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Copyright © 2001 College of American Pathologists Presentation Objectives By the end of this presentation you should know: –The content of the 3 core SNOMED.

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Presentation on theme: "Copyright © 2001 College of American Pathologists Presentation Objectives By the end of this presentation you should know: –The content of the 3 core SNOMED."— Presentation transcript:

1 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

2 Copyright © 2001 College of American Pathologists SNOMED CT Core Structure SNOMED CT Core Files –Principles behind SNOMED CT Core StructurePrinciples behind SNOMED CT Core Structure –Three Core tablesThree Core tables Loading the Core Tables into a Database –Microsoft AccessMicrosoft Access –Example SQL Table Definitions/Data LoadExample SQL Table Definitions/Data Load Help

3 Copyright © 2001 College of American Pathologists The Principles behind the SNOMED CT 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

4 Copyright © 2001 College of American Pathologists The Principles behind the SNOMED CT Structure Descriptions Kidney Disease Nephrosis Concept ID Disease of Kidney Renal Disorder Renal Disease

5 Copyright © 2001 College of American Pathologists The Principles behind the SNOMED CT Structure Hierarchical relationships ( ) Kidney disease ( ) Disorder of the urinary system Is a

6 Copyright © 2001 College of American Pathologists The Principles behind the SNOMED CT Structure Clinical attributes - logical definitions created through relationships with other concepts ( ) Kidney disease ( ) Kidney Has disorder site

7 Copyright © 2001 College of American Pathologists SNOMED CT Core Files The following slides show the 3 core files and the data fields that comprise them

8 Copyright © 2001 College of American Pathologists SNOMED CT Core Distribution Tables Concepts ConceptId Concept Status Full Specified Name CTV3ID SNOMEDID IsPrimitive Descriptions DescriptionId Description Status ConceptId Term Initial Capital Status Description Type Language Code Relationships RelationshipId ConceptId1 Relationship ConceptId2 Characteristic Type Refinability RelationshipGroup

9 Copyright © 2001 College of American Pathologists Concepts ConceptId Concept status Fully specified name CTV3ID SNOMEDID IsPrimitive SNOMED CT Concepts Table Sample Data

10 Copyright © 2001 College of American Pathologists DescriptionId Term ConceptId Description type Description status Initial capital status Language code Descriptions SNOMED CT Descriptions Table Sample Data

11 Copyright © 2001 College of American Pathologists SNOMED CT Relationships Table Relationships RelationshipId ConceptId1 Relationship ConceptId2 Characteristic Type Refinability RelationshipGroup Sample Data

12 Copyright © 2001 College of American Pathologists Loading 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 ImportMicrosoft Assess Import –Example - SQL table Definition/Data LoadSQL table Definition/Data Load

13 Copyright © 2001 College of American Pathologists More Information SNOMED CT Implementation Guide or contact us

14 Copyright © 2001 College of American Pathologists Concept Table Sample Data

15 Copyright © 2001 College of American Pathologists Description Table Sample Data

16 Copyright © 2001 College of American Pathologists Relationship Examples ( Terms shown for illustrative purposes only)

17 Copyright © 2001 College of American Pathologists Concept ID Item identifier Partition identifier Check-digit SNOMED 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

18 Copyright © 2001 College of American Pathologists Partition Identifier - Core Values

19 Copyright © 2001 College of American Pathologists Partition Identifier - For Extensions

20 Copyright © 2001 College of American Pathologists SCTID Namespace identifier Partition identifier Check-digit SNOMED 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

21 Copyright © 2001 College of American Pathologists Check 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 D 5 Check. See the SNOMED CT core specification for information about the Verhoff check-digit and sample program code.

22 Copyright © 2001 College of American Pathologists Item 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.

23 Copyright © 2001 College of American Pathologists Concept 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. 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.

24 Copyright © 2001 College of American Pathologists Concept Status Values

25 Copyright © 2001 College of American Pathologists Concept 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

26 Copyright © 2001 College of American Pathologists CTV3ID 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.

27 Copyright © 2001 College of American Pathologists The 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.

28 Copyright © 2001 College of American Pathologists Description ID Item identifier Partition identifier Check-digit SNOMED 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.

29 Copyright © 2001 College of American Pathologists Terms 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. FullySpecifiedName

30 Copyright © 2001 College of American Pathologists Description Type Values

31 Copyright © 2001 College of American Pathologists Description Status Values

32 Copyright © 2001 College of American Pathologists Initial 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 its case changed according to its position in a sentence without changing its 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.

33 Copyright © 2001 College of American Pathologists Description 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.ISO635 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.ISO3166IANA

34 Copyright © 2001 College of American Pathologists Description Language Code (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

35 Copyright © 2001 College of American Pathologists Relationship ID Item identifier Partition identifier Check-digit SNOMED 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.

36 Copyright © 2001 College of American Pathologists Relationship Characteristic Type Values

37 Copyright © 2001 College of American Pathologists Relationship Refinability Values

38 Copyright © 2001 College of American Pathologists Relationship - 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

39 Copyright © 2001 College of American Pathologists Loading 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 delimitedfiles are tab delimited –Field names are in the first row of each filefirst row of each file –Primary key is the Id field for each tablePrimary key

40 Copyright © 2001 College of American Pathologists Access Load - Tab Delimited SNOMED CT Files are tab delimited

41 Copyright © 2001 College of American Pathologists Access Load - First Row Has Field Names Field names for each table can be found in the first row.

42 Copyright © 2001 College of American Pathologists Access Load - Primary Keys

43 Copyright © 2001 College of American Pathologists Example SQL Table Definitions/Data Load 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 TableCreate Concept Table –Create Description TableCreate Description Table –Create Relationship TableCreate Relationship Table –Load Table DataLoad Table Data

44 Copyright © 2001 College of American Pathologists Example* SQL Definition for Concept Table CREATE 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.

45 Copyright © 2001 College of American Pathologists Example* SQL Definition for Description Table 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.

46 Copyright © 2001 College of American Pathologists Example* SQL Definition for Relationship Table CREATE 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.

47 Copyright © 2001 College of American Pathologists Example* - Load SNOMED CT Table Data LOAD DATA INFILE sct_Concepts_ txt INTO TABLE SNOMEDConcept FIELDS TERMINATED BY \t INGNORE 1 LINES; > LOAD DATA INFILE sct_Description_ txt INTO TABLE SNOMEDDescription FIELDS TERMINATED BY \t INGNORE 1 LINES; > LOAD DATA INFILE sct_Rels_ txt INTO TABLE SNOMEDRelationships FIELDS TERMINATED BY \t 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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