From ca0b877690bad000af94745ab6a2a6f3aecf3b47 Mon Sep 17 00:00:00 2001
From: Pip Liggins <philippa.liggins@dtc.ox.ac.uk>
Date: Tue, 14 Nov 2023 12:07:03 +0000
Subject: [PATCH] Add fio2_percent and oxygen_flow_rate (#188)

Creates fio2_percent as an observation, transforms oxygen_flow_volume_max into
oxygen_flow_rate to store L/min provision of oxygen.

Uses presence of an oxygen flow rate as a input to treatment_oxygen_therapy.
---
 docs/guide.rst                           |   8 +-
 isaric/parsers/ccp-cameroon.toml         |  74 +++++++-------
 isaric/parsers/ccp-ghana.toml            |  60 +++++++-----
 isaric/parsers/ccp-guinea.toml           |  43 +++++++++
 isaric/parsers/ccp-netherlands.toml      |  12 +++
 isaric/parsers/ccp-spain.toml            |  41 --------
 isaric/parsers/ccp-uganda-v2.toml        |  16 +++-
 isaric/parsers/cocoa_pediatrics.toml     |   8 +-
 isaric/parsers/idor-brazil.toml          |   7 ++
 isaric/parsers/isaric-ccpuk.toml         |  24 +++++
 isaric/parsers/isaric-core.toml          |  32 ++++++-
 isaric/parsers/isaric-ecmo.toml          | 117 ++++++++++++++---------
 isaric/parsers/isaric-followup-fr.toml   |  11 +++
 isaric/parsers/isaric-rapid.toml         |  37 +++++--
 isaric/parsers/ncov-france.toml          |  46 ++++++++-
 isaric/parsers/ncov-malaysia.toml        |  76 ++++++++++++---
 isaric/parsers/predicovid.toml           |   2 +-
 isaric/parsers/sprintsari-australia.toml |  10 ++
 isaric/parsers/stopcovid-russia.toml     |   5 +-
 schemas/dev/observation.schema.json      |   5 +-
 schemas/dev/parser.schema.json           |   4 +-
 templates/template_parser.toml           |   2 +-
 22 files changed, 448 insertions(+), 192 deletions(-)

diff --git a/docs/guide.rst b/docs/guide.rst
index 2af05e7e..80a6aff5 100644
--- a/docs/guide.rst
+++ b/docs/guide.rst
@@ -868,12 +868,16 @@ fields describing symptoms, here.
 
 **oxygen_o2hb**: Value (g/dL). Heamoglobin level, lab test.
 
-**oxygen_flow_volume_max**: Value. If the subject received O2 therapy,
-record the maximum flow volume.
+**oxygen_flow_rate**: Value (L/min). Flow rate of oxygen administered.
+Where possible, record the method of oxygen therapy being used, and whether
+this is a maximum or point value. Sometimes recorded in data as FiO2 (L/min).
 
 **oxygen_saturation_percent**: Value (20-100). Use context to note whether
 observation was made on room air, on while on oxygen.
 
+**fio2_percent**: Value (21-100): Fraction of inspired oxygen (concentration
+of oxygen in supplied gas mixture).
+
 **pao2_mmHg**: Value (25-150). Use context to record whether this is an arterial,
 venous or capillary measurement if data is provided. Use mmHg as the
 default unit.
diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml
index 08113507..e03aa546 100644
--- a/isaric/parsers/ccp-cameroon.toml
+++ b/isaric/parsers/ccp-cameroon.toml
@@ -487,7 +487,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q30_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -529,7 +529,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q28_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -571,7 +571,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q37_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -613,7 +613,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q19_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -647,7 +647,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q33_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q33_signs_symptoms", description = "33) Conjunctivitis", ref = "Y/N" }
@@ -691,7 +691,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q12_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -728,7 +728,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q12_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q12_signs_symptoms", description = "12) Cough / Toux", ref = "Y/N" }
@@ -758,7 +758,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q13_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q13_signs_symptoms", description = "13) Cough - with sputum production", ref = "Y/N" }
@@ -788,7 +788,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q14_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q14_signs_symptoms", description = "14) Cough - bloodysputum", ref = "Y/N" }
@@ -818,7 +818,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q32_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q32_signs_symptoms", description = "32) Diarrhoea", ref = "Y/N" }
@@ -848,7 +848,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q6_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q6_signs_symptoms", source_unit = "mmHg", description = "6) Diastolic BP" }
@@ -878,7 +878,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q17_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q17_signs_symptoms", description = "17) Ear pain", ref = "Y/N" }
@@ -908,7 +908,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q22_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q22_signs_symptoms", description = "22) Fatigue , Malaise", ref = "Y/N" }
@@ -938,7 +938,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q27_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q27_signs_symptoms", description = "27) Headache", ref = "Y/N" }
@@ -968,7 +968,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q3_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q3_signs_symptoms", description = "3) HR/ Fréquence cardiaque" }
@@ -998,7 +998,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q11_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q11_signs_symptoms", description = "11) History of fever", ref = "Y/N" }
@@ -1028,7 +1028,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q21_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q21_signs_symptoms", description = "21) Joint pain (Arthralgia)", ref = "Y/N" }
@@ -1068,7 +1068,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q24_signs_symptoms = { "!=" = "" } },
   ]
   [observation.is_present]
@@ -1103,7 +1103,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q24_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q24_signs_symptoms", description = "24) Loss of sense of smell", ref = "Y/N" }
@@ -1133,7 +1133,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q25_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q25_signs_symptoms", description = "25) Loss of flavour", ref = "Y/N" }
@@ -1163,7 +1163,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q26_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q26_signs_symptoms", description = "26) Lower chest wall indrawing", ref = "Y/N" }
@@ -1193,7 +1193,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q36_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q36_signs_symptoms", description = "36) Lymphadenopathy", ref = "Y/N" }
@@ -1223,7 +1223,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q20_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q20_signs_symptoms", description = "20) Muscle aches (Myalgia)", ref = "Y/N" }
@@ -1334,7 +1334,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q9_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q9_signs_symptoms", description = "9) Oxygen saturation" }
@@ -1416,7 +1416,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q4_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q4_signs_symptoms", description = "4) RR / Fréquence Respiratoire" }
@@ -1446,7 +1446,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q16_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q16_signs_symptoms", description = "16) Runny nose (Rhinorrhoea)", ref = "Y/N" }
@@ -1476,7 +1476,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q29_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q29_signs_symptoms", description = "29) Seizures /Convulsions", ref = "Y/N" }
@@ -1519,7 +1519,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q7_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q7_signs_symptoms", description = "7) Severe dehydration", ref = "Y/N" }
@@ -1549,7 +1549,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q23_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q23_signs_symptoms", description = "23) Shortness of breath (Dyspnea)", ref = "Y/N" }
@@ -1579,7 +1579,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q34_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q34_signs_symptoms", description = "34) Skin rash / Eruption cutanée", ref = "Y/N" }
@@ -1609,7 +1609,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q35_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q35_signs_symptoms", description = "35) Skin ulcers", ref = "Y/N" }
@@ -1639,7 +1639,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q15_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q15_signs_symptoms", description = "15) Sore throat", ref = "Y/N" }
@@ -1673,7 +1673,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q8_signs_symptoms = { "!=" = "" } },
     { q8_signs_symptoms = { "!=" = 3 } },
   ]
@@ -1705,7 +1705,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q5_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q5_signs_symptoms", description = "5) Systolic BP / Tension artérielle systolique", source_unit = "mmHg" }
@@ -1745,7 +1745,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q1_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -1780,7 +1780,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q31_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q31_signs_symptoms", description = "31) Vomiting / Nausea", ref = "Y/N" }
@@ -1810,7 +1810,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q18_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q18_signs_symptoms", description = "18) Wheezing", ref = "Y/N" }
diff --git a/isaric/parsers/ccp-ghana.toml b/isaric/parsers/ccp-ghana.toml
index cc012102..6e853c2b 100644
--- a/isaric/parsers/ccp-ghana.toml
+++ b/isaric/parsers/ccp-ghana.toml
@@ -841,6 +841,11 @@
     description = "Extracorporeal (ECMO) support?"
     ref = "Y/N/NK"
 
