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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 applied to subsequent intravocabulary concept relationships creation and formulation of essential concept names.
A numeric value (C-key) originating from the source was used as source code. The only exception - manually created CAP Protocols codes were created as modifications of the source file name.
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 propose to maintain parental relationships in name as a sequence separated by |-symbol, putting them in concept_synonym table. The left flanking word in this sequence is an exact concept_name, all the right-handed words are parents for it.
Concepts in CAP vocabulary belong to one of 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
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 Decision making: Approaches for CAP mapping.