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Separate entries in the concept dict by category (#3)
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* Separate entries in the concept dict by category.

* Use underscore in blood_gas.
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@mlondschien
mlondschien authored Mar 5, 2024
1 parent aea5685 commit 7fb95ea
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6,591 changes: 0 additions & 6,591 deletions inst/extdata/config/concept-dict.json
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689 changes: 689 additions & 0 deletions inst/extdata/config/concept-dict/blood_gas.json
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1,539 changes: 1,539 additions & 0 deletions inst/extdata/config/concept-dict/chemistry.json
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388 changes: 388 additions & 0 deletions inst/extdata/config/concept-dict/demographics.json
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{
"adm": {
"target": "id_tbl",
"levels": [
"med",
"surg",
"other"
],
"class": "fct_cncpt",
"description": "patient admission type",
"category": "demographics",
"sources": {
"aumc": [
{
"val_var": "specialty",
"table": "admissions",
"callback": "apply_map( c(Cardiochirurgie = 'surg', Cardiologie = 'med', ders = 'other', Gynaecologie = 'other', `Heelkunde Gastro-enterologie` = 'surg', `Heelkunde Longen/Oncologie` = 'surg', `Heelkunde Oncologie` = 'surg', Hematologie = 'med', `Intensive Care Volwassenen` = 'other', Inwendig = 'med', `Keel, Neus & Oorarts` = 'surg', Longziekte = 'med', `Maag-,Darm-,Leverziekten` = 'med', Mondheelkunde = 'surg', Nefrologie = 'med', Neurochirurgie = 'surg', Neurologie = 'med', Obstetrie = 'other', `Oncologie Inwendig` = 'med', Oogheelkunde = 'surg', Orthopedie = 'surg', `Plastische chirurgie` = 'surg', Reumatologie = 'med', Traumatologie = 'surg', Urologie = 'surg', Vaatchirurgie = 'surg', Verloskunde = 'other'))",
"class": "col_itm"
}
],
"eicu": [
{
"table": "admissiondx",
"val_var": "admitdxpath",
"callback": "eicu_adx",
"class": "col_itm"
}
],
"eicu_demo": [
{
"table": "admissiondx",
"val_var": "admitdxpath",
"callback": "eicu_adx",
"class": "col_itm"
}
],
"miiv": [
{
"table": "services",
"val_var": "curr_service",
"callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
"class": "col_itm"
}
],
"mimic": [
{
"table": "services",
"val_var": "curr_service",
"callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
"class": "col_itm"
}
],
"mimic_demo": [
{
"table": "services",
"val_var": "curr_service",
"callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
"class": "col_itm"
}
]
}
},
"age": {
"unit": "years",
"min": 0,
"max": 100,
"target": "id_tbl",
"description": "patient age",
"omopid": 4314456,
"category": "demographics",
"sources": {
"aumc": [
{
"val_var": "agegroup",
"table": "admissions",
"callback": "apply_map(c(`18-39` = 30, `40-49` = 45, `50-59` = 55, `60-69` = 65, `70-79` = 75, `80+` = 90))",
"class": "col_itm"
}
],
"eicu": [
{
"table": "patient",
"val_var": "age",
"callback": "transform_fun(eicu_age)",
"class": "col_itm"
}
],
"eicu_demo": [
{
"table": "patient",
"val_var": "age",
"callback": "transform_fun(eicu_age)",
"class": "col_itm"
}
],
"hirid": [
{
"table": "general",
"val_var": "age",
"class": "col_itm"
}
],
"miiv": [
{
"table": "patients",
"val_var": "anchor_age",
"class": "col_itm"
}
],
"mimic": [
{
"table": "patients",
"val_var": "dob",
"callback": "transform_fun(mimic_age)",
"class": "col_itm"
}
],
"mimic_demo": [
{
"table": "patients",
"val_var": "dob",
"callback": "transform_fun(mimic_age)",
"class": "col_itm"
}
],
"sic": [
{
"table": "cases",