+  [[visit.treatment_oxygen_therapy.fields]]
+    field = "fi02"
+    if.any = [{ fi02 = { ">" = 21 } }, { fi02 = 1 }]
+    apply = { function = "isNotNull" }
+
 [visit.treatment_prone_position]
   combinedType = "any"
   excludeWhen = "none"
@@ -882,38 +887,37 @@
   #   context = ["high-flow nasal cannula"]
 
 [[observation]]
+  name = "oxygen_flow_rate"
   phase = "study"
-  name = "oxygen_flow_volume_max"
   date.field = "outcome_date"
+  text = { field = "overall_oxygen_cmdose___1", values = { 1 = "1-5 L/min" } }
+  context = ["Maximum rate during hospital stay"]
 
-  [observation.text] # This is a multi-select, but we're only recording the MAX value
-    combinedType = "firstNonNull"
-    fields = [
-      { field = "overall_oxygen_cmdose___4", values = { 1 = ">15 L/min", 0 = "None", "" = "None" } },   # Stop-gap until if parsing improves
-      { field = "overall_oxygen_cmdose___3", values = { 1 = "11-15 L/min", 0 = "None", "" = "None" } },
-      { field = "overall_oxygen_cmdose___2", values = { 1 = "6-10 L/min", 0 = "None", "" = "None" } },
-      { field = "overall_oxygen_cmdose___1", values = { 1 = "1-5 L/min", 0 = "None", "" = "None" } },
-    ]
-
-  [observation.context]
-    combinedType = 'set'
-    excludeWhen = "none"
-    fields = [
-      { field = "daily_oxygen_cmtype_1", values = { 1 = "Nasal prongs", 2 = "HF nasal cannula", 3 = "Mask", 4 = "Mask with reservoir", 5 = "CPAP/NIV mask" } },
-    ]
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date.field = "outcome_date"
+  text = { field = "overall_oxygen_cmdose___2", values = { 1 = "6-10 L/min" } }
+  context = ["Maximum rate during hospital stay"]
 
-  [observation.if] # need to improve the auto-if for this,
-    any = [
-      { overall_oxygen_cmdose___4 = { "!=" = "" } },
-      { overall_oxygen_cmdose___3 = { "!=" = "" } },
-      { overall_oxygen_cmdose___2 = { "!=" = "" } },
-      { overall_oxygen_cmdose___1 = { "!=" = "" } },
-    ]
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date.field = "outcome_date"
+  text = { field = "overall_oxygen_cmdose___3", values = { 1 = "11-15 L/min" } }
+  context = ["Maximum rate during hospital stay"]
 
 [[observation]]
+  name = "oxygen_flow_rate"
   phase = "study"
-  name = "oxygen_flow_volume_max"
-  date.field = "o2_date"
+  date.field = "outcome_date"
+  text = { field = "overall_oxygen_cmdose___4", values = { 1 = ">15 L/min" } }
+  context = ["Maximum rate during hospital stay"]
+
+[[observation]]
+  phase = "admission"
+  name = "oxygen_flow_rate"
+  date = { ref = "admissionDateHierarchy" }
   text = { field = "daily_oxygen_cmdose_1", values = { 1 = "1-5 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min" } }
 
   [observation.context]
@@ -1380,6 +1384,12 @@
   date = { field = "icu_date" }
   value = { field = "ph", description = "pH" }
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "vitals_date" }
+  value = { field = "fi02", apply = { function = "Percentage" } }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
diff --git a/isaric/parsers/ccp-guinea.toml b/isaric/parsers/ccp-guinea.toml
index 800180c0..eae70c77 100644
--- a/isaric/parsers/ccp-guinea.toml
+++ b/isaric/parsers/ccp-guinea.toml
@@ -662,6 +662,13 @@
     { field = "non_inv_vent", ref = "Y/N" },
     { field = "inv_vent", ref = "Y/N" },
     { field = "ecls", ref = "Y/N" },
+    { field = "fio2", if = { fio2 = { ">" = 21 } }, apply = { function = "isNotNull" } },
+    { field = "any_supplemental_oxygen_value", if = { fio2_0_21_1_0_unit = 2 }, apply = { function = "isNotNull" } },
+    { field = "any_supplemental_oxygen_value", if.all = [
+      { fio2_0_21_1_0_unit = 1 },
+      { any_supplemental_oxygen_value = { ">" = 21 } },
+    ], apply = { function = "isNotNull" } },
+    { field = "daily_oxygen_cmdose_1", values = { 1 = true, 2 = true, 3 = true, 4 = true } },
   ]
 
