shyamvis / act-ontologies Goto Github PK

ACT Demographics, ACT Vital Signs - not expandable

HCPCS codes introduced in 2020AA and still active in 2020Ab are missing in V4 Ontology
HCPCS_2020AA_Missing_Codes.xlsx

1. Tooltip for all the 3 (ACT Demographics, ACT Social Determinants of Health, ACT Vital Signs) appear as "ACT Demographics".

2. ACT Social Determinants of Health:
   The entire ontology has Tooltip like "Vital signs\Blood Pressure\Diastolic (LOINC:8462-4): " OR
   "Vital signs\Body weight" OR "Body Mass Index" OR
   "Vital Signs\Oxygen Saturation"
   C_TOOLTIP column has changed.

3. Also the path includes the parent's LOINC code.

Current names

Patient Counts
Patient Count - At Least One Visit
Patient Count - Exists in Patient Table
Patient Counts - Distinct Patients with At Least One Diagnosis
Patient Counts - Distinct Patients with At Least One Lab
Patient Counts - Distinct Patients with At Least One Medication
Patient Counts - Distinct Patients with At Least One Procedure

Change to

Data Completeness
Patients With At Least One Visit
Patients In Patient Table
Patients With At Least One Diagnosis
Patients With At Least One Laboratory Test Result
Patients With At Least One Medication
Patients With At Least One Procedure

1.C56.1 Malignant neoplasm of Right ovary to be added (2011AA - 2020AB)
2. C64.1 Malignant neoplasm of Right Kidney to be added (2011AA - 2020AB)
3. C65.1 Malignant neoplasm of Right renal pelvis to be added (2011AA - 2020AB)
4. C66.1  Malignant neoplasm of Right ureter to be added (2011AA - 2020AB)
These codes represented 'Left' in 2010AB. In 2011AA, laterality has been changed.
5. D24.1 Benign neoplasm of right breast to be added(2011AA - 2020AB).

1. Under Tobacco Smoking Status:
   Light tobacco smoker |   |   | LA18982-1

is missing (only one missing in SDOH)

ACT COVID-19
Version_4.0RC1 - should be grayed out
Diagnostic Laboratory Tests / SARS-CoV-2 (Blood, Serum or Plasma)(Diagnostic Test) --> insert space between (Blood, Serum or Plasma) and (Diagnostic Test)
Total Patient Count --> is this the same as “Patients In Patient Table” in the ACT Demographics table? If so change it to “Patients In Patient Table”

ACT Diagnoses ICD-9-CM
in the tooltip the first 2 levels are in all caps --> change to lower case

ACT Diagnoses ICD-10 --> change to ICD-10-CM
These have codes at end of the string:
C00-D49 Neoplasms (C00-D49) [2011AA-2020AB]
E00-E89 Endocrine, Nutritional And Metabolic Diseases (E00-E89) [2011AA-2020AB]
K00-K95 Diseases Of The Digestive System (K00-K95) [2012AA-2020AB]
O00-O9A Pregcy, Childbirth And The Puerperium (O00-O9A) [2012AA-2020AB]
S00-T88 Injury, Poisoning And Certain Other Consequences Of External Causes (S00-T88) [2011AA-2020AB]
U00-U85 Codes For Special Purposes (U00-U85) [2020AB-2020AB]
D49-D49 Neoplasms Of Unspecified Behavior (D49) [2011AA-2020AB]
E70-E88 Metabolic Disorders (E70-E88) [2011AA-2020AB]
E89-E89 Postprocedural Endocrine And Metabolic Complications And Disorders, Not Elsewhere Classified (E89) [2011AA-2020AB]
G60-G65 Polyneuropathies And Other Disorders Of The Peripheral Nervous System (G60-G65) [2011AA-2020AB]
H55-H57 Other Disorders Of Eye And Adnexa (H55-H57) [2011AA-2020AB]
H59-H59 Intraoperative And Postprocedural Complications And Disorders Of Eye And Adnexa, Not Elsewhere Classified (H59) [2011AA-2020AB]
H95-H95 Intraoperative And Postprocedural Complications And Disorders Of Ear And Mastoid Process, Not Elsewhere Classified (H95) [2011AA-2020AB]
I10-I16 Hypertensive Diseases (I10-I16) [2016AB-2020AB]
K90-K95 Other Diseases Of The Digestive System (K90-K95) [2012AA-2020AB]
M04-M04 Autoinflammatory Syndromes (M04) [2016AB-2020AB]
M97-M97 Periprosthetic Fracture Around Internal Prosthetic Joint (M97) [2016AB-2020AB]
N40-N53 Diseases Of Male Genital Organs (N40-N53) [2011AA-2020AB]
O09-O09 Supervision Of High Risk Pregcy (O09) [2011AA-2020AB]
O80-O82 Encounter For Delivery (O80-O82) [2011AA-2020AB]
U00-U49 Provisional Assignment Of New Diseases Of Uncertain Etiology Or Emergency Use (U00-U49) [2020AB-2020AB]
X50-X50 Overexertion And Strenuous Or Repetitive Movements (X50) [2016AB-2020AB]
X52-X58 Accidental Exposure To Other Specified Factors (X52-X58) [2011AA-2020AB]
X92-Y09 Assault (X92-Y09) [2016AB-2020AB]
Y21-Y33 Event Of Undetermined Intent (Y21-Y33) [2011AA-2020AB]
Z18-Z18 Retained Foreign Body Fragments (Z18) [2011AA-2020AB]
Z19-Z19 Hormone Sensitivity Maligcy Status (Z19) [2016AB-2020AB]

