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

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186 | SNOMED CT Release Format 1 (RF1) Guide July 2012 LOINC Analyte Name(s) FENCLORVOS FENCHLORPHOS ENDOTOXIN KETOCONAZOLE KETOKONAZOLE MONACETYLDAPSONE MONOACETYLDAPSONE ACETYLMORPHINE MONOACETYLMORPHINE 6-MONOACETYLMORPHINE OXYCODINONE OXYCODONE 6-BETA NALTREXONE 6-BETA NALTREXOL METHABARBITAL METHARBITAL DESMETHYLDOXEPIN NORDOXEPIN HYDROXYALPRAZOLAM ALPHA HYDROXYALPRAZOLAM N-DESALKYLFLURAZEPAM DESALKYLFLURAZEPAM SNOMED CT ID Comments SNOMED CT ConceptId C-23151 22008009 C-36210 18127008 C-52B50 40232005 C-55296 123003007 C-606B3 118290009 C-606D0 55452001 C-60D22 116562004 C-61340 30676006 C-62285 96204007 C-64523 123010001 C-64521 117158005 C-64552 115558004 Fenclorvos is probably a "spelling variant" of fenchlorphos. We assume | endotoxin | and | bacterial endotoxin | are synonymous. Ketokonazole is probably a "spelling variant". Monacetyldapsone may be a "spelling variant" of monoacetyldapsone. We assume these are all the same as 6-Omonoacetylmorphine, the major metabolite of heroin (besides morphine). If this is true, it appears to result in some duplicate LOINC codes. Oxycodinone is probably another name for oxycodone, but we were unable to find the name Oxycodinone in MEDLINE or any major chemical/drug reference. The major metabolite of naltrexone is 6-beta naltrexol, also called 6-beta hydroxynaltrexone. We assume this is what is meant by 6-beta naltrexone. LOINC related names for Methabarbital says Barbitone (not the same! Barbitone is Ethylbarbital!) and also Metharbital (the correct name) is a synonym. "Methabarbital" does not occur in MEDLINE, though some lists of controlled substances also use this spelling. These are synonyms for the demethylated metabolite of doxepin, N-desmethyldoxepin. Probably hydroxyalprazolam is intended to include both alpha- and 4- hydroxyalprazolam... (C-64521 is the alpha form). Synonyms for a major metabolite of flurazepam, N-1-desalkylflurazepam. © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
LOINC Analyte Name(s) DESMETHYLAMIODARONE DESETHYLAMIODARONE LINDANE AMINOBENZOATE PARA AMINOBENZOATE FLUBIPROFEN FLURBIPROFEN 2-AMINOBUTYRATE 2-AMINOBUTYRIC A-1-IDURONIDASE KETOGENIC STEROIDS 17-KETOGENIC STEROIDS 17-HYDROXYKETOSTEROIDS 20-HYDROXYPROGESTERONE 11-DEOXYCORTISOL DEOXYCORTISOL SNOMED CT ID Comments SNOMED CT ConceptId C-80352 96295003 C-91170 77496001 C-93210 39707000 C-96050 54344006 F-65C04 115343006 F-6A928 86430005 F-B2430 46120009 F-B2430 46120009 F-B2460 52422003 F-B2480 22941009 The only important metabolite of amiodarone (particularly in humans) is DESETHYLAMIODARONE, which is the meaning we have chosen here. There are no MEDLINE references containing the word DESMETHYLAMIODARONE, and we have assumed the addition of the "M" may be a spelling error. Lindane is the gamma isomer of hexachlorocyclohexane (strictly speaking must contain over 99% pure gamma isomer). Para-aminobenzoic acid (PABA), UV screen, B vitamin. Although both m-aminobenzoic acid and o-aminobenzoic acid exist, they are probably not what is meant here. Flubiprofen is probably a "spelling variant" of flurbiprofen. 2-aminobutyrate. Alpha L iduronidase. Assume these mean the same. These steroids have an -OH on C17. They include all of the 17-hydroxycorticosteroids, plus pregnanetriol, cortol, cortolone, etc. Possibly means any steroids with a keto or hydroxy on carbon 17. Assume these are the 17-ketogenic steroids. F-B2460 is 20-Hydroxyprogesterone, but LOINC related names and the CAS number both point to 17-alpha hydroxyprogesterone, which is F-B2470 (and has a keto group at C20!). These two are assumed to be the same. Formats | 187 © 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
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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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Table 52: Changes to Relationships
Page 135 and 136: • The only Relationships that it
Page 137 and 138: ComponentId ConceptId ReleaseVersio
Page 139 and 140: A readme.txt file is distributed wi
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
Page 151 and 152: 3.2.9.3.2.3. ConceptId2 Table 84: -
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
Page 175 and 176: This discussion of rules is include
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 and 184: The value of the SNOMED CT / LOINC
Page 185: The SNOMED CT Relationships Table e
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
Page 197 and 198: 3.2.9.6.5.1.1. ComponentId Table 17
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
Page 207 and 208: Use of recommended additional indic
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
Page 217 and 218: Figure 41: Overview of Cross Map Sc
Page 219 and 220: Table 197: Cross Maps Sets Table Ma
Page 221 and 222: Table 201: Cross Maps Sets Table Ma
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
Page 229 and 230: 1. A record may contain many record
Page 231 and 232: • Temporally related to the selec
Page 233 and 234: CONCEPTID 95333004 7119001 95336007
Page 235 and 236: 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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