 [visit.treatment_prone_position]
@@ -1391,6 +1398,42 @@
   date = { field = "vitals_date" }
   value = { field = "temperature", description = "Value Temperature" }
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "admission"
+  date = { field = "constantes_date_t", source_date = "%d/%m/%Y %H:%M" }
+  value = { field = "any_supplemental_oxygen_value", apply = { function = "Percentage" }, if.any = [
+    { fio2_0_21_1_0_unit = 1 },                        # percentage
+    { any_supplemental_oxygen_value = { "!=" = "" } },
+  ] }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "admission"
+  date = { field = "constantes_date_t", source_date = "%d/%m/%Y %H:%M" }
+  text = { field = "daily_oxygen_cmdose_1", values = { 1 = "1-5", 2 = "6-10", 3 = "11-15", 4 = ">15" } }
+  [observation.context]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "daily_oxygen_cmtype_1", values = { 1 = "nasal cannula", 2 = "HFNC", 3 = "mask", 4 = "mask with reservoir", 5 = "CPAP/NIV mask", 6 = "Unknown" } },
+    ]
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "admission"
+  date = { field = "constantes_date_t", source_date = "%d/%m/%Y %H:%M" }
+  value = { field = "any_supplemental_oxygen_value", if.any = [
+    { fio2_0_21_1_0_unit = 2 },                        # L/min
+    { any_supplemental_oxygen_value = { "!=" = "" } },
+  ] }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "icu_date" }
+  value = { field = "fio2", apply = { function = "Percentage" } }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
diff --git a/isaric/parsers/ccp-netherlands.toml b/isaric/parsers/ccp-netherlands.toml
index 92e07e38..942dce7d 100644
--- a/isaric/parsers/ccp-netherlands.toml
+++ b/isaric/parsers/ccp-netherlands.toml
@@ -310,6 +310,8 @@
       { field = "patient_interventions#Highflow_nasal_canula_oxygen_therapy", values = { 1 = true, 0 = false } },
       { field = "patient_interventions#Extra_corporeal_life_support_ECLS", values = { 1 = true, 0 = false } },
       { field = "Extracorporeal_support", ref = "Y/N" },
+      { field = "fio2_1", if = { fio2_1 = { ">" = 21 } }, apply = { function = "isNotNull" } },
+      { field = "signssymp_L_oxygen", apply = { function = "isNotNull" } },
     ]
 
   [visit.treatment_prone_position]
@@ -709,6 +711,16 @@
       { field = "oxygen_saturation_on", values = { 1 = "room air", 2 = "on oxygen" } },
     ]
 
+[[observation]]
+  name = "fio2_percent"
+  date = { field = "assessment_dt" }
+  phase = "study"
+  value = { field = "fio2_1" }
+  if.all = [
+    { report_name_custom = { "=~" = "Daily case record form" } },
+    { fio2_1 = { "!=" = "" } },
+  ]
+
 [[observation]]
   name = "pao2_mmHg"
   date = { field = "assessment_dt" }
diff --git a/isaric/parsers/ccp-spain.toml b/isaric/parsers/ccp-spain.toml
index f9726c56..9fbf5025 100644
--- a/isaric/parsers/ccp-spain.toml
+++ b/isaric/parsers/ccp-spain.toml
@@ -540,44 +540,3 @@
   date = { field = "fchadminsion" }
   phase = "admission"
   is_present = { field = "ss_malest", ref = "Y/N/NK" } # this field onlz captured malaise, not fatigue
-
-  ### Obervation attributes not mapped here...
-  # bleeding
-  # has_immunosuppression
-  # avpu
-  # clinical_classification_critical_illness_scale
-  # clinical_classification_pneumonia_needing_oxygen
-  # clinical_frailty_score
-  # anorexia
-  # base_excess
-  # conjunctivitis
-  # cyanosis
-  # ear_pain
-  # fatigue_malaise
-  # feeding_intolerence_peadiatrics
-  # hepatomegaly
-  # inability_to_walk
-  # inability_to_walk_scale
-  # irritability_peadiatrics
-  # loss_of_taste
-  # lung_sounds
-  # lymphadenopathy
-  # lower_chest_wall_indrawing
-  # muscle_aches
-  # total_fluid_output_m
-  # heart_sounds
-  # mid_upper_arm_circumference_cm
-  # mean_arterial_blood_pressure_mmHg
-  # severe_dehydration
-  # skin_ulcers
-  # richmond_agitation-sedation_scale
-  # riker_sedation-agitation_scale
-  # pH
-  # transfer_from_other_facility
-  # time_of_admission
-  # sternal_capillary_refill_time_greater_2s
-  # runny_nose
-  # wheezing
-  # oxygen_flow_volume_max
-  # oxygen_o2hb
-  # sore_throat
diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml
index 8a7c0572..17940e75 100644
--- a/isaric/parsers/ccp-uganda-v2.toml
+++ b/isaric/parsers/ccp-uganda-v2.toml
@@ -327,6 +327,11 @@
       { field = "non_inv_vent", values = { 1 = true, 0 = false } },
       { field = "overall_extracorp_prtrt", values = { 1 = true, 0 = false } },
       { field = "ecls", ref = "Y/N" },
+      { field = "fi02", if.all = [
+        { fi02 = { ">" = 21 } },
+        { fi02 = { "!=" = 999 } },
+      ], apply = { function = "isNotNull" } },
+      { field = "ttl_oxy", if = { ttl_oxy = { "!=" = 999 } }, apply = { function = "isNotNull" } },
     ]
 
