Copyright © 2001 College of American Pathologists Presentation Objectives By the end of this...

Copyright © 2001 College of American Pathologists

Presentation Objectives

• By the end of this presentation you should know:

– The content of the 3 core SNOMED distribution files

– How to load the 3 core files into relational tables

Help


SNOMED CT Core StructureSNOMED CT Core Structure

• SNOMED CT Core Files

– Principles behind SNOMED CT Core Structure

– Three Core tables

• Loading the Core Tables into a Database

– Microsoft Access

– Example SQL Table Definitions/Data Load

Help


The Principles behind the SNOMED The Principles behind the SNOMED CT StructureCT Structure

• SNOMED is concept based

– Each concept represents a unit of meaning

– Each concept has one or more language terms that can be used to describe the concept

– Every concept has inter-relationships with other concepts that provide logical computer readable definitions



• Descriptions

Kidney Disease

Nephrosis

Concept ID -90708001

Disease of Kidney

Renal Disorder

Renal Disease



• Hierarchical relationships

(90708001)Kidney disease

(128606002)Disorder ofthe urinary

system

Is a



• Clinical attributes - logical definitions created through relationships with other concepts

(90708001)Kidney disease

(64033007)Kidney

Hasdisorder site


SNOMED CT Core FilesSNOMED CT Core Files

• The following slides show the 3 core files and the data fields that comprise them


SNOMED CT Core Distribution TablesSNOMED CT Core Distribution Tables

Concepts

ConceptIdConcept StatusFull Specified NameCTV3IDSNOMEDIDIsPrimitive

Descriptions

DescriptionIdDescription StatusConceptIdTermInitial Capital StatusDescription TypeLanguage Code

Relationships

RelationshipIdConceptId1RelationshipConceptId2Characteristic TypeRefinabilityRelationshipGroup


Concepts

ConceptIdConcept statusFully specified nameCTV3IDSNOMEDIDIsPrimitive

SNOMED CT Concepts TableSNOMED CT Concepts Table

Sample DataSample Data


DescriptionIdTermConceptIdDescription typeDescription statusInitial capital statusLanguage code

Descriptions

SNOMED CT Descriptions TableSNOMED CT Descriptions Table



SNOMED CT Relationships TableSNOMED CT Relationships Table

Relationships

RelationshipIdConceptId1RelationshipConceptId2Characteristic TypeRefinabilityRelationshipGroup



Loading the SNOMED CT FilesLoading the SNOMED CT Files

• SNOMED CT core files may be loaded directly into a relational database.

• The first row of each table contains the table column names for ease of import

– Example - Microsoft Assess Import

– Example - SQL table Definition/Data Load


More InformationMore Information

SNOMED CT

Implementation Guide

or contact us

www.snomed.org


ConceptId FullySpecifiedName ConceptStatus

SNOMEDId CTV3Id IsPrimitive

236003 Incision of vein 0 P1-38100 XUSTv 0237007 Annona 0 L-D2100 XUA2a 0238002 Heptachlor 0 C-23115 X8084 0239005 Ophthalmologic 0 G-B106 XUA53 0240007 Biopsy of scent gland 0 P1-40322 XUA6E 0241006 Epilepsia partialis continua 0 DA-30250 X007F 0242004 Noninfectious jejunitis 0 D5-41620 XUA8W 0243009 Replacement of cerebral

ventricular tube0 P1-91578 XUA9e 0

Concept Table Sample DataConcept Table Sample Data


Description Table Sample DataDescription Table Sample Data


Relationship ExamplesRelationship Examples

ConceptId1 Relationship ConceptId274400008 116676008 2358300374400008 116677004 6675400874400008 116680003 12676700974400008 116680003 18526009

ConceptId1 Relationship ConceptId2Appendicitis Associated Morpology InflammationAppendicitis Associated Topography Veriform AppendixAppendicitis Is a Inflammatory disorder

of intestineAppendicitis Is a Disease of appendix

(Terms shown for illustrative purposes only)


Concept ID

Item identifier

101291657896189 00 9

Partition identifier

Check-digit

SNOMED CT Concept IdentifierSNOMED CT Concept Identifier

• ConceptId is a 64 bit integer code that uniquely identifies each concept in SNOMED CT. This field is the primary key of the concepts file.Concepts

Relationships

Descriptions


PartitionIdentifier

Description

00 Concept01 Description02 Relationship03 Subset

Partition Identifier - Core ValuesPartition Identifier - Core Values


PartitionIdentifier

Description

10 Extra Concept11 Extra Description12 Extra Relationship13 Extra Subset

Partition Identifier - For ExtensionsPartition Identifier - For Extensions


SCTID

Namespace identifier

0101291 109

Partitionidentifier

Check-digit

SNOMED CT Extension IdentifierSNOMED CT Extension Identifier

• Extensions to the SNOMED CT are differentiated from the core through the “partition identifier”. Each extension has a namespace that identifies the author.

