SNOMED CT® Release Format 1 (RF1) Guide - ihtsdo

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76 | SNOMED CT Release Format 1 (RF1) Guide July 2012 Table 18: Released Extensions Extension U.S. Drug Extension Distribution International Release 2.3.4. Representational Forms for Expressions 2.3.4.1. SNOMED CT compositional grammar Extension Contents Actual manufactured drugs approved for distribution in the United States at the "actual medicinal product" (AMP) level. The AMP is a syntactic normal form consisting of: • Name (Proprietary); • Strength; • Dosage Form. All AMPs relate to "virtual medicinal product" (VMP) concepts in the SNOMED CT Core. All AMPs include the "has active ingredient"relationship where the active ingredient is a substance in the SNOMED CT Core. The SNOMED Composition Grammar is a lightweight syntax for representation of SNOMED CT expressions. It is has been proven to be both human readable and machine parsable. 2.3.4.1.1. Background 2.3.4.1.1.1. Prior versions and status of revision The SNOMED Composition Grammar was initial specified as part of the document "SNOMED Clinical Terms Abstract Logical Models and Representational Forms, External Draft for Comment Version". This was used extensively and was proven to be both human readable and machine parsable. The current specification which has now been adopted as an IHTSDO Standard, follows the prior version in most details. It includes the following enhancements: 1. The syntax of the grammar specification is now Augmented Backus-Naur Form (ABNF) 5 which provides a formal standards-based reference for the grammar's structure. 2. Unnecessary whitespace designators, , were removed from several places in the grammar. 3. The maximum length constraint for SNOMED Clinical Terms Identifiers (SCTIDs) is added to this grammar. SCTIDs consist of sequences of digits, from a minimum of 6 to a maximum of 18 digits in length. 4. The hex code for carriage return (CR) was incorrectly given as '0C' in the previous version. It is corrected to '0D' in this version. 5. Detailed character encoding information for UTF-8 is added. 6. The definition of term has been amended to allow correct parsing by the APG parser generator. 2.3.4.1.1.2. Compositional Grammar and the HL7 Code data type The SNOMED CT compositional grammar allows SNOMED CT expressions to be represented as a text string that can be carried in HL7 version 3 messages, in the Code data type. In particular, the grammar is intended to replace the qualifier mechanism that formerly was in the HL7 Concept Descriptor data type (CD data type), and which was removed in the HL7 version 3 data types Release 2. 5 ABNF as defined by Internet Standard 68, RFC 5234 © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
In May 2008, the HL7 Version 3 Standard "Data Types - Abstract Specification, Release 2" was released for Normative Ballot 2. This revised standard defined what can be carried in the Code data type as "the plain code symbol defined by the code system, or an expression in a syntax defined by the code system which describes the concept." The following details are quoted from the HL7 Version 3 Standard: Data Types - Abstract Specification, Release 2, Normative Ballot 2 - May 2008 (HL7 V3 DT R2), section 4.5.1 "Code (code): ST.SIMPLE": 6 Table 19: Code definition from HL7 Data Types Release 2 Code (code) :ST.SIMPLE Definition: The plain code symbol defined by the code system, or an expression in a syntax defined by the code system which describes the concept. (emphasis added) If provided, the code SHALL be an exact match to a plain code symbol or expression defined by the code System. If the code system defines a code or expression that includes whitespace, the code SHALL include the whitespace. An expression can only be used where the code System either defines an expression syntax, or there is a generally accepted syntax for the code System. (emphasis added) The syntax described herein is intended to satisfy the need for a "syntax defined by the code system" as stated above, when the "code System" is SNOMED CT. 6 http://www.hl7.org/v3ballot/html/infrastructure/datatypes_r2/datatypes_r2.htm Structure and Content Guide | 77 © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
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SNOMED CT ® Release Format 1 (RF1)
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Contents | 3 Release Format 1 - Det
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Chapter 1 Preface The purpose of th
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Table 3: Document Types Type Name a
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IHTSDO Glossary (DRAFT) • On line
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Chapter 2 Structure and Content Gui
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Figure 1: Multiple levels of granul
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Table 5: Example: Defining arthriti
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The full definitions of the concept
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Other components (i.e. Relationship
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2.1.2.2.1.3. Linking related Concep
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• Local content requirements that
Page 25 and 26: Consistent representation is a prer
Page 27 and 28: Figure 8: Abstract logical model of
Page 29 and 30: 1. As originally stated: : • | Ha
Page 31 and 32: 2.2.1.3.2.3.1. Supertype aspects of
Page 33 and 34: Figure 11: Example hierarchy with l
Page 35 and 36: Concept E F G H J K L M Note: Compr
Page 37 and 38: Concept M List of proximal primitiv
Page 39 and 40: Table 11: Non-redundant attribute v
Page 41 and 42: G. | Severe upper limb laceration |
Page 43 and 44: As a result of this limitation some
Page 45 and 46: 2.2.1.4.3. Historical relationships
Page 47 and 48: 2.2.2.1.1.2. Refinement attribute n
Page 49 and 50: 2.2.2.1.4.3. Use of "unapproved att
Page 51 and 52: Interim recommendations 1. Wherever
Page 53 and 54: 2.2.2.3.1. Close-to-user expression
Page 55 and 56: It is important to note that combin
Page 57 and 58: 2.2.2.3.6.1. Example of equivalent
