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

More documents

Recommendations

Info

84 | SNOMED CT Release Format 1 (RF1) Guide July 2012 2.3.4.2. Expression in definition forms An expression can be transformed to definition form and the representations applicable to this alternative form can then be applied. However, this approach is limited because several of the forms used to represent concept definitions do not support nesting. 2.3.4.3. Human-readable renderings An expression may be rendered according to particular rules to generate human-readable representations. Specific "simple" rules have been specified by NHS Connecting for Health in the UK. Alternative suggestions for more natural rendering have also been made to extend this initial outline proposal. Advice on this topic may be added to future revisions of this guide. 2.3.5. Stated Relationships Guide This part of the Guide provides information about the Stated relationships tables and the Web Ontology Language (OWL) transformation. 2.3.5.1. The Stated relationships tables The Stated Relationships Table contains the stated form of SNOMED CT. The stated form of a Concept is the logic definition that is directly edited by authors or editors. It consists of the stated | is a | relationships plus the defining relationships that exist prior to running a classifier on the logic definitions. Therefore, the stated form of a Concept is represented by a collection of relationships: one or more | Is a | relationships and zero or more defining relationships. The Stated Relationships Table is in the same table format as the Relationships Table, but the value of the characteristicTypeId field is | Stated relationship (core metadata concept) |. The stated form enables implementers to test a classifier for consistency, by comparing the results of classification with the distributed Relationships Table, which is the inferred form. 2.3.5.2. Description Logic (OWL or KRSS) Transform The Description Logic Transform Script, written in the Perl language, performs a transform of the Stated Relationships into Web Ontology Language (OWL) format or KRSS format. There are two options for the syntax of the OWL output: RDF/XML, or OWL Functional Syntax. The RDF/XML is more verbose and results in a file approximately double the size of the Functional Syntax file. 2.3.5.2.1. Object Properties SNOMED CT's attributes, the middle element of the concept- Relationship-concept triple, correspond to OWL Object Properties. The hierarchy under 410662002 | concept model attribute | contains all the attributes that have been approved for use as object properties. In addition, the subtype Relationships (i.e. | Is a | Relationships) between attributes in the | concept model attribute | hierarchy, as expressed in the stated relationships tables, are used by the script to automatically generate the corresponding sub-property axioms in OWL. For example, | Procedure site - Direct | appears as a subtype of | PROCEDURE SITE | in the stated relationships tables, and so the script automatically makes the OWL object property 'PROCEDURE SITE DIRECT' a sub-property of OWL object property 'PROCEDURE SITE'. 2.3.5.2.2. Relationship Grouping When transforming Relationships to OWL or KRSS, all rows that have a RelationshipType that are allowed to be grouped, even if a particular row is ungrouped (i.e. even if the row has a RelationshipGroup value meaning ‘ungrouped’), must be nested under an existential restriction that represents the (potential) grouping. © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
This existential restriction is labeled with the OWL object property name ‘RoleGroup’. It is anonymous in the sense that it has no SNOMED CT identifier and therefore is not named in the distributed concepts table. For example, in KRSS syntax, the stated definition of myConceptId1 with a stated definition that has a row with the triplet consisting of myConceptId1, myRelationshipType, myConceptId2 would translate into: (defprimconcept myConceptId1 (and parentConceptId (some RoleGroup (some myRelationshipType myConceptId2)))) Attributes that are never grouped: All RelationshipTypes are allowed to be grouped except | IS A |, and the following four: • 123005000 | PART OF | • 272741003 | LATERALITY | • 411116001 | HAS DOSE FORM | • 127489000 | HAS ACTIVE INGREDIENT | 2.3.5.2.3. Right Identities There has historically been limited use of right identities, also known as property chains, in SNOMED CT. The one property chain that is in the current release is | DIRECT SUBSTANCE | o | HAS ACTIVE INGREDIENT | -> | DIRECT SUBSTANCE |. The OWL transform properly represents this property chain in the OWL 2 EL Profile. It is not yet represented in the relationships tables, or anywhere else in the RF1 or RF2 format SNOMED CT distribution files. This is a recognized deficiency which has not yet been addressed partly because there is only one such declaration, and no inferences in standard release are affected by this single right identity declaration. 