Download Nebraska Lexicon © namespace content includes problem list

Nebraska Lexicon Release Documentation
Introduction
Purpose
This document summarizes the RF2 release set and supporting documents which publishes the Nebraska
Lexicon© extension namespace including content for the cancer synoptic reporting content mapping of
College of American Pathologists (CAP) and the associated RF2 mapping files and supportive
documentation. The Nebraska Lexicon© module is dependent upon the US extension and so
terminology developers wishing to classify this content should load the US extension 20160330 and
SNOMED CT Internal Release 20160130.
Scope
Nebraska Lexicon © namespace content includes problem list terminology developed and deployed by
UNMC as well as SNOMED CT and LOINC content developed in conjunction with the Observables project
sponsored by the IHTSDO and synoptic reporting terminology data developed in collaboration with the
College of American Pathologists (CAP) and the Royal College of Pathologists (MRCP).
Audience
This material is intended for SNOMED CT system managers and system analysts who may wish to
expand their SNOMED CT terminology for problem list, or have interest in employing SNOMED CT-LOINC
structured reporting of cancer synoptic data compliant with CAP check sheets.
Content development activity
Nebraska Lexicon extension set 1000004
(sct2_XXX_Snapshot_INT_20160725)
Table: Inventory of content by domain
Version SNOMED CT content domain
1.0
Clinical finding
Body structure
Substance
Observable entity
Procedure
Qualifiers
Situation
Relationships (stated)
Descriptions
Concepts
1496
61
8
197
1002
27
200
13958
12286
Derived products
SNOMED CT – HGNC Equivalence map
(der2_sRefset_SNOMED\NebbraskaLexicon-HGNCEquivalenceMapSnapshot_INT_20160725)
The SNOMED CT concept model for Body structures was extended for this publication in order to define
named genes (nucleotide sequences) of clinical importance, nucleotide sequence variants and
associated proteins. These extensions were necessary for full definition of Observable entities for
molecular pathology and cytogenetics. Genes are defined in this model as named nucleotide sequences
which are part of chromosome structures. Reference data for the gene definition resides in the
publication of the HUGO Gene Nomenclature Committee (HGNC) (http://www.genenames.org/). The
simple map reference set enclosed with this release includes the reference component gene locus
concept identifier such as 100670521000004106|BRAF gene locus(cell structure)| linked to the HGNC
record Identifier and a REST services call which will retrieve the supplemental data regarding the
nucleotide sequence identification (‘HGNC:1097^http://rest.genenames.org/fetch/symbol/BRAF’).
Figure: Concept model for 100670521000004106|BRAF gene locus(cell structure)|
Figure: REST services reference data from Human Gene Nomenclature reference
BRAF gene locus
SNOMED CT – LOINC Equivalence map
(der2_sRefset_SNOMED\NebbraskaLexicon-LOINCEquivalenceMapSnapshot_INT_20160725)
This work represents a portion of the deployment of the expanded Observable entity concept model
developed by the IHTSDO and the Regenstrief Institute. Use of this model in service of cancer synoptic
reporting identifies pre-existing Observable content in LOINC which are summarized in this simple map
for extension concepts. This RF2 refset is a mapping between the extension concept identifier assigned
by Nebraska to content modelled for this project and LOINC concept codes where pre-existing content
was identified in LOINC V2.54.
Annotated Synoptic Checksheets from College of American
Pathologists© CAP 2016
With permission of the College of American Pathologists (CAP), we enclose the CAP synoptic documents
in PDF format supplemented with hyperlinks in context to the Observable entity and valueset for all
checksheet data items. In most cases these are one-to-one matches with checksheet data items. In a
minority of cases, the information model implied by the checksheet structure was expanded or modified
in order to properly define the nature of the observation. An example of this can be found in the
colorectal cancer anatomic pathology checksheet on page 6. Since the checklist valueset for
Microscopic tumor extension required four types of observations, the last three items in the list (organ
adherence, direct invasion and penetration of visceral peritoneum) have unique observable entities
defined for a total of four observables for this checklist. The comprehensive set of observable entities,
valuesets and concept model definition are included immediately following the CAP checklist document.
To use the annotated checksheets, simply open the document in an Adobe browser. Scrolling down the
CAP checksheet to individual data sections, a ‘hand’ widget will appear when hovering over the
checklist. Clicking on this portion of the document will take the reader to the SNOMED CT observable
entity and the associated valueset in tabular form. Clicking a second time on the valueset table will
return the reader to the CAP document at the point of departure.
Publication
date
6/5/2016
6/13/2016
6/13/2016
6/14/2016
File name
CAP_colorectal_cancer_anatomic_pathology_20160613
Content
Annotated colorectal
checksheet with
observables and valuesets
CAP_colorectal_cancer_biomarkers_20160613
Annotated colorectal
biomarker checksheet
CAP_invasive_breast_cancer_anatomic_pathology_20160613 Annotated breast cancer
checksheet
CAP_breast_cancer_biomarkers_20160614
Annotated breast cancer
biomarkers checksheet
Technical notes
Publication history
Publication date
7/21/2016
Content
1)Nebraska lexicon post-coordinated problem list content
2)CAP checksheets includes histopathology and biomarkers for colon
and breast carcinoma
3) HGNC simple map refset for gene locus definition
4) LOINC simple map refset for extension observables concepts
Version
1.0