   [visit.treatment_prone_position]
@@ -861,6 +866,13 @@
       { field = "ox_type", values = { 1 = "Room air", 2 = "Oxygen therapy" } },
     ]
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "icu_date" }
+  value = { field = "fi02", apply = { function = "Percentage" } }
+  if.all = [{ fi02 = { "!=" = "" } }, { fi02 = { "!=" = 0 } }]
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
@@ -943,10 +955,10 @@
   if.all = [{ temp_study = { "!=" = "" } }, { temp_study = { "!=" = 0 } }]
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   date = { ref = "admissionDateHierarchy" }
   phase = "study"
-  value = { field = "ttl_oxy" }
+  value = { field = "ttl_oxy", description = "how many litres of oxygen?" }
   if.all = [{ ttl_oxy = { "!=" = "" } }, { ttl_oxy = { "!=" = 999 } }]
 
 [[observation]]
diff --git a/isaric/parsers/cocoa_pediatrics.toml b/isaric/parsers/cocoa_pediatrics.toml
index ac9d0f62..0535be17 100644
--- a/isaric/parsers/cocoa_pediatrics.toml
+++ b/isaric/parsers/cocoa_pediatrics.toml
@@ -286,6 +286,8 @@
     fields = [
       { field = "oxygen_prtrt_v3", description = "Oxygen therapy?", ref = "Y/N/NK" },
       { field = "noninvasive_prtrt_v3", description = "Non-invasive ventilation ? (e.g. BIPAP, CPAP)", ref = "Y/N/NK" },
+      { field = "xygn_thrpintfc_trt_v3", values = { 1 = true, 2 = true } },
+      { field = "xygn_thrpintfc_mask_v3", apply = { function = "isNotNull" } },
     ]
 
   [visit.treatment_oxygen_mask_prongs]
@@ -559,16 +561,16 @@
     ]
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "study"
   start_date = { field = "hostdat" }
   date = { field = "dsstdtc" }
   duration_type = "event"
-  context = ["over entire visit"]
+  context = ["Maximum flow rate over entire visit", "Nasal prongs/mask"]
 
   [observation.value]
     field = "xygn_thrpintfc_mask_v3"
-    description = "If NP or Mask selected what wa the maximum flow rate recorded in L/min"
+    description = "If NP or Mask selected what was the maximum flow rate recorded in L/min"
 
 [[observation]]
   name = "oxygen_saturation_percent"
diff --git a/isaric/parsers/idor-brazil.toml b/isaric/parsers/idor-brazil.toml
index 2ea0d3ce..c667e53f 100644
--- a/isaric/parsers/idor-brazil.toml
+++ b/isaric/parsers/idor-brazil.toml
@@ -594,6 +594,7 @@
     { field = "noninvasive_proccur", ref = "Y/N/NK" },
     { field = "daily_noninvasive_prtrt", ref = "Y/N/NK" },
     { field = "daily_ecmo_prtrt", ref = "Y/N/NK" },
+    { field = "daily_fio2_lborres", if = { daily_fio2_lborres = { ">" = 0.21 } }, apply = { function = "isNotNull" } },
   ]
 
 [visit.treatment_cardiovascular_support]
@@ -922,6 +923,12 @@
   date = { ref = "admissionDate" }
   is_present = { field = "skinulcers_ceoccur_v2", ref = "Y/N/NK" }
 
+[[observation]]
+  name = "fio2_percent"
+  phase.ref = "phaseFromRedcapEvent"
+  date = { ref = "dailyDate" }
+  value = { field = "daily_fio2_lborres", apply = { function = "Percentage" } }
+
 [[observation]]
   name = "pao2_mmHg"
   phase.ref = "phaseFromRedcapEvent"
diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml
index 947799e2..8a2cfaec 100644
--- a/isaric/parsers/isaric-ccpuk.toml
+++ b/isaric/parsers/isaric-ccpuk.toml
@@ -611,6 +611,12 @@
       { field = "daily_noninvasive_prtrt", ref = "Y/N/NK" },
       { field = "extracorp_prtrt", ref = "Y/N/NK" },
       { field = "daily_ecmo_prtrt", ref = "Y/N/NK" },
+      { field = "daily_fio2_lborres", if.all = [
+        { daily_fio2_lborres = { ">" = 0.21 } },
+        { daily_fio2_lborres = { "<=" = 1 } },
+      ], apply = { function = "isNotNull" } },
+      { field = "daily_fio2b_lborres", if = { daily_fio2b_lborres = { ">" = 21 } }, apply = { function = "isNotNull" } },
+      { field = "daily_fio2c_lborres", apply = { function = "isNotNull" } },
     ]
 
 
@@ -1077,6 +1083,24 @@
   date = { field = "daily_dsstdat", description = "Date of assessment" }
   context = ['Highest']
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "daily_dsstdat", description = "Date of assessment" }
+  value = { field = "daily_fio2b_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "daily_dsstdat", description = "Date of assessment" }
+  value = { field = "daily_fio2_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date = { field = "daily_dsstdat", description = "Date of assessment" }
+  value = { field = "daily_fio2c_lborres" }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
diff --git a/isaric/parsers/isaric-core.toml b/isaric/parsers/isaric-core.toml
index fa00bd9f..fe0c7af9 100644
--- a/isaric/parsers/isaric-core.toml
+++ b/isaric/parsers/isaric-core.toml
@@ -517,6 +517,10 @@
   description = "Employed a a healthcare worker?"
   ref = "Y/N/NK"
 
+[subject.works_lab]
+  field = "labwork_erterm"
+  values = { 1 = true }
+
 [subject.works_microbiology_lab]
   field = "labwork_erterm"
   description = "Employed in a microbiology laboratory?"
@@ -876,6 +880,23 @@
     description = "Mechanical Ventilation?"
     values = { 1 = true, 2 = true, 3 = true, 4 = true }
 
+  [[visit.treatment_oxygen_therapy.fields]]
+    field = "daily_fio2_lborres"
+    if.all = [
+      { daily_fio2_lborres = { ">" = 0.21 } },
+      { daily_fio2_lborres = { "<=" = 1 } },
+    ]
+    apply = { function = "isNotNull" }
+
+  [[visit.treatment_oxygen_therapy.fields]]
+    field = "daily_fio2b_lborres"
+    if = { daily_fio2_lborres = { ">" = 21 } }
+    apply = { function = "isNotNull" }
+
+  [[visit.treatment_oxygen_therapy.fields]]
+    field = "daily_fio2c_lborres"
+    apply = { function = "isNotNull" }
+
 [visit.treatment_oxygen_mask_prongs]
   field = "oxygen_cminterface"
   values = { 1 = false, 2 = true, 3 = true, 4 = false }
@@ -1671,8 +1692,8 @@
   duration_type = "event"
   text = { field = "flw2_other_symp" }
 
