Observational Health Data Sciences and Informatics

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===== Adding PROM data to CDM =====
  * Requestor: Colin Orr and Catherine Kerr, ICON plc
  * Discussion: here

==== Background ====
ICON plc is currently engaged in a project with [[http://www.ichom.org/|ICHOM (International Consortium for Health Outcomes Measurement]]. 

//"ICHOM's mission is to unlock the potential of value-based healthcare by defining global Standard Sets of outcome measures that really matter to patients for the most relevant medical conditions and by driving adoption and reporting of these measures worldwide."// 

ICHOM brings together patient representatives, clinician leaders, and registry leaders from all over the world to develop Standard Sets, comprehensive yet parsimonious sets of outcomes and case-mix variables for specific medical conditions that ICHOM recommends all providers track.

Each Standard Set focuses on patient-centered results, and provides an internationally-agreed upon method for measuring each of these outcomes. ICHOM believes that standardized outcomes measurement will open up new possibilities to compare performance globally, allow clinicians to learn from each other, and rapidly improve the care provided to patients.

ICHOM Standard Sets include baseline conditions and risk factors to enable meaningful case-mix adjustment globally, ensuring that comparisons of outcomes will take into account the differences in patient populations across not just providers, but also countries and regions. They also include high-level treatment variables to allow stratification of outcomes by major treatment types. A comprehensive data dictionary, as well as scoring guides for patient-reported outcomes is provided for each Standard Set.

==== Proposal ====
ICON plc is developing a platform to ingest, store and analyse the outcome measures and is using the OMOP Common Data Model to store the data. The current CDM satisfies many of the requirements, but there are some gaps, specifically:
  - We need to store data relating to each PROM (Patient_reported Outcome Measure) questionnaire that is completed by a patient. We propose introducing a new SURVEY table.
  - The patient responses are stored as key-value pairs in the OBSERVATION table, but we need to be able to group responses together according to the survey they belong to. We also need to know the timing of the observation in relation to the treatment the patient received - for example, 'baseline', or 'six month followup', so that we can compare outcomes. We propose adding three new columns to the OBSERVATION table, described below.
  - Patient responses (in most cases) will be stored as concepts in the OBSERVATION table. We require an extension to the concept table to include the ICHOM Vocabulary. The ICHOM Vocabulary includes a concept for each data point in each Standard Set AND a concept for each allowable response for every question. The ICHOM Vocabulary will grow with each Standard Set that is defined by ICHOM. Each Standard Set is likely to generate 200 to 300 concepts and the objective is for 50 Standard Sets, thus requiring 15,000 new concepts.
  
===== SURVEY table =====
^ Field                ^ Required  ^ Type         ^ Description ^
| SURVEY_ID            | Yes       | integer      | Unique identifer for each completed survey |
| SURVEY_CONCEPT_ID    | Yes       | integer      | A foreign key that refers to a survey Concept identifier in the Standardized Vocabularies |
| PERSON_ID            | Yes       | integer      | A foreign key identifier to the Person in the PERSON table about whom the survey was completed |
| VISIT_OCCURRENCE_ID  | No        | integer      | A foreign key to the visit in the visit table during which the the treatment was carried out that relates to this survey |
| SURVEY_DATE          | Yes       | date         | Date on which the survey was completed |
| ASSISTED_IND_CONCEPT_ID | No     | integer      | A foreign key that refers to a data source Concept identifier in the Standardized Vocabularies |
| ASSISTED_IND         | No   | varchar(10)  | ICHOM code representing whether patient required assistance to complete the survey - 1=Completed without assistance, 2=Completed with assistance |
| DATA_SOURCE_CONCEPT_ID | No      | integer      | A foreign key that refers to a data source Concept identifier in the Standardized Vocabularies |
| DATA_SOURCE           | No   | varchar(10)  | ICHOM code representing role of person who completed the survey - e.g. 1=Administrative, 2=Clinician, 3=Patient-reported |
| TIMING_CONCEPT_ID    | No        | integer      | A foreign key that refers to a timing Concept identifier in the Standardized Vocabularies |
| TIMING_SOURCE_VALUE  | No        | varchar(100) | Text string representing the timing of the survey |
| COLLECTION_METHOD_CONCEPT_ID | No | varchar(10)  | A foreign key that refers to a collection method Concept identifier in the Standardized Vocabularies |
| COLLECTION_METHOD    | No        | varchar(10)  | ICHOM code representing method of capturing responses in survey - e.g. 1=Paper, 2=Telephone, 3=Electronic Questionnaire |
| DURATION             | No        | varchar(50)  | Time taken to complete survey HH:MM:SS |
| SURVEY_SOURCE_VALUE  | No        | varchar(100) | Unique identifier for each completed survey in source system |
| SURVEY_NAME          | No        | varchar(50)  | Name of the survey - e.g. HOOSPS, EQ5D-3L, VR12 |

