes: 47 additions & 17 deletions PRIMED_phenotype_data_model.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "PRIMED Phenotype Data Model",
"description": "Data model for phenotype data in the PRIMED consortium",
"version": "1.7",
"version": "1.8",
"tables": [
{
"table": "subject",
Expand Down Expand Up @@ -628,7 +628,7 @@
{
"table": "cmqt_hematology",
"url": "https://docs.google.com/spreadsheets/d/1LTGvRdGTsc0gYiFrNHOvKsRE5E4ohxoI466pt4fXyjY/edit#gid=768778505",
"version": "1.0",
"version": "1.1",
"columns": [
{
"column": "subject_id",
Expand Down Expand Up @@ -660,77 +660,107 @@
{
"column": "rbc_1",
"description": "Red blood cell count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "hemoglobin_1",
"description": "Hemoglobin",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "hematocrit_1",
"description": "Hematocrit",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "mcv_1",
"description": "Mean corpuscular volume",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 1000
},
{
"column": "mch_1",
"description": "Mean corpuscular hemoglobin",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 1000
},
{
"column": "mchc_1",
"description": "Mean corpuscular hemoglobin concentration",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 1000
},
{
"column": "rdw_1",
"description": "Red blood cell distribution width",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "wbc_1",
"description": "White blood cell count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 10000
},
{
"column": "basophil_count_1",
"description": "Relative basophil count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "eosinophil_count_1",
"description": "Relative eosinophil count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "lymphocyte_count_1",
"description": "Relative lymphocyte count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "monocyte_count_1",
"description": "Relative monocyte count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "neutrophil_count_1",
"description": "Relative neutrophil count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
},
{
"column": "platelet_count_1",
"description": "Platelet count",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 10000
},
{
"column": "mean_platelet_volume_1",
"description": "Mean platelet volume",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 100
}
]
},
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2 changes: 1 addition & 1 deletion sheets_to_JSON_phenotype.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ library(jsonlite)
url <- "https://docs.google.com/spreadsheets/d/1kpWz-6QfjMPVtm62fQwm4hoxzXhR0dnKxVt02fbx9ks"
model_name <- "PRIMED Phenotype Data Model"
model_description <- "Data model for phenotype data in the PRIMED consortium"
model_version <-"1.7"
model_version <-"1.8"

# table metadata
meta <- read_sheet(url, sheet="Description", skip=1, col_types="c") %>%
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