-[[observation]] # PL: look at this one
-  name = "oxygen_flow_volume_max"
+[[observation]]
+  name = "oxygen_flow_rate"
   phase = "study"
   start_date = { ref = "admissionDateHierarchy" }
   date = { field = "dsstdtc" }
@@ -1981,3 +2002,10 @@
   phase = "study"
   date = { field = "daily_dsstdat" }
   value = { field = "daily_fio2_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date = { field = "daily_dsstdat" }
+  value = { field = "daily_fio2c_lborres" }
+  context = ["Maximum value over 24hrs"]
diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml
index 1e28677c..11e8f27d 100644
--- a/isaric/parsers/isaric-ecmo.toml
+++ b/isaric/parsers/isaric-ecmo.toml
@@ -638,51 +638,51 @@
       { field = "icu_hostdat", if = { "Date Of ICU Admission  (Treatment) 6.1 Date of ICU admission [dischargeoutcome_arm_1][icu_hostdat]" = "" } },
     ]
 
-[visit.transfer_from_other_facility]
-  field = "hooccur"
-  values = { 1 = true, 2 = true, 3 = false }
+  [visit.transfer_from_other_facility]
+    field = "hooccur"
+    values = { 1 = true, 2 = true, 3 = false }
 
-[visit.treatment_antivirals]
-  field = "antiviral_cmyn"
-  ref = "Y/N/NK"
-  description = "Antiviral agent?"
+  [visit.treatment_antivirals]
+    field = "antiviral_cmyn"
+    ref = "Y/N/NK"
+    description = "Antiviral agent?"
 
-[visit.treatment_antiviral_type]
-  combinedType = "set"
-  description = "Antiviral ot COVID-19 targeted agent"
-  excludeWhen = 'none'
-  fields = [
-    { field = "antiviral_cmtrt___1", values = { 1 = "Ribavirin" } },
-    { field = "antiviral_cmtrt___2", values = { 1 = "Lopinavir/Ritonavir" } },
-    { field = "antiviral_cmtrt___3", values = { 1 = "Interferon alpha" } },
-    { field = "antiviral_cmtrt___4", values = { 1 = "Interferon beta" } },
-    { field = "antiviral_cmtrt___5", values = { 1 = "Neuraminidase inhibitor" } },
-    { field = "antiviral_cmtrt___6", values = { 1 = "Other" } },
-    { field = "antiviral_cmtrt___7", values = { 1 = "Remdesivir" } },
-    { field = "antiviral_cmtrt___9", values = { 1 = "IL6 inhibitor" } },
-    { field = "antiviral_cmtrt___10", values = { 1 = "Convalescent plasma" } },
-    { field = "antiviral_cmtrt___11", values = { 1 = "Anti-influenza antiviral" } },
-  ]
-  
-[visit.treatment_antiviral_type_other]
-  combinedType = "set"
-  excludeWhen = "none"
-  fields = [{ field = "antiviral_cmtype" }]
+  [visit.treatment_antiviral_type]
+    combinedType = "set"
+    description = "Antiviral ot COVID-19 targeted agent"
+    excludeWhen = 'none'
+    fields = [
+      { field = "antiviral_cmtrt___1", values = { 1 = "Ribavirin" } },
+      { field = "antiviral_cmtrt___2", values = { 1 = "Lopinavir/Ritonavir" } },
+      { field = "antiviral_cmtrt___3", values = { 1 = "Interferon alpha" } },
+      { field = "antiviral_cmtrt___4", values = { 1 = "Interferon beta" } },
+      { field = "antiviral_cmtrt___5", values = { 1 = "Neuraminidase inhibitor" } },
+      { field = "antiviral_cmtrt___6", values = { 1 = "Other" } },
+      { field = "antiviral_cmtrt___7", values = { 1 = "Remdesivir" } },
+      { field = "antiviral_cmtrt___9", values = { 1 = "IL6 inhibitor" } },
+      { field = "antiviral_cmtrt___10", values = { 1 = "Convalescent plasma" } },
+      { field = "antiviral_cmtrt___11", values = { 1 = "Anti-influenza antiviral" } },
+    ]
 
-[visit.treatment_antimalarial]
-  field = "antiviral_cmtrt___8"
-  values = { 1 = true }
+  [visit.treatment_antiviral_type_other]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [{ field = "antiviral_cmtype" }]
 
-[visit.treatment_antimalarial_type]
-  combinedType = "set"
-  excludeWhen = "none"
-  fields = [
-    { field = "antiviral_cmtrt___8", values = { 1 = "Chloroquine/Hydroxychloroquine" } },
-  ]
+  [visit.treatment_antimalarial]
+    field = "antiviral_cmtrt___8"
+    values = { 1 = true }
 
-[visit.treatment_neuromuscular_blocking_agents]
-  field = "daily_neuro_cmtrt"
-  ref = "Y/N/NK"
+  [visit.treatment_antimalarial_type]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "antiviral_cmtrt___8", values = { 1 = "Chloroquine/Hydroxychloroquine" } },
+    ]
+
+  [visit.treatment_neuromuscular_blocking_agents]
+    field = "daily_neuro_cmtrt"
+    ref = "Y/N/NK"
 
   [visit.treatment_antibiotics]
     description = "Antibiotics?"
@@ -832,6 +832,12 @@
       { field = "daily_ecmo_prtrt", ref = "Y/N/NK" },
       # { field = "pronevent_prtrt", description = "Ventilation in prone position?", ref = "Y/N/NK" },
       { field = "daily_prone_cmtype", description = "Prone while on invasive ventilation", values = { 1 = true } },
+      { field = "daily_fio2_lborres", if.all = [
+        { daily_fio2_lborres = { ">" = 0.21 } },
+        { daily_fio2_lborres = { "<=" = 1 } },
+      ], apply = { function = "isNotNull" } },
+      { field = "daily_fio2b_lborres", if = { daily_fio2b_lborres = { ">" = 21 } }, apply = { function = "isNotNull" } },
+      { field = "daily_fio2c_lborres", apply = { function = "isNotNull" } },
     ]
 
