Terminology Mapping - OHDSI/ETL--PulmonaryHypertensionRegistries GitHub Wiki
Storing the information as a code that represents a single unique concept does not always convey all the information necessary for clinical care, population management, and research. The data modeling methods applied to address the issue are Pre- and Post-coordination. These approaches either provide the usage of complex structures (Post-coordination) or explicit all-in-one entities (Pre-coordination) to cover the source semantics.
Read more about it here.
The data stored as The Medical Dictionary for Regulatory Activities (MedDRA) terms are usually adverse events and medical history terms. The majority of classified terms are used to relate the medical events to specific drug or device exposures. Predominantly, these events are clinical findings and laboratory test abnormalities. The terms from the vocabulary are mapped to the appropriate OMOP standards by the following rules:
- Clinical events such as symptoms and signs, conditions and other clinical findings (excluding some allergic reactions) are mapped to explicit pre-coordinated OMOP entities, with some cases of usage of independent post-coordinated facts or 1-to-many mapping.
- Laboratory abnormalities, allergies are mapped to the post-coordianted pairs of events and its dependent attributive value (e.g. substance resulted in allergy, measurement result (high/low), dynamic (fluctuating/changing) or binary (presence/absence) attribute).
The most frequently utilized terms related to PH diagnosis and treatment are already a part of OMOP vocabulary with provided mappings to Standard. To look up and download the terms and mappings in Athena the user has to be a license owner.
To look up the MedDRA mapping of the PH and related conditions click here.
The WHO Drug dictionary is an international classification of medicines created by the WHO Programme for International Drug Monitoring and managed by the Uppsala Monitoring Centre. Data sources may contain the drug prescription and administration information represented by these codes . However, the approach to ETL the data into OMOP is not established due to license issues yet.
The most common data elements originate from non-ontological sources and presented as free text values and/or their combinations. The data are usually describes the main diagnosis and its essential attributes such as:
- Diagnosis-defining or confirmatory procedures and tests,
- medications used for treatment of PH and comorbid conditions,
- medical history (both personal and family),
- adverse events,
- data about causality, severity of events.
Examples of mapping can be found here.
According to OMOP conventions, different types of clinical facts should be reflected as events in appropriate Domains according to their mapping.
The tables below provide the examples of mappings performed on both MedDRA and free text source terms (excluding the PH diagnosis described here).
| Source_vocabulary | Source_code | Source_code_description | target_entity_type | target_concept_id | target_concept_code | target_concept_name | target_concept_class_id | target_domain_id | target_vocabulary_id |
| FreeText | Right heart catheterization | Right heart catheterization | event | 4223626 | 40403005 | Catheterization of right heart | Procedure | Procedure | SNOMED |
| FreeText | CABG | CABG | event | 4336464 | 232717009 | Coronary artery bypass graft | Procedure | Procedure | SNOMED |
| MedDRA | 10011077 | Coronary artery bypass | event | 4336464 | 232717009 | Coronary artery bypass graft | Procedure | Procedure | SNOMED |
| Source_vocabulary | Source_code | Source_code_description | target_eentity_type | target_concept_id | target_concept_code | target_concept_name | target_concept_class_id | target_domain_id | target_vocabulary_id |