Extension item identifier

99999999


Check DigitCheck Digit

• It is not envisaged that users will routinely type SCTID values, but the check digit is available to check for errors in transcription or communication of the SCTID.

• The right most digit of any SCTID is the check digit.

• This digit is generated and checked using the “Verhoff check”, which is a Dihedral D5 Check. See the SNOMED CT core specification for information about the Verhoff check-digit and sample program code.


Item Identifier - Core ContentItem Identifier - Core Content

• The item identifier for core content will be an integer with a value between 100 (3 digits) and 999,999,999,999,999 (15 digits).

• Combined with the partition identifier and the check sum, this make the total length of the SCTID somewhere between 6 and 18 digits.


Concept Status FlagConcept Status Flag

• “Concept status” is an integer value that specifies the current status of a given concept. The permitted values can be viewed in the table Concept Status Values.

• A value of zero indicates that the concepts in current use.

• A full documentation can be found in the SNOMED CT Implementation Guide.


Status Description0 Current1 Retired2 Duplicate3 Outdated4 Ambiguous5 Erroneous6 Limited

Concept Status ValuesConcept Status Values


Concept Fully Specified NameConcept Fully Specified Name

• The “Fully Specified Name” is a unique string which describes the concept in a way that is intended to be unambiguous.

• Note that the fully specified name for a concept also appears in the descriptions table. Although this creates redundancy of data storage, the designers of SNOMED felt it important to include a human readable representation in the concepts table.

Concepts

Descriptions


CTV3ID and SNOMEDIDCTV3ID and SNOMEDID

• The CTV3ID and SNOMED ID are alpha-numeric codes that are attached to a concept for historical reasons. SNOMED CT was formed by the merger of SNOMED RT and Clinical Terms Version 3 (formerly know as the Read codes).

• These codes will continue to be allocated and stored for the purpose of backward compatibility with the source terminologies.


The “Is Primitive” FlagThe “Is Primitive” Flag

• “IsPrimitive” is a Boolean field (true/false).

• It has important application for developers who which to manipulate SNOMED CT concepts using description logic. Primitive concepts can not have children assigned to them automatically based on the clinical attributes of the concept.

• For more information on this field, see the SNOMED CT implementation guide.


Description ID

Item identifier

101291 019


Check-digit

SNOMED CT Description IdentifierSNOMED CT Description Identifier

• DescriptionId is a 64 bit integer code that uniquely identifies each description in SNOMED CT. This field is the primary key of the descriptions file.


TermsTerms

• “Term” is a text string which can be used to describe the associated concept. Each term is not unique within the descriptions table, since the same term may be used to describe more than one concept. For example the term “Fundus” is associated with several different anatomical concepts, so it will appear in multiple rows of the descriptions table. In such cases, the concept FullySpecifiedName should be examined by a user, to differentiate meaning between these concepts.


Description Type ValuesDescription Type Values

Type Description0 Unspecified1 Preferred2 Synonym3 Fully Specified Name


Description Status ValuesDescription Status Values

Status Description0 Current1 Retired2 Duplicate3 Outdated4 Erroneous7 Inappropriate8 Retained


Initial Capitalization StatusInitial Capitalization Status

• This field indicates whether the capitalization of the first character of the term is significant.

• If this field has a value of ‘0’ the first character may have it’s case changed according to it’s position in a sentence without changing it’s meaning.

• If it is ‘1’, the case of the first character must not be changed, but must be displayed as it appears in the description table.


Description Language CodeDescription Language Code

• This field is a string identifying the language, and if appropriate the dialect in which the description is valid. It consists of a code and, optionally, a sub-code. If a sub-code is present it is separated from the code by a dash (“-”).

• The code is the ISO635 language code.

• The sub-code is a two letter ISO3166 country code, or a string of more than two letters, which is registered with IANA as a sub-code for the language.


Description Language Code Description Language Code (Definitions) (Definitions)

• ISO639 is the International Standard for “Codes for the representation of languages”

• ISO3166 is the International Standard for “Codes for the representation of names of countries”

• IANA is the “Internet Assigned Numbers Authority”


Relationship ID

Item identifier

101291 029


Check-digit

SNOMED CT Relationship IdentifierSNOMED CT Relationship Identifier

• RelationshipId is a 64 bit integer code that uniquely identifies each concept in SNOMED CT. This field is the primary key of the concepts file.