   [visit.treatment_inhaled_nitric_oxide]
@@ -1168,6 +1174,31 @@
   date = { field = "daily_dsstdat" }
   value = { field = "daily_temp_vsorres", unit = "°C", source_unit = { field = "daily_temp_vsorresu", values = { 1 = "°C", 2 = "°F" } } }
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { ref = "dailyDateHierarchy" }
+  value = { field = "daily_fio2b_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { ref = "dailyDateHierarchy" }
+  value = { field = "daily_fio2_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date = { ref = "dailyDateHierarchy" }
+  value = { field = "daily_fio2c_lborres" }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date = { field = "daily_dsstdat" }
+  text = { field = "oxygen_cmdose", values = { 1 = "<2 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min", 6 = "2-5 L/min" } }
+  context = ['Maximum dose over entire visit']
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
@@ -1225,12 +1256,6 @@
   value = { field = "sas_vsorres", apply = { function = "getFloat" } }
   # if.any = [{ sas_vsyn = 1 }, { rass_sas_vsyn = 4 }]
 
-[[observation]]
-  name = "oxygen_flow_volume_max"
-  phase = "study"
-  date = { field = "daily_dsstdat" }
-  text = { field = "oxygen_cmdose", values = { 1 = "<2 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min", 6 = "2-5 L/min" } }
-
 [[observation]]
   name = "altered_consciousness_confusion"
   date = { ref = "admissionDateHierarchy" }
diff --git a/isaric/parsers/isaric-followup-fr.toml b/isaric/parsers/isaric-followup-fr.toml
index b79ecbbc..c5d7a2d1 100644
--- a/isaric/parsers/isaric-followup-fr.toml
+++ b/isaric/parsers/isaric-followup-fr.toml
@@ -72,6 +72,11 @@
     field = "subjid"
     sensitive = true
 
+  [visit.treatment_oxygen_therapy]
+    field = "fio2_pao2"
+    if = { fio2_pao2 = { ">" = 21 } }
+    apply = { function = "isNotNull" }
+
   [visit.outcome]
     field = "ca_hospit"
     values = { 1 = "hospitalised" }
@@ -262,6 +267,12 @@
   date = { field = "ca_date" }
   value = { field = "ca_hb_lborres", unit = "g/dL", source_unit = { field = "ca_hb_lborresu", values = { 1 = "g/L", 2 = "g/dL", 3 = "mg/dl" } } } #, 4 = "mmol/L"
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "followup"
+  date = { field = "abg_date" }
+  value = { field = "fio2_pao2", unit = "%" }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "followup"
diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml
index a10faf33..0b1fe870 100644
--- a/isaric/parsers/isaric-rapid.toml
+++ b/isaric/parsers/isaric-rapid.toml
@@ -873,6 +873,12 @@
     { fieldPattern = ".*noninvasive_proccur", ref = "Y/N/NK", description = "Non-invasive ventilation?" },
     { field = "ccm_b_noninvasive_prtrt", ref = "Y/N/NK", description = "Non-invasive ventilation?" },
     { fieldPattern = ".*extracorp_prtrt", ref = "Y/N/NK" },
+    { field = "ccm_a_fio2_lborres", if.all = [
+      { ccm_a_fio2_lborres = { ">" = 0.21 } },
+      { ccm_a_fio2_lborres = { "<=" = 1 } },
+    ], apply = { function = "isNotNull" } },
+    { field = "ccm_a_fio2b_lborres", if = { daily_fio2b_lborres = { ">" = 21 } }, apply = { function = "isNotNull" } },
+    { field = "ccm_a_fio2c_lborres", apply = { function = "isNotNull" } },
   ]
 
 [visit.treatment_prone_position]
@@ -1815,6 +1821,24 @@
   value = { field = "daily_temp_vsorres" } # there is no source unit field
   context = ['Most abnormal reading']
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "ccm_a_dat" }
+  value = { field = "ccm_a_fio2b_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "ccm_a_dat" }
+  value = { field = "ccm_a_fio2_lborres", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "oxygen_flow_rate"
+  phase = "study"
+  date = { field = "ccm_a_dat" }
+  value = { field = "ccm_a_fio2c_lborres" }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
@@ -1853,11 +1877,10 @@
   value = { field = "ccm_a_baseex_lborres" }
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "admission"
   date = { ref = "admissionDateHierarchy" }
   text = { field = "oxygen_cmdose", values = { 1 = "1-5 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min" } }
-  if.all = [{ oxygen_cmoccur = 1 }, { oxygen_cmdose = { "!=" = 5 } }]
 
   [observation.context]
     combinedType = "set"
@@ -1867,14 +1890,10 @@
     ]
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "study"
   date = { field = "daily_date" }
   text = { field = "daily_oxygen_cmdose", values = { 1 = "1-5 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min" } }
-  if.all = [
-    { daily_oxygen_cmoccur = 1 },
-    { daily_oxygen_cmdose = { "!=" = 5 } },
-  ]
 
   [observation.context]
     combinedType = "set"
@@ -1884,12 +1903,12 @@
     ]
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "study"
   startdate = { ref = "admissionDateHierarchy" }
   date = { field = "dsstdtc" }
   duration_type = "event"
-  # text = { field = "overall_oxygen_cmdose", values = { 1 = "1-5 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min" } }
+  context = ["Maxiumum dose over entire visit"]
 