| MedDRA | 10001720 | Allergic reaction to antibiotics | event | 439224 | 416098002 | Allergy to drug | Clinical Finding | Observation | SNOMED |
| 10001720 | Allergic reaction to antibiotics | value | 1035150 | LA30299-4 | Antibiotic | Answer | Meas Value | LOINC | |
| MedDRA | 10014313 | Effusion pleural | event | 254061 | 60046008 | Pleural effusion | Clinical Finding | Condition | SNOMED |
| FreeText | CHRONIC PLEURAL EFFUSION | CHRONIC PLEURAL EFFUSION | event | 254061 | 60046008 | Pleural effusion | Clinical Finding | Condition | SNOMED |
| MedDRA | 10059296 | Intermittent headache | event | 37016721 | 712826000 | Intermittent headache | Clinical Finding | Condition | SNOMED |
| FreeText | HEADACHES, INTERMITTENT | HEADACHES, INTERMITTENT | event | 37016721 | 712826000 | Intermittent headache | Clinical Finding | Condition | SNOMED |
| Source_vocabulary | Source_code | Source_code_description | target_entity_type | target_concept_id | target_concept_code | target_concept_name | target_concept_class_id | target_domain_id | target_vocabulary_id |
| FreeText | trandolapril|TRANDOLAPRIL||ORAL | trandolapril|TRANDOLAPRIL||ORAL | event | 1342439 | 38454 | trandolapril | Ingredient | Drug | RxNorm |
| FreeText | TELMISARTAN|TELMISARTAN|MG|80 | TELMISARTAN|TELMISARTAN|MG|80 | event | 1317678 | 316765 | telmisartan 80 MG | Clinical Drug Comp | Drug | RxNorm |
| MedDRA | ADEMPAS 1 MG TAB||||1|1 | ADEMPAS 1 MG TAB||| | event | 44506640 | 1439896 | riociguat 1 MG Oral Tablet [Adempas] | Branded Drug | Drug | RxNorm |
| FreeText | sildenafilo|SILDENAFIL||ORAL | sildenafilo|SILDENAFIL||ORAL | event | 1316262 | 136411 | sildenafil | Ingredient | Drug | RxNorm |
| MedDRA | 10062117 | Steroid therapy | event | 4180039 | 297279009 | Administration of steroid | Procedure | Procedure | SNOMED |
| FreeText | STEROIDS (UNKNOWN)||||| | STEROIDS (UNKNOWN)||||| | event | 4180039 | 297279009 | Administration of steroid | Procedure | Procedure | SNOMED |
| Source_vocabulary | Source_code | Source_code_description | target_entity_ type | target_concept_id | target_concept_code | target_concept_name | target_concept_class_id | target_domain_id | target_vocabulary_id |
| FreeText | OTHER SIGNS OF RIGHT HEART FAILURE: ELEVATED BNP OF 2,293 PG/ML | OTHER SIGNS OF RIGHT HEART FAILURE: ELEVATED BNP OF 2,293 PG/ML | event | 4307029 | 390917008 | Brain natriuretic peptide measurement | Procedure | Measurement | SNOMED |
| FreeText | OTHER SIGNS OF RIGHT HEART FAILURE: ELEVATED BNP OF 2,293 PG/ML | OTHER SIGNS OF RIGHT HEART FAILURE: ELEVATED BNP OF 2,293 PG/ML | value | 21498551 | LA25349-4 | Elevation | Answer | Meas Value | LOINC |
| FreeText | PCO2|MM/HG | Partial Pressure Carbon Dioxide|MM/HG | event | 4099545 | 25284008 | Carbon dioxide measurement, partial pressure | Procedure | Measurement | SNOMED |
| MedDRA | 10071033 | Walking distance test | event | 4012948 | 165263003 | Walking distance | Observable Entity | Measurement | SNOMED |
| MedDRA | 10071032 | Walking distance test abnormal | event | 4012948 | 165263003 | Walking distance | Observable Entity | Measurement | SNOMED |
| FreeText | SIXMW106 | SIXMW1-Distance at 6 Minutes | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | PATIENT DESAT'S TO 83% WITH 6MWALK TESTING. | PATIENT DESAT'S TO 83% WITH 6MWALK TESTING. | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | THE SUBJECT DESATURATED TO 80% DURING 6 MINUTE HALL WALK DESPITE BEING ON OXYGEN @ 2L/MIN. | THE SUBJECT DESATURATED TO 80% DURING 6 MINUTE HALL WALK DESPITE BEING ON OXYGEN @ 2L/MIN. | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | PATIENT DESATURATING TO 84% WITH ACTIVITY DURING 6 MWALK | PATIENT DESATURATING TO 84% WITH ACTIVITY DURING 6 MWALK | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | PER