===== OBSERVATION table - new columns =====
^ Field                ^ Required  ^ Type         ^ Description ^
| SURVEY_ID	           | No        | integer      | A foreign key to the survey in the SURVEY table to which the observation belongs |	
| TIMING_CONCEPT_ID    | No        | integer      | A foreign key that refers to a timing Concept identifier in the Standardized Vocabularies |
| TIMING_SOURCE_VALUE  | No        | varchar(100) | Text string representing the timing of the survey |

Note: The TIMING columns are required in the OBSERVATION table as well as the SURVEY table because many observations are collected by clinicians and administrators as opposed to patient-completed surveys.

==== Use Cases ==== 
Example is for observation made through Question 1 (HPS1) on the HOOSPS survey (Hip Disability and Osteoarthritis Outcome Score). The question asks the degree of difficulty in descending stairs due to the patient's hip problem. The patient answers "Moderate".

===== CONCEPT table - example =====

^ CONCEPT_ID ^ CONCEPT_NAME ^ DOMAIN_ID ^ VOCABULARY_ID ^ CONCEPT_CLASS_ID ^ STANDARD_CONCEPT ^ CONCEPT_CODE ^ 
| 2020 | HPS1 | Metadata | Domain | Domain |  | ICHOM generated | 
| 2021 | None | HPS1 | ICHOM Observation | PRO Measure | S | 0 | 
| 2022 | Mild | HPS1 | ICHOM Observation | PRO Measure | S | 1 | 
| 2023 | Moderate | HPS1 | ICHOM Observation | PRO Measure | S | 2 | 
| 2024 | Severe | HPS1 | ICHOM Observation | PRO Measure | S | 3 | 
| 2025 | Extreme | HPS1 | ICHOM Observation | PRO Measure | S | 4 | 

===== SURVEY table - example =====

^ Column ^ Value ^ Comment ^
| SURVEY_ID | 19073 |  |
| SURVEY_CONCEPT_ID | 3501 | Concept for HOOSPS survey |
| PERSON_ID | 21405 |  |
| VISIT_OCCURRENCE_ID | 13403 |  |
| SURVEY_DATE | 42565 |  |
| ASSISTED_IND_CONCEPT_ID | 3601 | Concept for "Completed without assistance" |
| ASSISTED_IND | 1 | ICHOM value for "Completed without assistance" |
| DATA_SOURCE_CONCEPT_ID | 3611 | Concept for "Patient-reported" |
| DATA_SOURCE | 3 | ICHOM value for "Patient-reported" |
| TIMING_CONCEPT_ID | 3621 | Concept for "BASELINE" timing |
| TIMING_SOURCE_VALUE | BASELINE |  |
| COLLECTION_METHOD_CONCEPT_ID | 3631 | Concept for "Electronic questionnaire" |
| COLLECTION_METHOD | 3 | ICHOM value for "Electronic questionnaire" |
| DURATION | 00:07:45 | Patient took 7 minutes and 45 seconds to complete online survey |
| SURVEY_SOURCE_VALUE | HS001234 |  |
| SURVEY_NAME | HOOSPS |  |

===== OBSERVATION table - example =====

^ Column ^ Value ^ Comment ^
| OBSERVATION_ID | 794657 |  |
| PERSON_ID | 21405 |  |
| OBSERVATION_CONCEPT_ID | 2020 | Concept for HPS1 |
| OBSERVATION_DATE | 42565 |  |
| OBSERVATION_DATETIME |  |  |
| OBSERVATION_TYPE_CONCEPT_ID | 1001 | Concept for 'PRO Measure' |
| VALUE_AS_NUMBER |  |  |
| VALUE_AS_STRING |  |  |
| VALUE_AS_CONCEPT_ID | 2023 | Concept for "Moderate" |
| QUALIFIER_CONCEPT_ID |  |  |
| UNIT_CONCEPT_ID |  |  |
| PROVIDER_ID |  |  |
| VISIT_OCCURRENCE_ID | 13403 |  |
| OBSERVATION_SOURCE_VALUE |  |  |
| OBSERVATION_SOURCE_CONCEPT_ID |  |  |
| UNIT_SOURCE_VALUE |  |  |
| QUALIFIER_SOURCE_VALUE |  |  |
| SURVEY_ID | 19073 |  |
| TIMING | BASELINE |  |