   [observation.text]
     combinedType = "firstNonNull"
diff --git a/isaric/parsers/ncov-france.toml b/isaric/parsers/ncov-france.toml
index 2c082d77..1acae087 100644
--- a/isaric/parsers/ncov-france.toml
+++ b/isaric/parsers/ncov-france.toml
@@ -466,14 +466,35 @@
   is_present = { field = "signes_clin___6", values = { 1 = true } }
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "admission"
   date = { ref = "admissionDate" }
+
   [observation.value]
-    combinedType = "max"
+    combinedType = "firstNonNull"
     fields = [
       { field = "a_o2_on", description = "O2 flow (L/min), nasal O2" },
       { field = "a_of_o2", description = "O2 flow (L/min), HFNC" },
+      # { field = "a_vni_ti", description = "Inspiratory trigger (L/min)" },
+      { field = "a_vm_di", description = "Inspiratory flow (L/min)" },
+    ]
+
+  [observation.context]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "a_o2_on", apply = { function = "textIfNotNull", params = [
+        "Nasal O2",
+      ] } },
+      { field = "a_of_o2", apply = { function = "textIfNotNull", params = [
+        "HFNC",
+      ] } },
+      { field = "a_vni_ti", apply = { function = "textIfNotNull", params = [
+        "Non-invasive ventilation",
+      ] } },
+      { field = "a_vm_di", apply = { function = "textIfNotNull", params = [
+        "Mechanical ventilation",
+      ] } },
     ]
 
 [[observation]]
@@ -494,6 +515,27 @@
   date = { ref = "admissionDate" }
   value = { field = "ph_dose", description = "pH" }
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "admission"
+  date = { ref = "admissionDate" }
+  value = { field = "a_of_fio2", apply = { function = "Percentage" } }
+  context = ['nasal oxygen']
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "admission"
+  date = { ref = "admissionDate" }
+  value = { field = "a_vni_fio2", apply = { function = "Percentage" } }
+  context = ['non-invasive ventilation']
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "admission"
+  date = { ref = "admissionDate" }
+  value = { field = "a_vm_fio2", apply = { function = "Percentage" } }
+  context = ['mechanical ventilation']
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "admission"
diff --git a/isaric/parsers/ncov-malaysia.toml b/isaric/parsers/ncov-malaysia.toml
index d6c57dc5..182b5a7f 100644
--- a/isaric/parsers/ncov-malaysia.toml
+++ b/isaric/parsers/ncov-malaysia.toml
@@ -351,7 +351,7 @@
       { field = "mx_antiviral_type___4", values = { 1 = "Interferon beta" } },
       { field = "mx_antiviral_type___5", values = { 1 = "Neuraminidase inhibitor" } },
       { field = "mx_antiviral_type___6", values = { 1 = "Ritonavir" } },
-      { field = "mx_antiviral_type___7", values = { 1 = "Favipravir" } },
+      { field = "mx_antiviral_type___7", values = { 1 = "Favipiravir" } },
       { field = "mx_antiviral_type___8", values = { 1 = "Atazanavir" } },
       { field = "type_antiviral_dc___1", values = { 1 = "Ribavirin" } },
       { field = "type_antiviral_dc___2", values = { 1 = "Lopinavir/Ritonavir" } },
@@ -359,7 +359,7 @@
       { field = "type_antiviral_dc___4", values = { 1 = "Interferon beta" } },
       { field = "type_antiviral_dc___5", values = { 1 = "Neuraminidase inhibitor" } },
       { field = "type_antiviral_dc___6", values = { 1 = "Ritonavir" } },
-      { field = "type_antiviral_dc___7", values = { 1 = "Favipravir" } },
+      { field = "type_antiviral_dc___7", values = { 1 = "Favipiravir" } },
       { field = "type_antiviral_dc___8", values = { 1 = "Atazanavir" } },
     ]
 
@@ -472,6 +472,9 @@
       { field = "prone_dc", ref = "Y/N", description = "Prone Ventilation?" },
       { description = "Oxygen interface - HFNC", field = "oxy_interface", values = { 1 = false, 2 = true, 3 = false, 4 = false, 5 = false, 6 = false } },
       { field = "type_oxy_dc", values = { 1 = false, 2 = true, 7777 = false } },
+      { field = "daily_fio2_data", if = { daily_fio2_data = { ">" = 0.21 } }, apply = { function = "isNotNull" } },
+      { field = "fio_prone", if = { fio_prone = { ">" = 0.21 } }, apply = { function = "isNotNull" } },
+      { field = "oxy_flow", apply = { function = "isNotNull" } },
     ]
 
   [visit.treatment_prone_position]
@@ -909,6 +912,40 @@
     field = "daily_ph_data"
     description = "pH"
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "admission"
+  if.all = [
+    { redcap_event_name = "on_admission_arm_1" },
+    { daily_fio2_data = { "!=" = "" } },
+    { daily_fio2_data = { "!=" = "9999" } },
+  ]
+  date = { field = "daily_assess_date" }
+  value = { field = "daily_fio2_data", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  if.all = [
+    { redcap_event_name = "daily_progress_arm_1" },
+    { daily_fio2_data = { "!=" = "" } },
+    { daily_fio2_data = { "!=" = "9999" } },
+  ]
+  date = { field = "daily_assess_date" }
+  value = { field = "daily_fio2_data", apply = { function = "Percentage" } }
+
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  if.all = [
+    { redcap_event_name = "daily_progress_arm_1" },
+    { fio_prone = { "!=" = "" } },
+    { fio_prone = { "!=" = "9999" } },
+  ]
+  date = { field = "daily_assess_date" }
+  value = { field = "fio_prone", apply = { function = "Percentage" } }
+  context = ["FiO2 while in prone position"]
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "admission"
@@ -1083,13 +1120,6 @@
     field = "t_sx"
     unit = "°C"
 
