documentation:vocabulary:cap
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documentation:vocabulary:cap [2020/05/05 14:58] dimshitc1 [3. Domains and Concept Classes] |
documentation:vocabulary:cap [2024/09/02 10:05] (current) jcruz Depreciation of page and posting of corresponding link in Github wiki |
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| ======= CAP vocabulary ======== | ======= CAP vocabulary ======== | ||
| - | ===== Overview ===== | + | Thank you for visiting the wiki! This page has moved to https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-CAP. |
| - | + | ||
| - | Snapshot of CAP (College of American Pathologists) eCC protocols for Breast Cancer is implemented as a source vocabulary for the purpose of having a set of concepts to capture relevant pathological report data. | + | |
| - | + | ||
| - | ==== Source ==== | + | |
| - | XML files provided by CAP were used to retrieve the data. | + | |
| - | The source items hierarchy was reflected in concept relationships and concept_synonym_names. | + | |
| - | See below | + | |
| - | + | ||
| - | ===== Concept characteristics ===== | + | |
| - | + | ||
| - | ==== 1.Concept code ==== | + | |
| - | + | ||
| - | A numeric value (**//C-key//**) originating from the source was used as a source code. | + | |
| - | The only exception - manually created CAP Protocol codes were created as modifications of a source file name. | + | |
| - | + | ||
| - | ==== 2. Names ==== | + | |
| - | + | ||
| - | Descriptions attached to distinct codes were designated as their **concept names**. | + | |
| - | + | ||
| - | **Alternative concept name** was used to preserve a maximum of relevant source data. We keep parental relationships in a concept_synonym_name as a sequence separated by **|**-symbol, putting them in //**concept_synonym table**//. | + | |
| - | Composite name starts from the lowest hierarchy level concept and ends with the highest one reflecting the actual hierarchy. | + | |
| - | ==== 3. Domains and Concept Classes ==== | + | |
| - | + | ||
| - | Concepts in CAP vocabulary belong to one of the three Domains: | + | |
| - | + | ||
| - | |**Domain**|**Class**|**Description**| | + | |
| - | |Observation|CAP Protocol, CAP Header|Concepts, describe items providing information from which distinct protocol or from which variables-values logic group it originates from.| | + | |
| - | |Meas Value|CAP Value|Concepts somehow corresponding to distinct clinical entities.| | + | |
| - | |Measurement|CAP Variable|Concepts expressing the meaning of report question-element.| | + | |
| - | + | ||
| - | Class and subsequently domain recognition was performed based on listed rules: | + | |
| - | + | ||
| - | |**Class**|**HTML-tag accessory**|**Name restrictions**| | + | |
| - | |CAP Value|LI|No| | + | |
| - | |CAP Header|S|Not equals 'Distance'| | + | |
| - | |CAP Variable|Q,S|For Q-tag all items included, for S-tag name equality to 'Distance' was needed| | + | |
| - | |CAP Protocol|Not Applicable|Not Applicable| | + | |
| - | + | ||
| - | Original //**DI**//-tag was considered as a comment, guide for a pathologist, not significant for Observational research | + | |
| - | + | ||
| - | ===== Relationships ===== | + | |
| - | + | ||
| - | **1. Internal relationships** | + | |
| - | + | ||
| - | CAP vocabulary includes a set of hierarchical and attributive relationships. | + | |
| - | + | ||
| - | |**Relationship**|**Reverse relationship**|**Linked concepts**| | + | |
| - | |CAP Value of|Has CAP value|Cap Value <-> Cap Variable| | + | |
| - | |Has CAP parent item|CAP parent item of|Any concept_class <-> Any concept_class| | + | |
| - | |Has CAP protocol|CAP protocol of|Any concept_class <-> Cap Protocol| | + | |
| - | + | ||
| - | **2. External relationships** | + | |
| - | + | ||
| - | Nebraska Lexicon as SNOMED extension was used as a primary mapping target. | + | |
| - | Also, other OMOP CDM standard vocabularies were used to represent clinically relevant CAP entities. | + | |
| - | We provide parallel relations to each Ckey mapped to Nebraska Lexicon where relationship 'CAP-Nebraska category' reflects more general mapping, | + | |
| - | and 'CAP-Nebraska equivalent' is used to preserve maximal possible granularity. | + | |
| - | + | ||
| - | |**Relationship**|**Reverse relationship**|**Linked concepts**| | + | |
| - | |Maps to|Mapped from|Cap codes <-> OMOP Standards| | + | |
| - | |CAP to Nebraska Lexicon equivalent|Nebraska Lexicon to CAP equivalent|Cap codes <-> Nebraska Lexicon/SNOMED codes with maximal granularity preserved| | + | |
| - | |CAP to Nebraska Lexicon category|Nebraska Lexicon to CAP category|Cap codes <-> Nebraska Lexicon/SNOMED codes with less than maximal granularity preserved| | + | |
| - | + | ||
| - | Issues detected performing mapping are described in [[https://docs.google.com/presentation/d/13H5aneGgeoJkIHRFkwJsGOw-Iz7SZk0gqkKDq7Grjis/edit#slide=id.p |Decision making: Approaches for CAP mapping]]. | + | |
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documentation/vocabulary/cap.1588690735.txt.gz · Last modified: 2020/05/05 14:58 by dimshitc1
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