132 lines
8.2 KiB
Markdown
132 lines
8.2 KiB
Markdown
|
The NOTE table captures unstructured information that was recorded by a provider about a patient in free text notes on a given date.
|
|||
|
|
|
|||
|
|
Field|Required|Type|Description
|
|||
|
|
:--------------------|:--------|:------------|:--------------------------------------------------------
|
|||
|
|
|note_id |Yes|integer|A unique identifier for each note.|
|
|||
|
|
|person_id |Yes|integer|A foreign key identifier to the Person about whom the Note was recorded. The demographic details of that Person are stored in the PERSON table.|
|
|||
|
|
|note_date |Yes|date|The date the note was recorded.|
|
|||
|
|
|note_datetime |No|datetime|The date and time the note was recorded.|
|
|||
|
|
|note_type_concept_id |Yes|integer|A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the type, origin or provenance of the Note.|
|
|||
|
|
|note_class_concept_id |Yes| integer| A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the HL7 LOINC Document Type Vocabulary classification of the note.|
|
|||
|
|
|note_title |No| varchar(250)| The title of the Note as it appears in the source.|
|
|||
|
|
|note_text |Yes|varchar(MAX)|The content of the Note.|
|
|||
|
|
|encoding_concept_id |Yes |integer| A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the note character encoding type|
|
|||
|
|
|language_concept_id |Yes |integer |A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the language of the note|
|
|||
|
|
|provider_id |No|integer|A foreign key to the Provider in the PROVIDER table who took the Note.|
|
|||
|
|
|visit_occurrence_id |No|integer|A foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken.|
|
|||
|
|
|visit_detail_id |No|integer|A foreign key to the Visit in the VISIT_DETAIL table when the Note was taken.|
|
|||
|
|
|note_source_value |No|varchar(50)|The source value associated with the origin of the Note|
|
|||
|
|
|
|||
|
|
### Conventions
|
|||
|
|
* The NOTE table contains free text (in ASCII, or preferably in UTF8 format) taken by a healthcare Provider.
|
|||
|
|
* The Visit during which the note was written is recorded through a reference to the VISIT_OCCURRENCE table. This information is not always available.
|
|||
|
|
* The Provider making the note is recorded through a reference to the PROVIDER table. This information is not always available.
|
|||
|
|
* The type of note_text is CLOB or varchar(MAX) depending on RDBMS
|
|||
|
|
* note_class_concept_id is a foreign key to the CONCEPT table to describe a standardized combination of five LOINC axes (role, domain, setting, type of service, and document kind). See below for description.
|
|||
|
|
|
|||
|
|
### Mapping of clinical documents to Clinical Document Ontology (CDO) and standard terminology
|
|||
|
|
|
|||
|
|
HL7/LOINC CDO is a standard for consistent naming of documents to support a range of use cases: retrieval, organization, display, and exchange. It guides the creation of LOINC codes for clinical notes. CDO annotates each document with 5 dimensions:
|
|||
|
|
|
|||
|
|
* **Kind of Document:** Characterizes the generalc structure of the document at a macro level (e.g. Anesthesia Consent)
|
|||
|
|
* **Type of Service**: Characterizes the kind of service or activity (e.g. evaluations, consultations, and summaries). The notion of time sequence, e.g., at the beginning (admission) at the end (discharge) is subsumed in this axis. Example: Discharge Teaching.
|
|||
|
|
* **Setting:** Setting is an extension of CMS<4D>s definitions (e.g. Inpatient, Outpatient)
|
|||
|
|
* **Subject Matter Domain (SMD):** Characterizes the subject matter domain of a note (e.g. Anesthesiology)
|
|||
|
|
* **Role:** Characterizes the training or professional level of the author of the document, but does not break down to specialty or subspecialty (e.g. Physician)
|
|||
|
|
|
|||
|
|
Each combination of these 5 dimensions should roll up to a unique LOINC code. For example, Dentistry Hygienist Outpatient Progress note (LOINC code 34127-1) has the following dimensions:
|
|||
|
|
|
|||
|
|
* According to CDO requirements, only 2 of the 5 dimensions are required to properly annotate a document: Kind of Document and any one of the other 4 dimensions.
|
|||
|
|
* However, not all the permutations of the CDO dimensions will necessarily yield an existing LOINC code.2 HL7/LOINC workforce is committed to establish new LOINC codes for each new encountered combination of CDO dimensions. 3
|
|||
|
|
|
|||
|
|
Automation of mapping of clinical notes to a standard terminology based on the note title is possible when it is driven by ontology (aka CDO). Mapping to individual LOINC codes which may or may not exist for a particular note type cannot be fully automated. To support mapping of clinical notes to CDO in OMOP CDM, we propose the following approach:
|
|||
|
|
|
|||
|
|
#### 1. Add all LOINC concepts representing 5 CDO dimensions to the Concept table. For example:
|
|||
|
|
|
|||
|
|
Field | Record 1 | Record 2
|
|||
|
|
:-- | :-- | :--
|
|||
|
|
concept_id | 55443322132 | 55443322175
|
|||
|
|
concept_name | Administrative note | Against medical advice note
|
|||
|
|
concept_code | LP173418-7 | LP173388-2
|
|||
|
|
vocabulary_id | LOINC | LOINC
|
|||
|
|
|
|||
|
|
#### 2. Represent CDO hierarchy in the Concept_Relationship table using the <20>Subsumes<65> <20> <20>Is a<> relationship pair. For example:
|
|||
|
|
|
|||
|
|
Field | Record 1 | Record 2
|
|||
|
|
:-- | :-- | :--
|
|||
|
|
concept_id_1 | 55443322132 | 55443322175
|
|||
|
|
concept_id_2 | 55443322175 | 55443322132
|
|||
|
|
relationship_id | Subsumes | Is a
|
|||
|
|
|
|||
|
|
#### 3. Add LOINC document codes to the Concept table (e.g. Dentistry Hygienist Outpatient Progress note, LOINC code 34127-1). For example:
|
|||
|
|
|
|||
|
|
Field | Record 1 | Record 2
|
|||
|
|
:-- | :-- | :--
|
|||
|
|
concept_id | 193240 | 193241
|
|||
|
|
concept_name | Dentistry Hygienist Outpatient Progress note | Consult note
|
|||
|
|
concept_code | 34127-1 | 11488-4
|
|||
|
|
vocabulary_id | LOINC | LOINC
|
|||
|
|
|
|||
|
|
#### 4. Represent dimensions of each document concept in Concept_Relationship table by its relationships to the respective concepts from CDO.
