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

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20 | SNOMED CT Release Format 1 (RF1) Guide July 2012 component that is a member of the set and may associate some additional information with the referenced component. Some types of Reference Set may also be represented by a set of rules referred to as an 'intensional Refset definition'. 2.1.2.2. Navigation Hierarchies SNOMED CT subtype Relationships provide a logical semantic hierarchy. Often it is possible to view parts of the terminology and select particular Concepts by navigating through this subtype hierarchy. However, there are many situations in which the pure subtype hierarchy does not provide an ideal route for navigating the hierarchy. Navigation links are used to provide an alternative route through parts of the terminology. A navigation link can link any two Concepts together to identify a useful route for navigation. Each of the navigation links is directional, linking a navigational parent Concept to a more refined navigational child Concept. However, unlike the subtype relationship the presence or absence of a navigation link neither adds to nor subtracts from the definition of either of the Concepts that it links. Some Concepts may exist only to provide nodes in a navigation hierarchy. These Concepts are subtypes of |Navigational Concept | and play no part in the semantic definitions of any other Concept. 2.1.2.2.1. Uses of Navigational Hierarchies 2.1.2.2.1.1. Breaking down a subtype into manageable categories Some Concepts have a large number of subtype children that cannot be logically divided into intermediate subtypes. At the user interface these result in long lists of options, which are difficult to visualize and navigate. Navigational Concepts with appropriate navigational links to the supertype parent and its subtype children provide an intermediate layer without disrupting the semantic definitions. The | clinical finding | top-level Concept has a large number of subtype children. Intermediate navigation Concepts group some of these together in a convenient way. Example: Three subtypes related to pregnancy are grouped together under a single natural navigational Concept: • Disorder of pregnancy / labor / delivery / puerperium [navigation concept]; • Disorder of pregnancy; • Disorder of labor / delivery; • Disorder of puerperium. 2.1.2.2.1.2. Bypassing levels in the subtype hierarchy Some Concepts that are members of the same rational set of choices may be found at different levels in the subtype hierarchy. This may occur because some have intervening subtypes and some of these intervening concepts may not be required for data entry. Addition of new concepts in a release may change the concepts available at some levels in the subtype hierarchy. Navigation links can "bypass" levels in the subtype hierarchy to represent a rational sets of choices for use in a particular situation. Example: While it is semantically correct to nest | common cold | in the following subtype hierarchy, a user may reasonably expect to see "common cold" as an immediate navigational child of | upper respiratory infection |. • | upper respiratory infection | • | Viral upper respiratory tract infection | • | common cold | © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
2.1.2.2.1.3. Linking related Concepts of different types Navigational links can also be used to provide access to connected Concepts even when they are from different hierarchy branches. Example: A navigation links could associate: • "hypertension" (the disorder) with | blood pressure | (the observation); • | cataract | (disorder / finding) with "cataract surgery" (the procedure). 2.1.2.2.1.4. Ordering the display of subtypes Sibling Concepts in a subtype hierarchy are not ordered. However, at the user interface a particular order may be useful to highlight commonly used Concepts or to mirror a conventional ordering. Example: Vertebrae, cranial nerves, disease stages, etc. Navigational links are ordered and are used to impose order, even when the set of navigational children is the same as the set of subtype children. 2.1.2.2.1.5. Providing alternative hierarchies The subtype hierarchy is logically defined and there can only be one such hierarchy. However, as navigation hierarchies have no definitional consequences, it is possible to have different hierarchies for different groups of users with differing needs. Initial releases of SNOMED CT will contain a single set of navigation links but those engaged in technical implementation should be aware that in the future there may be separate sets of navigation links for use in different environments. 2.1.2.3. Cross Maps Structure and Content Guide | 21 SNOMED CT specifications and content include resources that support cross mapping to and from other code systems, classifications and terminologies. These resources support simple mapping, where there is a one-to-one Relationship between a SNOMED CT concept and code in a target scheme, and more complex maps where these are required. More complex mapping requirements supported by the SNOMED CT cross mapping model include: • Maps from a single SNOMED CT concept to a combination of codes (rather than a single code) in the target scheme. • Maps from a single SNOMED CT concept to choice of codes in the target scheme. In this case, the resolution of the choices may involve: • Manual selection supported by advisory notes. • Automated selection based on rules that test other relevant characteristics in the source data (e.g. age and sex of the subject, presence or absence of co-existing conditions, etc). • A combination of automated processing with manual confirmation or selection where rules are insufficient to make the necessary decisions. Note: In Release Format 1 cross maps are represented using three tables. These tables contains rows that represent the following types of information: • Cross Map Set: metadata about a set of maps from SNOMED CT to a target scheme; • Cross Map: a map from a concept to a representation of the concept in the target scheme; © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
Page 1 and 2: SNOMED CT ® Release Format 1 (RF1)
Page 3 and 4: Contents | 3 Release Format 1 - Det
Page 5 and 6: Chapter 1 Preface The purpose of th
Page 7 and 8: Table 3: Document Types Type Name a
Page 9 and 10: IHTSDO Glossary (DRAFT) • On line
Page 11 and 12: Chapter 2 Structure and Content Gui
Page 13 and 14: Figure 1: Multiple levels of granul
Page 15 and 16: Table 5: Example: Defining arthriti
Page 17 and 18: The full definitions of the concept
Page 19: Other components (i.e. Relationship
Page 23 and 24: • 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
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2.3.3.3.1.4. Procedures 2.3.3.3.1.4
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1. Every Concept in an Extension:
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Table 17: Processing Transfers betw
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In May 2008, the HL7 Version 3 Stan
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An expression supports combinations
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digitNonZero= %x31-39 The first cha
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excision of left fallopian tube. No
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This existential restriction is lab
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• In order to generate the OWL ve
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• Though there are many candidate
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2.3.7.2.2.1. Single byte encoding C
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9 0 9 Table 29: The full array for
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else {document.getElementById("out"
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http://www.augustana.ab.ca/~mohrj/a
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version. It seems unwise to prevent
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Table DescDualKey Table ConcDualKey
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The IHTSDO recognizes that, while i
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3.2.2. Release Format 1 - Structure
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3.2.3.2. Core Tables Data - Structu
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Data Fields InitialCapitalStatus De
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3.2.4.1. Subset Mechanism - Structu
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Data Fields ContextId 3.2.4.2.2. Su
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Subset SNOMED CT Top Level Navigati
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• as a combination of codes; •
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Table 41: Cross Mapping Tables Cros
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Table 44: Cross Map Targets Table K
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The History Mechanism is also used
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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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