"val_var": "AgeOnAdmission",
"class": "col_itm"
}
]
}
},
"bmi": {
"concepts": [
"weight",
"height"
],
"description": "patient body mass index",
"omopid": 4245997,
"category": "demographics",
"callback": "bmi",
"target": "id_tbl",
"class": "rec_cncpt"
},
"height": {
"unit": "cm",
"min": 10,
"max": 230,
"target": "id_tbl",
"description": "patient height",
"omopid": 607590,
"category": "demographics",
"sources": {
"aumc": [
{
"val_var": "heightgroup",
"table": "admissions",
"callback": "apply_map(c(`159-` = 150, `160-169` = 165, `170-179` = 175, `180-189` = 185, `190+` = 200))",
"class": "col_itm"
}
],
"eicu": [
{
"table": "patient",
"val_var": "admissionheight",
"class": "col_itm"
}
],
"eicu_demo": [
{
"table": "patient",
"val_var": "admissionheight",
"class": "col_itm"
}
],
"hirid": [
{
"ids": 10000450,
"table": "observations",
"sub_var": "variableid",
"class": "hrd_itm"
}
],
"miiv": [
{
"ids": 226707,
"table": "chartevents",
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
}
],
"mimic": [
{
"ids": [
920,
1394,
3485,
4187,
4188,
3486,
226707
],
"table": "chartevents",
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
}
],
"mimic_demo": [
{
"ids": [
920,
1394,
3485,
4187,
4188,
3486,
226707
],
"table": "chartevents",
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
}
],
"sic": [
{
"table": "cases",
"val_var": "HeightOnAdmission",
"class": "col_itm"
}
]
}
},
"sex": {
"target": "id_tbl",
"levels": [
"Female",
"Male"
],
"class": "fct_cncpt",
"description": "patient sex",
"omopid": 37116947,
"category": "demographics",
"sources": {
"aumc": [
{
"val_var": "gender",
"table": "admissions",
"callback": "apply_map(c(Vrouw = 'Female', Man = 'Male'))",
"class": "col_itm"
}
],
"eicu": [
{
"table": "patient",
"val_var": "gender",
"class": "col_itm"
}
],
"eicu_demo": [
{
"table": "patient",
"val_var": "gender",
"class": "col_itm"
}
],
"hirid": [
{
"table": "general",
"val_var": "sex",
"callback": "apply_map(c(M = 'Male', F = 'Female'))",
"class": "col_itm"
}
],
"miiv": [
{
"table": "patients",
"val_var": "gender",
"callback": "apply_map(c(M = 'Male', F = 'Female'))",
"class": "col_itm"
}
],
"mimic": [
{
"table": "patients",
"val_var": "gender",
"callback": "apply_map(c(M = 'Male', F = 'Female'))",
"class": "col_itm"
}
],
"mimic_demo": [
{
"table": "patients",
"val_var": "gender",
"callback": "apply_map(c(M = 'Male', F = 'Female'))",
"class": "col_itm"
}
],
"sic": [
{
"table": "cases",
"val_var": "Sex",
"callback": "apply_map(c(`735` = 'Male', `736` = 'Female'))",
"class": "col_itm"
}
]
}
},
"weight": {
"unit": "kg",
"min": 1,
"max": 500,
"target": "id_tbl",
"description": "patient weight",
"omopid": 4099154,
"category": "demographics",
"sources": {
"aumc": [
{
"val_var": "weightgroup",
"table": "admissions",
"callback": "apply_map(c(`59-` = 50, `60-69` = 65, `70-79` = 75, `80-89` = 85, `90-99` = 95, `100-109` = 105, `110+` = 120))",
"class": "col_itm"
}
],
"eicu": [
{
"table": "patient",
"val_var": "admissionweight",
"class": "col_itm"
}
],
"eicu_demo": [
{
"table": "patient",
"val_var": "admissionweight",
"class": "col_itm"
}
],
"hirid": [
{
"ids": 10000400,
"table": "observations",
"sub_var": "variableid",
"class": "hrd_itm"
}
],
"miiv": [
{
"ids": 226512,
"table": "chartevents",
"sub_var": "itemid"
}
],
"mimic": [
{
"ids": [
762,
4183,
226512
],
"table": "chartevents",
"sub_var": "itemid"
}
],
"mimic_demo": [
{
"ids": [
762,
4183,
226512
],
"table": "chartevents",
"sub_var": "itemid"
}
],
"sic": [
{
"table": "cases",
"val_var": "WeightOnAdmission",
"class": "col_itm",
"callback": "transform_fun(binary_op(`/`, 1000))"
}
]
}
}
}
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