How did Malignant get abbreviated to Maligt? - I like it

Several paths seem to be missing from V4-RC1 for Meds VA.
A few are listed below (I noticed this incidentally). Additionally I looked at the row counts for each version:
V4 row count is 1244941
V4-RC1 row count is 1244825

Missing concept examples:

\ACT\Medications\MedicationsByVaClass\V2_09302018\VA000\IP000\IP900
\ACT\Medications\MedicationsByVaClass\V2_09302018\VA000\OT000\OT400
\ACT\Medications\MedicationsByVaClass\V2_09302018\VA000\IM000\IM400\

I have not done a full compare, but based on the row count differences, that seems critical prior to finalizing.

RXNORM: 798274 has 2 different paths and both are present in Med_Alpha.

\ACT\Medications\MedicationsByAlpha\V2_12112018\RxNormUMLSRxNav\LPreparations\1007132\1656958\798274\ -- (2015AB - 2020 AA)
\ACT\Medications\MedicationsByAlpha\V2_12112018\RxNormUMLSRxNav\LPreparations\1007132\798270\798274\ -- (2008AA - 2015AA)
The new path(2015AB - 2020AA) has 2 more siblings(1657893, 1657894) compared to the old path (2008AB - 2015AA).

This RxNorm is absent in Med_VA as this Ingredient is not in RxClass.

Currently the names are Fully-Specified Names, eg,
Body Temperature:Temp:Pt:Axillary:Qn (8328-7)
Body Temperature:Temp:Pt:Urinary Bladder:Qn:Via Foley (76278-1)

Use instead Long common names, eg,
Axillary temperature (8328-7)
Bladder temperature via Foley (76278-1)

Also, add LOINC to the code at the end, eg,
Axillary temperature (LOINC: 8328-7)
Bladder temperature via Foley (LOINC: 76278-1)

Abbreviations like AST, ALT, GGT appear like Title case 'Ast, Alt, Ggt,'.
The following can be changed to UPPERCASE:
Ast - AST
Alt - ALT
Ggt - GGT
Csf - CSF
Vdrl -VDRL
Rpr - RPR
Igg - IgG
IgA - IgA
IgM - IgM
Hplc - HPLC
Ifcc - IFCC
Jds/Jscc - JDS/JSCC
Ria - RIA
Hiv - HIV
Rna - RNA
PT, INR
Aptt- aPTT
Esr- ESR
Mch - MCH
Mchc - MCHC
Mcv - MCV
Rbc - RBC
Rdw - RDW
Wbc - WBC.

ACT Diagnoses ICD-10-CM (ACT_4.0_Alpha_UMLS_2020AB) names sometimes have codes at the end of the name that should be removed. It seems to occur only in the top 2 levels.

C00-D49 Neoplasms (C00-D49)
E00-E89 Endocrine, Nutritional And Metabolic Diseases (E00-E89)
K00-K95 Diseases Of The Digestive System (K00-K95)
O00-O9A Pregnancy, Childbirth And The Puerperium (O00-O9A)
S00-T88 Injury, Poisoning And Certain Other Consequences Of External Causes (S00-T88)
U00-U85 Codes For Special Purposes (U00-U85)
D49-D49 Neoplasms Of Unspecified Behavior (D49)
E36-E36 Intraoperative Complications Of Endocrine System (E36)
E70-E88 Metabolic Disorders (E70-E88)
E89-E89 Postprocedural Endocrine And Metabolic Complications And Disorders, Not Elsewhere Classified (E89)
G60-G65 Polyneuropathies And Other Disorders Of The Peripheral Nervous System (G60-G65)
H55-H57 Other Disorders Of Eye And Adnexa (H55-H57)
H90-H94 Other Disorders Of Ear (H90-H94)
H95-H95 Intraoperative And Postprocedural Complications And Disorders Of Ear And Mastoid Process, Not Elsewhere Classified (H95)
10-I16 Hypertensive Diseases (I10-I16)
K55-K64 Other Diseases Of Intestines (K55-K64)
M04-M04 Autoinflammatory Syndromes (M04)
M97-M97 Periprosthetic Fracture Around Internal Prosthetic Joint (M97)
N40-N53 Diseases Of Male Genital Organs (N40-N53)
O09-O09 Supervision Of High Risk Pregnancy (O09)
O80-O82 Encounter For Delivery (O80-O82)
U00-U49 Provisional Assignment Of New Diseases Of Uncertain Etiology Or Emergency Use (U00-U49)
X50-X50 Overexertion And Strenuous Or Repetitive Movements (X50)
X52-X58 Accidental Exposure To Other Specified Factors (X52-X58)
X92-Y09 Assault (X92-Y09)
Y21-Y33 Event Of Undetermined Intent (Y21-Y33)
Z18-Z18 Retained Foreign Body Fragments (Z18)
Z19-Z19 Hormone Sensitivity Malignancy Status (Z19)
Z20-Z29 Persons With Potential Health Hazards Related To Communicable Diseases (Z20-Z29)

1. LDH Issue: Ldh appears twice and not expanding in the test 01 UI.

The FA term Ldh duplicated (1 more- for Cardiovascular path, 1 more - Enzymes path)
The 3 LA terms - For Enzymes path - okay appear only once
- For Cardiovascular path - appears 4 times (3 rows for each term have to be removed).

