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CAP vocabulary


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.


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:

ObservationCAP Protocol, CAP HeaderConcepts, describe items providing information from which distinct protocol or from which variables-values logic group it originates from.
Meas ValueCAP ValueAnswers in CAP form, for example “3 o'clock position”
MeasurementCAP VariableQuestion in CAP form, for example “tumor position clockwise”

Class and subsequently domain recognition was performed based on listed rules:

ClassHTML-tag accessoryName restrictions
CAP HeaderSNot equals 'Distance'
CAP VariableQ,SFor Q-tag all items included, for S-tag name equality to 'Distance' was needed
CAP ProtocolNot ApplicableNot Applicable

Original DI-tag was considered as a comment, guide for a pathologist, not significant for Observational research


1. Internal relationships

CAP vocabulary includes a set of hierarchical and attributive relationships.

RelationshipReverse relationshipLinked concepts
CAP Value ofHas CAP valueCap Value ↔ Cap Variable
Has CAP parent itemCAP parent item ofAny concept_class ↔ Any concept_class
Has CAP protocolCAP protocol ofAny 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 Decision making: Approaches for CAP mapping.

documentation/vocabulary/cap.txt · Last modified: 2020/05/05 15:04 by dimshitc1