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

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184 | SNOMED CT Release Format 1 (RF1) Guide July 2012 Table 160: Sample of LOINC codes that would be captured in a retrieval of all Urinalysis procedures METHOD_TYP SCALE_TYP SYSTEM TIME_ASPCT PROPERTY COMPONENT LOINC_NUM MICROSCOPY.LIGHT ORD URNS PT ACNC TUBULAR CELLS 11276-3 MICROSCOPY.LIGHT.HPF QN URNS PT NARIC SQUAMOUS CELLS 11277-1 MICROSCOPY.LIGHT.HPF QN URNS PT NARIC BLADDER CELLS 11278-9 MICROSCOPY.LIGHT NAR URNS PT FIND URINE SEDIMENT COMMENT 11279-7 MICROSCOPY.LIGHT ORD URNS PT ACNC RENAL CELLS 12248-1 MICROSCOPY.LIGHT.HPF ORD URNS PT ACNC SQUAMOUS CELLS 12258-0 TEST STRIP QN UR PT MCNC KETONES^ POST CFST 12448-7 MICROSCOPY.LIGHT ORD URNS PT ACNC BRUSHITE CRYSTALS 12512-0 © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434 QN URNS PT NCNC EPITHELIAL CELLS.RENAL 13653-1 MICROSCOPY.LIGHT.HPF QN URNS PT NARIC ERYTHROCYTES 13945-1 QN UR 24H SRAT ASCORBATE 15033-4 QN UR PT MCNC ASCORBATE 16408-7 QN UR PT MCNC ACETOACETATE 1702-0 MICROSCOPY.LIGHT QN URNS 12H NRAT LEUKOCYTES 18407-7 MICROSCOPY.LIGHT.LPF QN URNS PT NARIC BROAD CASTS 18487-9 TEST STRIP QN UR PT NCNC ERYTHROCYTES 20409-9 MICROSCOPY.LIGHT ORD URNS PT ACNC EPITHELIAL CELLS 20453-7 TEST STRIP QN UR PT NCNC ERYTHROCYTES 20409-9
The SNOMED CT Relationships Table enables even broader searches such as, for example, all body fluid analyzes . Since Urinalysis is a Body fluid analysis all the LOINC codes shown above would be included in the search, in addition to LOINC codes for CSF analyzes , joint fluid analyzes , etc. The SNOMED CT - LOINC Integration provides a mechanism that reflects the complementary relationship between LOINC and SNOMED CT.This integration yields formally defined appropriately classified laboratory terms that can be implemented in the design of robust laboratory analysis applications. Table 161: Comments on Some LOINC Analyte Names and Their Corresponding SNOMED CT Codes LOINC Analyte Name(s) ENTEROTOXIN ANTHRAQUINONE 9,10-ANTRHACENEDIONE BUTANE N-BUTANE HEXANE N-HEXANE DIOXANE 1,4-DIOXANE HEXACHLOROCYCLOHEXANE GAMMA HEXACHLOROCYCLOHEXANE SNOMED CT ID SNOMED CT ConceptId C-00226 116554007 C-10097 ---------- 116283009 C-20522 73229004 C-20524 40647006 C-20529 123008003 C-21304 27247007 C-23112 49490007 C-91170 77496001 Comments This may represent an assay for bacterial enterotoxins, but rotavirus also produces an enterotoxin, and so we use the more general parent term C-00226 Enterotoxin, instead of the more specific term C-36205 Bacterial enterotoxin. LOINC lists 9,10 anthracenedione as a related name for ANTHRAQUINONE, with CAS number 84-65-1 (the number for 9,10anthracenedione. The SNOMED CT code means the class of anthraquinones, which includes anthraquinone antineoplastics (e.g. mitoxantrone) as well as anthraquinone laxatives and anthraquinone dyes. We assume an anthraquinone assay would measure any anthraquinone, not just 9,10anthracenedione. Butane and n-butane are generally regarded as synonyms. In other words, ordinarily isobutane (C-20527) is specified explicitly, and is not counted as a subtype of butane. Unlike butane, hexane is a general term for 6-carbon saturated hydrocarbons. N-hexane is one isoform. Assume dioxane is 1,4-diethylene dioxide, same as 1,4-dioxane. LOINC lists CAS 608-73-1, but this refers to hexachlorocyclohexane mixed isomers (SNOMEDcode C-20885). We assume a hexachlorocyclohexane assay would measure any isomer or mixture of isomers, so the parent term C-23112 is the right one, even though it does not correspond to CAS 608-73-1. © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434 Formats | 185
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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
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Consistent representation is a prer
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Figure 8: Abstract logical model of
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1. As originally stated: : • | Ha
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2.2.1.3.2.3.1. Supertype aspects of
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Figure 11: Example hierarchy with l
