CAP vocabulary

Overview

This vocabulary is based on a conversion of the CAP (College of American Pathologists) eCC protocols. It is implemented as a source vocabulary for improving ETL steps from concepts capturing 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.

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. A 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