|
|||
|
|
|
|||
|
|
* Use the <20>Member Of<4F> <20> <20>Has Member<65> (new) relationship pair.
|
|||
|
|
* Using example from the Dentistry Hygienist Outpatient Progress note (LOINC code 34127-1):
|
|||
|
|
|
|||
|
|
concept_id_1 | concept_id_1 | relationship_id
|
|||
|
|
:-- | :-- | :--
|
|||
|
|
193240 | 55443322132 | Member Of
|
|||
|
|
55443322132 | 193240 | Has Member
|
|||
|
|
193240 | 55443322175 | Member Of
|
|||
|
|
55443322175 | 193240 | Has Member
|
|||
|
|
193240 | 55443322166 | Member Of
|
|||
|
|
55443322166 | 193240 | Has Member
|
|||
|
|
193240 | 55443322107 | Member Of
|
|||
|
|
55443322107 | 193240 | Has Member
|
|||
|
|
193240 | 55443322146 | Member Of
|
|||
|
|
55443322146 | 193240 | Has Member
|
|||
|
|
|
|||
|
|
Where concept codes represent the following concepts:
|
|||
|
|
|
|||
|
|
Content | Description
|
|||
|
|
:---------- | :--------------------------------------------------------------------
|
|||
|
|
193240 | Corresponds to LOINC 34127-1, Dentistry Hygienist Outpatient Progress note
|
|||
|
|
55443322132 | Corresponds to LOINC LP173418-7, Kind of Document = Note
|
|||
|
|
55443322175 | Corresponds to LOINC LP173213-2, Type of Service = Progress
|
|||
|
|
55443322166 | Corresponds to LOINC LP173051-6, Setting = Outpatient
|
|||
|
|
55443322107 | Corresponds to LOINC LP172934-4, Subject Matter Domain <20>= Dentistry
|
|||
|
|
55443322146 | Corresponds to LOINC LP173071-4, Role = Hygienist
|
|||
|
|
|
|||
|
|
Most of the codes will not have all 5 dimensions. Therefore, they may be represented by 2-5 relationship pairs.
|
|||
|
|
|
|||
|
|
#### 5. If LOINC does not have a code corresponding to a permutation of the 5 CDO encountered in the source, this code will be generated as OMOP vocabulary code.
|
|||
|
|
|
|||
|
|
* Its relationships to the CDO dimensions will be represented exactly as those of existing LOINC concepts (as described above). If/when a proper LOINC code for this permutation is released, the old code should be deprecated. Transition between the old and new codes should be represented by <20>Concept replaces<65> <20> <20>Concept replaced by<62> pairs.
|
|||
|
|
|
|||
|
|
#### 6. Mapping from the source data will be performed to the 2-5 CDO dimensions.
|
|||
|
|
|
|||
|
|
Query below finds LOINC code for Dentistry Hygienist Outpatient Progress note (see example above) that has all 5 dimensions:
|
|||
|
|
|
|||
|
|
```sql
|
|||
|
|
SELECT
|
|||
|
|
FROM Concept_Relationship
|
|||
|
|
WHERE relationship_id = <20>Has Member<65> AND
|
|||
|
|
(concept_id_1 = 55443322132
|
|||
|
|
OR concept_id_1 = 55443322175
|
|||
|
|
OR concept_id_1 = 55443322166
|
|||
|
|
OR concept_id_1 = 55443322107
|
|||
|
|
OR concept_id_1 = 55443322146)
|
|||
|
|
GROUP BY concept_ID_2
|
|||
|
|
```
|
|||
|
|
|
|||
|
|
If less than 5 dimensions are available, `HAVING COUNT(n)` clause should be added to get a unique record at the intersection of these dimensions. n is the number of dimensions available:
|
|||
|
|
|
|||
|
|
```sql
|
|||
|
|
SELECT
|
|||
|
|
FROM Concept_Relationship
|
|||
|
|
WHERE relationship_id = <20>Has Member<65> AND
|
|||
|
|
(concept_id_1 = 55443322132
|
|||
|
|
OR concept_id_1 = 55443322175
|
|||
|
|
OR concept_id_1 = 55443322146)
|
|||
|
|
GROUP BY concept_ID_2
|
|||
|
|
HAVING COUNT(*) = 3
|
|||
|
|
```
|