======= CAP vocabulary ========

===== Overview =====

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|Answers in CAP form, for example "3 o'clock position"|
|Measurement|CAP Variable|Question in CAP form, for example "tumor position clockwise"|

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 concept <->  OMOP Standard concept (full match or mapping to more generic concept)                                     |
| CAP to Nebraska Lexicon equivalent  | Nebraska Lexicon to CAP equivalent  | Cap concept <->  Nebraska Lexicon/SNOMED concept - full match                                                              |
| CAP to Nebraska Lexicon category    | Nebraska Lexicon to CAP category    | Cap concept <->  Nebraska Lexicon/SNOMED concept not a full match, some granularity is missing in Nebraska/SNOMED concept  |

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]].