MD ASSESSMENT & NOTES, PATIENT WITH +2 BLE EDEMA ; 6MWD MUCH SHORTER COMPARED WITH ENROLLMENT VISIT 6MWD. | PER MD ASSESSMENT & NOTES, PATIENT WITH +2 BLE EDEMA ; 6MWD MUCH SHORTER COMPARED WITH ENROLLMENT VISIT 6MWD. | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | Six min walk test: distance walked|ft | Six min walk test: distance walked|ft | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | Six min walk test: distance walked|m | Six min walk test: distance walked|m | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | Six min walk test: distance walked| | Six min walk test: distance walked| | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | SMWTTWD| | Distance Walked| | event | 44806532 | 821761000000100 | 6 minute walk test distance | Observable Entity | Measurement | SNOMED |
| FreeText | BNPPRONT|pg/mL | N-Terminal ProB-type Natriuretic Peptide|pg/mL | event | 3029187 | 33762-6 | Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma | Lab Test | Measurement | LOINC |
| FreeText | BNPPRONT|ng/L | N-Terminal ProB-type Natriuretic Peptide|ng/L | event | 3029187 | 33762-6 | Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma | Lab Test | Measurement | LOINC |
| FreeText | BNPPRONT|pmol/L | N-Terminal ProB-type Natriuretic Peptide|pmol/L | event | 3029435 | 33763-4 | Natriuretic peptide.B prohormone N-Terminal [Moles/volume] in Serum or Plasma | Lab Test | Measurement | LOINC |
| FreeText | Brain Natriuretic Peptide (BNP)|pg/ml | Brain Natriuretic Peptide (BNP)|pg/ml | event | 3031569 | 42637-9 | Natriuretic peptide B [Mass/volume] in Blood | Lab Test | Measurement | LOINC |
| FreeText | BMI | Body Mass Index | event | 4245997 | 60621009 | Body mass index | Observable Entity | Measurement | SNOMED |
| MedDRA | 10005895 | Body mass index decreased | event | 4245997 | 60621009 | Body mass index | Observable Entity | Measurement | SNOMED |
| MedDRA | 10005895 | Body mass index decreased | value | 4053347 | 1250004 | Decreased | Qualifier Value | Meas Value | SNOMED |
| MedDRA | 10007578 | Cardiac index increased | event | 4208254 | 54993008 | Cardiac index | Observable Entity | Measurement | SNOMED |
| MedDRA | 10007578 | Cardiac index increased | value | 4146067 | 35105006 | Increased | Qualifier Value | Meas Value | SNOMED |
| MedDRA | 10007577 | Cardiac index decreased | event | 4208254 | 54993008 | Cardiac index | Observable Entity | Measurement | SNOMED |
| MedDRA | 10007577 | Cardiac index decreased | value | 4053347 | 1250004 | Decreased | Qualifier Value | Meas Value | SNOMED |
| FreeText | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | event | 4208254 | 54993008 | Cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | event | 4040920 | 118433006 | Pulmonary artery wedge pressure | Observable Entity | Measurement | SNOMED |
| FreeText | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | event | 4221102 | 82799009 | Cardiac output | Observable Entity | Measurement | SNOMED |
| FreeText | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | event | 4353611 | 250767002 | Pulmonary artery pressure | Observable Entity | Measurement | SNOMED |
| FreeText | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | CARDIAC OUTPUT 11.8L/M, CARDIAC INDEX 5.8L/M/M2, PAP MEAN 60, PCWP 12 MEAN, 18 AT END EXPIRATION | event | 4353611 | 250767002 | Pulmonary artery pressure | Observable Entity | Measurement | SNOMED |