Page 59 and 60: Figure 25: Alternative expressions
Page 61 and 62: Figure 27: Possible expressions of
Page 63 and 64: Figure 28: SCTID Short Format - App
Page 65 and 66: PartitionId 05 Description A Cross
Page 67 and 68: SctId 999999990989121104 2.3.2.9. T
Page 69 and 70: 2.3.3.2. Specification for Namespac
Page 71 and 72: 2.3.3.3.1.4. Procedures 2.3.3.3.1.4
Page 73 and 74: 1. Every Concept in an Extension:
Page 75: Table 17: Processing Transfers betw
Page 79 and 80: An expression supports combinations
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Page 83 and 84: excision of left fallopian tube. No
Page 85 and 86: This existential restriction is lab
Page 87 and 88: • In order to generate the OWL ve
Page 89 and 90: • Though there are many candidate
Page 91 and 92: 2.3.7.2.2.1. Single byte encoding C
Page 93 and 94: 9 0 9 Table 29: The full array for
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Page 97 and 98: http://www.augustana.ab.ca/~mohrj/a
Page 99 and 100: version. It seems unwise to prevent
Page 101 and 102: Table DescDualKey Table ConcDualKey
Page 103 and 104: The IHTSDO recognizes that, while i
Page 105 and 106: 3.2.2. Release Format 1 - Structure
Page 107 and 108: 3.2.3.2. Core Tables Data - Structu
Page 109 and 110: Data Fields InitialCapitalStatus De
Page 111 and 112: 3.2.4.1. Subset Mechanism - Structu
Page 113 and 114: Data Fields ContextId 3.2.4.2.2. Su
Page 115 and 116: Subset SNOMED CT Top Level Navigati
Page 117 and 118: • as a combination of codes; •
Page 119 and 120: Table 41: Cross Mapping Tables Cros
Page 121 and 122: Table 44: Cross Map Targets Table K
Page 123 and 124: The History Mechanism is also used
Page 125 and 126: In addition, the ReferencedId field
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Table Descriptions Descriptions Rel
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Table 49: Relationships depending o
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Table 51: Changes to Relationships
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Table 52: Changes to Relationships
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• The only Relationships that it
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ComponentId ConceptId ReleaseVersio
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A readme.txt file is distributed wi
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Value 6 10 11 Limited Moved elsewhe
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As new concepts are added to SNOMED
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Table 73: DescriptionStatus Values
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3.2.9.2.2.4. InitialCapitalStatus T
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3.2.9.3. relationships tables Each
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3.2.9.3.2.3. ConceptId2 Table 84: -
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An integer value that expresses an
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3.2.9.4.1.2.4. SubsetType Table 95:
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A string that identifies a Context
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3.2.9.4.2.1.2. Data Fields Table 10
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• MemberStatus 3.2.9.4.2.3.1.1. S
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3.2.9.4.2.4.1.3. MemberStatus Table
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3.2.9.4.2.5.2. Data Fields Table 11
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3.2.9.4.2.7.1.1. SubsetId Table 124
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3.2.9.4.2.8.1.3. MemberStatus Table
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3.2.9.4.3. Subset Definition File P
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3.2.9.5.1.2.3. MapSetSchemeId Table
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This discussion of rules is include
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3.2.9.5.1.3.2.3. MapRule Table 151:
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3.2.9.5.1.4.2.3. TargetRule Table 1
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RELAT_NMS = column in the LOINC tab
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The value of the SNOMED CT / LOINC
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The SNOMED CT Relationships Table e
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LOINC Analyte Name(s) DESMETHYLAMIO
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LOINC Analyte Name(s) COMPLEMENT IC
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The information provided includes d
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3.2.9.6.4.1.2. ReleaseVersion Table
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Value 6 7 8 9 10 11 Note: Name Limi
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3.2.9.6.5.1.1. ComponentId Table 17
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Release Format 1 is represents a sn
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RF1 Descriptions Table Descriptions
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Table 177: Concepts Table Use of re
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Use of recommended additional indic
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Use of recommended additional indic
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Table 184: Cross Map Sets Table Use
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Keys Partition Size Type Field Name
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Table 192: Word Equivalents Table U
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3.2.10. The Stated relationships ta
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Figure 41: Overview of Cross Map Sc
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Table 197: Cross Maps Sets Table Ma
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Table 201: Cross Maps Sets Table Ma
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Table 205: Cross Map Sets Table Map
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If this approach is followed, there