-    # Not very useful without fluid input, disabling
-    # [[observation]] # THIS NEEDS DISCUSSION
-    #   name = "total_fluid_output_ml"
-    #   phase = "study"
-    #   date = { field = "daily_assess_date" }
-    #   value = { field = "mx_fluid_out" }
-
 [[observation]]
   name = "vomiting_nausea"
   phase = "admission"
@@ -1114,7 +1144,7 @@
     ref = "Y/N"
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   date = { field = "daily_assess_date" }
   phase = "admission"
   if.all = [
@@ -1122,11 +1152,20 @@
     { oxy_flow = { "!=" = "" } },
     { oxy_flow = { "!=" = "9999" } },
   ]
-  text = { field = "oxy_flow", values = { 1 = "1-5 l/min", 2 = "6-10 l/min", 3 = "11-15 l/min", 4 = ">15 l/min" } }
-  context = ['Maximum over 24hr period']
+  text = { field = "oxy_flow", values = { 1 = "1-5 L/min", 2 = "6-10 L/min", 3 = "11-15 L/min", 4 = ">15 L/min" } }
+
+  [observation.context]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "oxy_flow", apply = { function = "textIfNotNull", params = [
+        'Maximum rate over 24hr period',
+      ] } },
+      { field = "oxy_interface", values = { 1 = "Nasal prongs", 2 = "HFNC", 3 = "Mask", 4 = "Mask with reservoir", 5 = "CPAP/NIV mask", 6 = "Invasive ventilation" } },
+    ]
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   date = { field = "daily_assess_date" }
   phase = "study"
   if.all = [
@@ -1135,7 +1174,16 @@
     { oxy_flow = { "!=" = "9999" } },
   ]
   text = { field = "oxy_flow", values = { 1 = "1-5 l/min", 2 = "6-10 l/min", 3 = "11-15 l/min", 4 = ">15 l/min" } }
-  context = ['Maximum over 24hr period']
+
+  [observation.context]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "oxy_flow", apply = { function = "textIfNotNull", params = [
+        'Maximum rate over 24hr period',
+      ] } },
+      { field = "oxy_interface", values = { 1 = "Nasal prongs", 2 = "HFNC", 3 = "Mask", 4 = "Mask with reservoir", 5 = "CPAP/NIV mask", 6 = "Invasive ventilation" } },
+    ]
 
 [[observation]]
   name = "heart_sounds"
diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml
index 53f04052..2ab05de1 100644
--- a/isaric/parsers/predicovid.toml
+++ b/isaric/parsers/predicovid.toml
@@ -77,7 +77,7 @@
       { field = "other_ethnic" },
     ]
 
-  [subject.works_microbiology_lab]
+  [subject.works_lab]
     field = "labwork_erterm"
     ref = "Y/N/NK"
 
diff --git a/isaric/parsers/sprintsari-australia.toml b/isaric/parsers/sprintsari-australia.toml
index 40ecee16..1f753844 100644
--- a/isaric/parsers/sprintsari-australia.toml
+++ b/isaric/parsers/sprintsari-australia.toml
@@ -388,6 +388,10 @@
     { field = "daily_noninvasive_prtrt", description = "Non-invasive ventilation (e.g. BIPAP, CPAP)?", ref = "Y/N" },
     { field = "daily_invasive_prtrt", description = "Invasive ventilation?", ref = "Y/N" },
     { field = "daily_ecmo_prtrt", description = "ECMO?", ref = "Y/N" },
+    { field = "daily_fio2_lborres", if.all = [
+      { daily_fio2_lborres = { ">" = 0.21 } },
+      { daily_fio2_lborres = { "<=" = 1 } },
+    ], apply = { function = "isNotNull" } },
   ]
 
 [visit.treatment_prone_position]
@@ -702,6 +706,12 @@
     field = "daily_ph_lborres"
     description = "pH Document from same ABG with the worst P:F ratio"
 
+[[observation]]
+  name = "fio2_percent"
+  phase = "study"
+  date = { field = "daily_dsstdat" }
+  value = { field = "daily_fio2_lborres", apply = { function = "Percentage" } }
+
 [[observation]]
   name = "pao2_mmHg"
   phase = "study"
diff --git a/isaric/parsers/stopcovid-russia.toml b/isaric/parsers/stopcovid-russia.toml
index 0ac2fcaa..debc1aed 100644
--- a/isaric/parsers/stopcovid-russia.toml
+++ b/isaric/parsers/stopcovid-russia.toml
@@ -656,15 +656,16 @@
     5 = 4 # You are unable to walk about?
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   phase = "study"
   duration_type = "block"
   date.field = "dsstdtc"
   start_date.ref = "admissionDate"
   text.field = "oxygen_cmdose"
+  context = ["Maximum value"]
 
   [observation.text.values]
-    1 = "< 2 L/min"
+    1 = "<2 L/min"
     6 = "2-5 L/min"
     2 = "6-10 L/min"
     3 = "11-15 L/min"
diff --git a/schemas/dev/observation.schema.json b/schemas/dev/observation.schema.json
index 77ff735a..1e89f4f7 100644
--- a/schemas/dev/observation.schema.json
+++ b/schemas/dev/observation.schema.json
@@ -53,7 +53,7 @@
       ],
       "properties": {
         "name": {
-          "const": "oxygen_flow_volume_max"
+          "const": "oxygen_flow_rate"
         }
       }
     },
@@ -64,7 +64,7 @@
       ],
       "properties": {
         "name": {
-          "const": "oxygen_flow_volume_max"
+          "const": "oxygen_flow_rate"
         }
       }
     },
@@ -430,7 +430,6 @@
         "initial_illness",
         "pre-admission",
         "admission",
-        "initial_illness",
         "study",
         "followup"
       ],
diff --git a/schemas/dev/parser.schema.json b/schemas/dev/parser.schema.json
index 746ead61..47899024 100644
--- a/schemas/dev/parser.schema.json
+++ b/schemas/dev/parser.schema.json
@@ -787,7 +787,7 @@
                   "other_symptom",
                   "acvpu",
                   "avpu",
-                  "oxygen_flow_volume_max"
+                  "oxygen_flow_rate"
                 ]
               }
             }
@@ -811,7 +811,7 @@
                   "mid_upper_arm_circumference_cm",
                   "oxygen_o2hb",
                   "oxygen_saturation_percent",
-                  "oxygen_flow_volume_max",
+                  "oxygen_flow_rate",
                   "fio2_percent",
                   "pao2_mmHg",
                   "pco2_mmHg",
diff --git a/templates/template_parser.toml b/templates/template_parser.toml
index dbdef4ff..4c921917 100644
--- a/templates/template_parser.toml
+++ b/templates/template_parser.toml
@@ -1001,7 +1001,7 @@
   # if = {  = { "!=" = } }
 
 [[observation]]
-  name = "oxygen_flow_volume_max"
+  name = "oxygen_flow_rate"
   date = ""
   phase = ""
   is_present = { field = "", ref = "Y/N/NK" }