| FreeText | Calculated TD Cardiac Index|L/min/m2 | Calculated TD Cardiac Index|L/min/m2 | event | 4208254 | 54993008 | Cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | Calculated Fick Cardiac Index|L/min/m2 | Calculated Fick Cardiac Index|L/min/m2 | event | 4208254 | 54993008 | Cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | RHCCI| | Cardiac Index (CI)| | event | 4177046 | 427990004 | Right ventricular cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | RHCCI|THERMODILUTION METHOD | Cardiac Index (CI)|THERMODILUTION METHOD | event | 4177046 | 427990004 | Right ventricular cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | RHCCI|UNKNOWN | Cardiac Index (CI)|UNKNOWN | event | 4177046 | 427990004 | Right ventricular cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | RHCCI|FICK METHOD | Cardiac Index (CI)|FICK METHOD | event | 4177046 | 427990004 | Right ventricular cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | CARDIND|L/min/m2|RIGHT HEART CATHETERIZATION | Cardiac Index|L/min/m2|RIGHT HEART CATHETERIZATION | event | 4177046 | 427990004 | Right ventricular cardiac index | Observable Entity | Measurement | SNOMED |
| FreeText | SLEEP APNEA, OBESITY , BMI 51, HYPERCAPNIA | SLEEP APNEA, OBESITY , BMI 51, HYPERCAPNIA | event | 4060985 | 162864005 | Body mass index 30+ - obesity | Clinical Finding | Observation | SNOMED |
| FreeText | BMI >60 | BMI >60 | event | 4060985 | 162864005 | Body mass index 30+ - obesity | Clinical Finding | Observation | SNOMED |
| FreeText | HYPERLIPIDEMIA BODY MASS INDEX 30+ - OBESITY | HYPERLIPIDEMIA BODY MASS INDEX 30+ - OBESITY | event | 4060985 | 162864005 | Body mass index 30+ - obesity | Clinical Finding | Observation | SNOMED |
| FreeText | HYPERLIPIDEMIA, ASTHMA BODY MASS INDEX 30+ - OBESITY | HYPERLIPIDEMIA, ASTHMA BODY MASS INDEX 30+ - OBESITY | event | 4060985 | 162864005 | Body mass index 30+ - obesity | Clinical Finding | Observation | SNOMED |
| FreeText | OBESITY. LAST BODY MASS INDEX IS 37.12 KG/(M^2) DONE ON 06-SEP-2016. | OBESITY. LAST BODY MASS INDEX IS 37.12 KG/(M^2) DONE ON 06-SEP-2016. | event | 4060985 | 162864005 | Body mass index 30+ - obesity | Clinical Finding | Observation | SNOMED |
| Source_vocabulary | Source_code | Source_code_description | target_entity_ type | target_concept_id | target_concept_code | target_concept_name | target_concept_class_id | target_domain_id | target_vocabulary_id |
| FreeText | PAH WHO Functional Class I | PAH WHO Functional Class I | event | 2bil | Pulmonary Arterial Hypertension (PAH) WHO Functional Class | Pulmonary Arterial Hypertension (PAH) WHO Functional Class | Staging / Scales | Observation | custom |
| FreeText | PAH WHO Functional Class I | PAH WHO Functional Class I | value | 36307969 | LA28404-4 | Class I | Answer | Meas Value | LOINC |
| MedDRA | 10077739 | Pulmonary arterial hypertension WHO functional class I | event | 2bil | Pulmonary Arterial Hypertension (PAH) WHO Functional Class | Pulmonary Arterial Hypertension (PAH) WHO Functional Class | Staging / Scales | Observation | custom |
| MedDRA | 10077739 | Pulmonary arterial hypertension WHO functional class I | value | 36307969 | LA28404-4 | Class I | Answer | Meas Value | LOINC |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | event | 4214956 | 417662000 | History of clinical finding in subject | Context-dependent | Observation | SNOMED |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | value | 312437 | 267036007 | Dyspnea | Clinical Finding | Condition | SNOMED |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | value | 442588 | 78275009 | Obstructive sleep apnea syndrome | Clinical Finding | Condition | SNOMED |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | value | 318800 | 235595009 | Gastroesophageal reflux disease | Clinical Finding | Condition | SNOMED |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | value | 313217 | 49436004 | Atrial fibrillation | Clinical Finding | Condition | SNOMED |
| FreeText | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | AFIB,GERD 19/NOV/2009, CHF UNK/2014, OSA UNK/2017, DYSPNEA 14/JAN/2015 | value | 444031 | 48447003 | Chronic heart failure | Clinical Finding | Condition | SNOMED |