2. Protein Issue:
   LP15838-3 Protein appears under both Chemistry & Urinalysis.
   Chemistry\Protein includes Urine tests (3) .
   Urinalysis\Protein includes all the Protein (Blood/Serum/Plasma tests) and its children from Chemistry also. There is duplication of that portion both in Chemistry & Urinalysis.

ACT COVID-19 V4.0:

H_LEVEL 4 - has C_FULLNAME as "\ACT\UMLS_C0031437\SNOMED_3947185011\UMLS_C0242656\DISEASE_SEVERITY" in the Ontology File;
But the UI and C_TOOLTIP shows as "....\Illness severity". This occurs throughout down the ontology (H_LEVEL 5, 6, 7 & all)

1. H_LEVEL 5, 6 Terms - Abnormal Chest CT, Abnormal Chest CT (Derived, Abnormal Chest Imaging, Other nonspecific abnormal finding of lung field (R91.8),) missing in the Test 01 UI.
   Path: ACT Phenotypes\COVID-19 Related Terms\Course of Illness\Other Variables of Interest\Abnormal Chest Imaging*xxxxxx*
2. The following ICD10 Ventilation Procedures are missing in the H tree:
   ACT Phenotype\COVID-19 related Terms\Course of illness\Respiratory Therapy Management\Mechanical ventilation\ Ventilation Procedures\ ICD 10Ventilation Procedures 5A0935 & its children,
   5A0945 & its children,
   5A0955 & its children need to be added in the tree. They are present in the Onto. File.

ACT COVID-19 V4.0:

1. Difference in the Test 01 tree & the Tooltip for the 2 Top level terms
   Test 01 UI show as "ACT COVID – 19\Version_4.0Alpha" whereas Tooltip shows as "ACT Phenotype\ COVID-19 Related Terms" ….this recurs throughout the entire ontology.
2. 5 newly added ICD10CM codes under: Course of Illness\Conditions\ M35.81, M35.89, Z11.52, Z20.822, Z86.16 - all have ‘N17.9 Acute kidney failure, Unspecified’ in their Tooltips
3. COVID-19 Vaccines Folder: Tooltip for the Parent and all the children have ‘Abnormal Chest CT’ instead of COVID-19 Vaccines
4. ANY Active Infection Lab Test Equivocal - has C_TOOLTIP = ANY Nucleic Acid Lab Test Equivocal
   ANY Antibody Lab Test Equivocal - has C_TOOLTIPO = ANY Equivocal Antibody Test
5. ACT Social Determinants of Health has 'ACT Demographics' as tooltip; All its children have 'Vital Signs' tooltip

COVID_Ontology_V4_Issues.docx
COVID_Ontology_V4_Issues.docx

1. Medications: Anticoagulants,
   Non-Steroidal Anti-Inflammatory Drugs (NSAIDs)
   Dexmedetomidine
   Loop Diuretics
   Sympathomimetics (Adrenergics) --- these categories have NDCs listed in the Test 01 tree; but missing in the Ontology file.
2. Some medications have NDCs missing in the tree, but present in the file. Need to be added - by changing C_VISUAL ATTRIBUTES from LA --> FA. (List attached)
3. In the ONTOLOGY File - Medications which are present both under 'Severe Illness' & 'Medications' have NDCs only under the Medications Folder. In the Severe Illness Medications only have RXNORM.

Place Of Service Codes For Professional Claims (1021863) folder (present as leaf icon) - 48 children are missing in the ontology table and the test 01 UI.

ACT COVID-19 V4.0:

1. 4. COVID-19 Vaccines Folder: H_LEVEL = 8 has Terminal nodes with NDC codes like Jannsen COVID-19 vaccine (NDC:59676058015). Appear like Folder instead of a terminal leaf node.
      C_VISUAL ATTRIBUTES in the Ontology file appear as ‘LA’ only.

The following Hierarchical terms are to be removed:

1. G60-G64 Polyneuropathies And Other Disorders Of The Peripheral Nervous System
2. H55-H59 Other Disorders Of Eye And Adnexa
3. H90-H95 Other Disorders Of Ear
4. I10-I15 Hypertensive Diseases
5. N40-N51 Diseases Of Male Genital Organs - to be removed from UI
6. X92-Y08 Assault
7. Y20-Y33 Event Of Undetermined Intent
8. Z20-Z28 Persons With Potential Health Hazards Related To Communicable Diseases

--

--

--

--

--