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Concept E F G H J K L M Note: Compr
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Concept M List of proximal primitiv
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Table 11: Non-redundant attribute v
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G. | Severe upper limb laceration |
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As a result of this limitation some
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2.2.1.4.3. Historical relationships
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2.2.2.1.1.2. Refinement attribute n
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2.2.2.1.4.3. Use of "unapproved att
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Interim recommendations 1. Wherever
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2.2.2.3.1. Close-to-user expression
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It is important to note that combin
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2.2.2.3.6.1. Example of equivalent
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Figure 25: Alternative expressions
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Figure 27: Possible expressions of
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Figure 28: SCTID Short Format - App
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PartitionId 05 Description A Cross
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SctId 999999990989121104 2.3.2.9. T
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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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Page 135 and 136: • The only Relationships that it
Page 137 and 138: ComponentId ConceptId ReleaseVersio
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Page 141 and 142: Value 6 10 11 Limited Moved elsewhe
Page 143 and 144: As new concepts are added to SNOMED
Page 145 and 146: Table 73: DescriptionStatus Values
Page 147 and 148: 3.2.9.2.2.4. InitialCapitalStatus T
Page 149 and 150: 3.2.9.3. relationships tables Each
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Page 153 and 154: An integer value that expresses an
Page 155 and 156: 3.2.9.4.1.2.4. SubsetType Table 95:
Page 157 and 158: A string that identifies a Context
Page 159 and 160: 3.2.9.4.2.1.2. Data Fields Table 10
Page 161 and 162: • MemberStatus 3.2.9.4.2.3.1.1. S
Page 163 and 164: 3.2.9.4.2.4.1.3. MemberStatus Table
Page 165 and 166: 3.2.9.4.2.5.2. Data Fields Table 11
Page 167 and 168: 3.2.9.4.2.7.1.1. SubsetId Table 124
Page 169 and 170: 3.2.9.4.2.8.1.3. MemberStatus Table
Page 171 and 172: 3.2.9.4.3. Subset Definition File P
Page 173 and 174: 3.2.9.5.1.2.3. MapSetSchemeId Table
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Page 177 and 178: 3.2.9.5.1.3.2.3. MapRule Table 151:
Page 179 and 180: 3.2.9.5.1.4.2.3. TargetRule Table 1
Page 181 and 182: RELAT_NMS = column in the LOINC tab
Page 183: The value of the SNOMED CT / LOINC
Page 187 and 188: LOINC Analyte Name(s) DESMETHYLAMIO
Page 189 and 190: LOINC Analyte Name(s) COMPLEMENT IC
Page 191 and 192: The information provided includes d
Page 193 and 194: 3.2.9.6.4.1.2. ReleaseVersion Table
Page 195 and 196: Value 6 7 8 9 10 11 Note: Name Limi
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Page 199 and 200: Release Format 1 is represents a sn
Page 201 and 202: RF1 Descriptions Table Descriptions
Page 203 and 204: Table 177: Concepts Table Use of re
Page 205 and 206: Use of recommended additional indic
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Page 209 and 210: Table 184: Cross Map Sets Table Use
Page 211 and 212: Keys Partition Size Type Field Name
Page 213 and 214: Table 192: Word Equivalents Table U
Page 215 and 216: 3.2.10. The Stated relationships ta
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Page 223 and 224: Table 205: Cross Map Sets Table Map
Page 225 and 226: If this approach is followed, there
Page 227 and 228: This approach allows a more consist
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Page 231 and 232: • Temporally related to the selec
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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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