documentation:next_cdm:metadata
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documentation:next_cdm:metadata [2016/10/26 19:46] vojtechhuser |
documentation:next_cdm:metadata [2017/07/10 16:26] (current) clairblacketer |
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| + | ====Metadata==== | ||
| + | ===Proposals are now tracked as github issues=== | ||
| + | [[https://github.com/OHDSI/CommonDataModel/issues/79|link to github issue]] | ||
| + | |||
| Proposing person: Vojtech Huser | Proposing person: Vojtech Huser | ||
| Line 8: | Line 12: | ||
| ====== Use case ====== | ====== Use case ====== | ||
| - | - only run certain data quality checks when they are appropriate to the dataset (e.g., general population dataset) | + | - display metadata within Atlas-Achilles Web (when reviewing data characterization plots and tables) |
| - | - display metadata within Atlas-Achilles Web | + | - allow organizations with multiple OMOP CDM datasets to have a mechanism to store dataset metadata (analysis of this use will provide input for phase 2 of metadata standardization) |
| + | - only run certain data quality checks when they are appropriate to the dataset (e.g., general population dataset; this use case depends on proper concept level standardization) | ||
| ====== CDM changes ====== | ====== CDM changes ====== | ||
| - | The proposal is adding a single table to the CDM specs. | + | The proposal is adding a single table to the CDM specs. In phase 1, we are trying to provide a mechanism for sites to capture metadata. The concept level standardization is planned in phase 2. |
| ===== new METADATA table ===== | ===== new METADATA table ===== | ||
| Line 28: | Line 34: | ||
| | NAME |Name of the CONCEPT_ID stored in METADATA_CONCEPT_ID or in the event there is not an applicable CONCEPT_ID NAME can be used to represent the data stored (e.g. CDM_BUILDER VERSION) |VARCHAR(250) | | | NAME |Name of the CONCEPT_ID stored in METADATA_CONCEPT_ID or in the event there is not an applicable CONCEPT_ID NAME can be used to represent the data stored (e.g. CDM_BUILDER VERSION) |VARCHAR(250) | | ||
| | VALUE |Store the metadata value you wish to capture |NVCHAR | | | VALUE |Store the metadata value you wish to capture |NVCHAR | | ||
| + | |||
| + | |||
| + | **Modified proposal** | ||
| + | |||
| + | ^ Column ^ Description ^ Data_type | Required | | ||
| + | | METADATA_CONCEPT_ID | OMOP Vocabulary CONCEPT_ID that identifies the information you with to track (e.g. 8 for metadata about a Visit) | INT | | | ||
| + | | METADATA_TYPE_CONCEPT_ID | OMOP Vocabulary CONCEPT_ID that identifies the type information you with to track (e.g. 1 for metadata about Domains such as a Visit) | INT | | | ||
| + | | NAME | Name of the CONCEPT_ID stored in METADATA_CONCEPT_ID or in the event there is not an applicable CONCEPT_ID NAME can be used to represent the data stored (e.g. CDM_BUILDER VERSION) | VARCHAR(250) | | | ||
| + | | VALUE_AS_STRING | Store the metadata value (string) | NVCHAR | | | ||
| + | | VALUE_AS_CONCEPT_ID | OMOP Vocabulary CONCEPT_ID that reflects the metadata value | int | No | | ||
| + | | METADATA_DATETIME | The date and time associated with metadata | datetime | No | | ||
| + | | METADATA_DATE | date | date | No | | ||
| + | |||
| + | |||
| **Example records:** | **Example records:** | ||
| - | ^ METADATA_CONCEPT_ID ^ METADATA_TYPE_CONCEPT_ID ^ NAME ^ VALUE ^ | + | ^ METADATA_ CONCEPT_ID ^ METADATA_TYPE_ CONCEPT_ID ^ NAME ^ VALUE ^ |
| + | | 51 | 1 | PERSON | Person information is pulled from insurance enrollment data where the individual both has medical and prescription benefits. The month of birth is not provided however for enrollees who start their enrollment the year they are born we extrapolate their month of birth from the month where their enrollment starts, for the majority of patients only year of birth is available. Persons who change gender over their enrollments or change year of birth are excluded. | | ||
| + | | 0 | 1 | OBSERVATION PERIOD | An observation period is a representation of when a patient was enrolled in a health insurance plan and had prescription benefits. Periods of continuous enrollment are consolidated by combining monthly records as long as the time between the end of one enrollment period and the start of the next is 32 days or less. | | ||