Relationship Characteristic Type Relationship Characteristic Type ValuesValues

Type Description0 Defining1 Qualifier2 Additional


Relationship Refinability ValuesRelationship Refinability Values

Type Description0 Not refinable1 Optional2 Mandatory


Relationship - Relationship GroupRelationship - Relationship Group

• An integer value that expresses an association between two or more Relationships.

• The default relationship group value is zero and this applies to all relationships that have not been stated to be associated with any other Relationships. All Relationships that share the same ConceptId1 and the same non-zero Relationship group value are associated with one another. Any Relationships that share the same ConceptId1 but have different Relationship group values are not associated with one another


Loading into Microsoft AccessLoading into Microsoft Access

• SNOMED CT tables can be loaded directly into Access via the “File/Get External Data/Import” menu option.

• Some important parameters involved in the load process are as follows: -

– SNOMED CT files are tab delimited

– Field names are in the first row of each file

– Primary key is the “Id” field for each table


Access Load - Tab DelimitedAccess Load - Tab Delimited

SNOMED CT Files are “tab” delimited


Access Load - First Row Has Field Access Load - First Row Has Field NamesNames

Field names for each table can be found in the first row.


Access Load - Primary KeysAccess Load - Primary Keys

Primary Keys for each tableConcepts ConceptIdDescriptions DescriptionIdRelationships RelationshipId


Example SQL Table Definitions/Data Example SQL Table Definitions/Data LoadLoad

• SNOMED CT tables can be created and loaded using SQL scripts or by entering SQL at the command line. The following slides show illustrative examples. You should consult your own SQL manuals for the exact commands applicable to your relational database management system (RDMS).

– Create Concept Table

– Create Description Table

– Create Relationship Table

– Load Table Data


Example* SQL Definition for ‘Concept’ Example* SQL Definition for ‘Concept’ TableTableCREATE TABLE SNOMEDConcept

(ConceptId BIGINT UNSIGNED NOT NULL,

ConceptStatus TINYINT NOT NULL,

FullySpecifiedName TEXT,

CTV3ID TINYTEXT,

SNOMEDID TINYTEXT NOT NULL,

PRIMARY KEY (ConceptId),

KEY (SNOMEDID)

);

* Example shown uses ‘MySQL’ data types. See your own RDBMS documentation for the correct syntax and data types for the create table command.


Example* SQL Definition for ‘Description’ Example* SQL Definition for ‘Description’ TableTable

CREATE TABLE SNOMEDDescription

(DescriptionId BIGINT UNSIGNED NOT NULL

ConceptId BIGINT UNSIGNED NOT NULL REFERENCES SNOMEDConcept,

DescriptionStatus TINYINT NOT NULL,

DescriptionType TINYINT NOT NULL

InitialCapitalStatus TINYINT,

LanguageCode TINYTEXT,

PRIMARY KEY (DescriptionId)

);

* Example shown uses ‘MySQL’ data types. See your own RDBMS documentation for the correct syntax and data types for the create table command.


Example* SQL Definition for ‘Relationship’ Example* SQL Definition for ‘Relationship’ TableTableCREATE TABLE SNOMEDRelationship

(RelationshipId BIGINT UNSIGNED NOT NULL

ConceptId1 BIGINT UNSIGNED NOT NULL REFERENCES SNOMEDConcept,

RelationshipType BIGINT UNSIGNED NOT NULL REFERENCES SNOMEDConcept,

ConceptId2 BIGINT UNSIGNED NOT NULL REFERENCES SNOMEDConcept,

CharacteristicType TINYINT

Refinability TINYINT,

PRIMARY KEY (RelationshipId)

KEY (ConceptId1),

KEY (ConceptId2)

);

* Example shown uses ‘MySQL’ data types. See your own RDBMS documentation for the correct syntax and data types for the CREATE TABLE command.


Example* - Load SNOMED CT Table DataExample* - Load SNOMED CT Table Data

LOAD DATA INFILE ‘sct_Concepts_01232002.txt’

INTO TABLE SNOMEDConcept

FIELDS TERMINATED BY ‘\t’

INGNORE 1 LINES;

>

LOAD DATA INFILE ‘sct_Description_01232002.txt’

INTO TABLE SNOMEDDescription


INGNORE 1 LINES;

>

LOAD DATA INFILE ‘sct_Rels_01232002.txt’

INTO TABLE SNOMEDRelationships


INGNORE 1 LINES;

* Examples shown use ‘MySQL’ syntax. See your own RDBMS documentation for the correct syntax of the LOAD DATA command

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