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This approach allows a more consist
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1. A record may contain many record
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• Temporally related to the selec
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CONCEPTID 95333004 7119001 95336007
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CONCEPTID 109778006 109788007 15270
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CONCEPTID 417163006 417746004 12820
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CONCEPTID 102706005 1677001 9145400
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CONCEPTID 399023006 399154007 39905
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CONCEPTID 399306005 399239005 39937
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CONCEPTID 125086000 78678003 388393
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CONCEPTID 339008 47002008 128419007
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CONCEPTID 16817006 15367004 1580700
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CONCEPTID 14509009 39250009 8627300
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CONCEPTID 122868007 122465003 78817
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CONCEPTID 19207007 74923002 6639100
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CONCEPTID 54305003 84100007 3216600
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CONCEPTID 255496004 255499006 24646
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CONCEPTID 62834003 5668004 34810001
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CONCEPTID 53224005 4150005 74636004
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CONCEPTID 47538007 19359003 3011000
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3.2.13. Enumerated values Value 0 1
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Table and Field Subsets SubsetType
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3.3. Release Format 2 Update Guide
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• The Release Format should minim
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3.3.3.4. Backward compatibility The
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3.3.4.5. Field Ordering Records in
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externalised structures such as Ref
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ContextId If either the RealmId fie
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eplaced by more descriptive ones if
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descriptions associated with concep
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Figure 45: Illustration of module d
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was inactivated. Each Reference ind
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Finally, add members to the Referen
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3.4.1. File Naming Convention - Ove
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• Test/Beta Release File("xsct",
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In certain cases, an RF1 data file
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VersionDate refers to the official,
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Example: Excluding the Fully Specif
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4.2.1.3. Pre-processing of distribu
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• Reject, highlight or apply othe
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Table 236: Essential concept Identi
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The purpose of this section of the
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Table 240: Example results for a Se
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• For each dual key, add rows to
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• Description104951019 is elimina
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4.4.1.4.1. Avoiding multiple hits o
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Table 248: Relationship Example Con
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• Since the depth of the hierarch
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4.4.2.5. Using navigation Subsets t
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Table 253: Concepts used in the Exa
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SubsetId Mem
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• 302402006 | radius and/or ulna
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Now we have tree nodes and their ch
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Subsets may be used to derive table
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• One Subset can be used as the b
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• A Context Concept Subset only r
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• A Navigation Subset specifies a
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• A RealmID identifies the specia
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4.5. Testing and traversing subtype
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This approach removes the need for
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4.5.5.2.4. Using the transitive clo
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Figure 55: Terminology server provi
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A field in the Component History Ta
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Cross maps table A data table consi
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• References Table Inactive compo
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A field in the Cross Maps Table tha
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A Subset that specifies sets of Nav
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A field in the Concepts Table that
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TargetId A SNOMED CT Identifier tha
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WordText A field in the Word Equiva
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