| + | | 57 | 1 | CARE SITE | There is not clear care site information in this source so no data will be captured within this table. | | ||
| | 8 | 1 | VISIT | For the outpatient visits, all activity that is recorded on a single day for a person is considered to have occurred during one visit with the visit start and end date corresponding to this date. | | | 8 | 1 | VISIT | For the outpatient visits, all activity that is recorded on a single day for a person is considered to have occurred during one visit with the visit start and end date corresponding to this date. | | ||
| + | | 55 | 1 | PROVIDER | Unique list of health care providers (physicians). Truven does provide some provider information however some of the providers listed by Truven may also be considered care sites or organizations. Since there is not clear way to decipher between all items identified as providers by Truven, regardless if they are truly organizations or care sites, they will be added to this table. | | ||
| + | | 0 | 1 | DEATH | Death in Truven can be captured at discharge from an inpatient visits or in some cases by diagnosis code. The death data in this source should not be considered complete, for example if a patient left a hospital and later died at home that would not be captured. Additionally if a death was recorded however if the patient continues to have services charges after 30 days of the death date we assume the death data was faulty. | | ||
| + | |19|1|CONDITION|Condition records are primarily recorded as codified claims data (e.g. ICD9 or ICD10 records that are submitted associated with a service). Additional condition information comes from patients who also have Health Risk Assessment data from Truven.| | ||
| + | |13|1|DRUG|Drug exposure records are primarily recorded as codified claims data (e.g. an NDC code or a procedure code that includes a drug). If the OMOP Vocabulary deems a code of a non-traditional drug centric vocabulary is in fact a drug exposure, the record will move to this table (e.g. CPT4- 90690- “Typhoid vaccine, live, oral” maps to drug concept in the OMOP Vocabularies so the CDM_BUILDER will move the record to the DRUG_EXPOSURE table instead of the procedure table). Additional drug exposure information comes from patients who also have Health Risk Assessment data from Truven.| | ||
| + | |10|1|PROCEDURE|Procedure occurrence records are recorded as codified claims data (e.g. a CPT4 code or ICD9 procedure code). If the OMOP Vocabulary deems a procedure code to be of a type of another domain (e.g. CPT4- 90690- “Typhoid vaccine, live, oral” maps to drug concept in the OMOP Vocabularies so the CDM_BUILDER will move the record to the DRUG_EXPOSURE table instead of the procedure table) however in the case of the primary procedure code those will always write a record to this table in order to maintain cost data. | | ||
| + | |21|1|MEASUREMENT|Measurement data traditionally comes from lab data supplied from laboratory service vendors however data vendors such as Truven do not have 100% representation with their lab results (e.g. they will only receive lab data of vendors they have contracted with like a Quest Diagnostics). If the OMOP Vocabulary deems a code of a non-traditional measurement centric vocabulary is in fact a measurement, the record will move to this table (e.g. ICD9- V85.22- “Body Mass Index 26.0-26.9, adult” usually thought of as a diagnosis code maps to a measurement concept in the OMOP Vocabularies so the CDM_BUILDER will move the record to the MEASUREMENT table). Additional measurement information comes from patients who also have Health Risk Assessment data from Truven.| | ||
| + | |27|1|OBSERVATION|Codified data or Health Risk Assessment data that is not a diagnosis, drug exposure, procedure, or measurement will become an observation.| | ||
| | 0 | 0 | CDM_BUILDER VERSION | 1.8.0.9 | | | 0 | 0 | CDM_BUILDER VERSION | 1.8.0.9 | | ||
| |0|0|DATASET_TYPE|Clinical Trial Data| | |0|0|DATASET_TYPE|Clinical Trial Data| | ||
| + | The proposal encourages all CDM adopters to fully populate and utilize the existing CDM_SOURCE table. | ||
| ===== END OF PROPOSAL ===== | ===== END OF PROPOSAL ===== | ||
documentation/next_cdm/metadata.1477511199.txt.gz · Last modified: 2016/10/26 19:46 by vojtechhuser
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