2.3.5.2.4. Running the Perl transform script Run the script according to the pattern: perl where • is the name of the file containing the transform script • In the January 2012 release this Perl script file is named: tls2_StatedRelationshipsToOwlKRSS_INT_20120131.pl • can be KRSS, OWL, or OWLF • KRSS causes output to be formatted according to KRSS2 which is parsable by the OWL API 3.2.2, or by CEL or other classifiers • OWL causes output to be formatted according to OWL XML/RDF • OWLF causes output to be formatted according to the OWL functional syntax • is the name of the file containing the RF2 format SNOMED CT Concepts Table snapshot • In the Jan 2012 release this file is named: sct2_Concept_Snapshot_INT_20120131.txt • is the name of the file containing the RF2 format SNOMED CT Descriptions Table snapshot • In the Jan 2012 release this file is named: sct2_Description_Snapshot-en_INT_20120131.txt • is the name of the file containing the RF2 format SNOMED CT Stated relationships tables • In the Jan 2012 release this file is named: sct2_StatedRelationship_Snapshot_INT_20120131.txt • is the name of the output file. Any valid file name can be used. • for example: res_StatedOWLF_INT_20120131.owl Structure and Content Guide | 85 © 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 and 20:
Other components (i.e. Relationship
Page 21 and 22:
2.1.2.2.1.3. Linking related Concep
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
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 and 76: Table 17: Processing Transfers betw
Page 77 and 78: In May 2008, the HL7 Version 3 Stan
Page 79 and 80: An expression supports combinations
Page 81 and 82: digitNonZero= %x31-39 The first cha
Page 83: excision of left fallopian tube. No
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
Page 95 and 96: else {document.getElementById("out"
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
Page 127 and 128: Table Descriptions Descriptions Rel
Page 129 and 130: Table 49: Relationships depending o
Page 131 and 132: Table 51: Changes to Relationships
Page 133 and 134: 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 and 186:
The SNOMED CT Relationships Table e
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
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
Page 237 and 238:
CONCEPTID 417163006 417746004 12820
Page 239 and 240:
CONCEPTID 102706005 1677001 9145400
Page 241 and 242:
CONCEPTID 399023006 399154007 39905
Page 243 and 244:
CONCEPTID 399306005 399239005 39937
Page 245 and 246:
CONCEPTID 125086000 78678003 388393
Page 247 and 248:
CONCEPTID 339008 47002008 128419007
Page 249 and 250:
CONCEPTID 16817006 15367004 1580700
Page 251 and 252:
CONCEPTID 14509009 39250009 8627300
Page 253 and 254:
CONCEPTID 122868007 122465003 78817
Page 255 and 256:
CONCEPTID 19207007 74923002 6639100
Page 257 and 258:
CONCEPTID 54305003 84100007 3216600
Page 259 and 260:
CONCEPTID 255496004 255499006 24646
Page 261 and 262:
CONCEPTID 62834003 5668004 34810001
Page 263 and 264:
CONCEPTID 53224005 4150005 74636004
Page 265 and 266:
CONCEPTID 47538007 19359003 3011000
Page 267 and 268:
3.2.13. Enumerated values Value 0 1
Page 269 and 270:
Table and Field Subsets SubsetType
Page 271 and 272:
3.3. Release Format 2 Update Guide
Page 273 and 274:
• The Release Format should minim
Page 275 and 276:
3.3.3.4. Backward compatibility The
Page 277 and 278:
3.3.4.5. Field Ordering Records in
Page 279 and 280:
externalised structures such as Ref
Page 281 and 282:
ContextId If either the RealmId fie
Page 283 and 284:
eplaced by more descriptive ones if
Page 285 and 286:
descriptions associated with concep
Page 287 and 288:
Figure 45: Illustration of module d
Page 289 and 290:
was inactivated. Each Reference ind
Page 291 and 292:
Finally, add members to the Referen
Page 293 and 294:
3.4.1. File Naming Convention - Ove
Page 295 and 296:
• Test/Beta Release File("xsct",
Page 297 and 298:
In certain cases, an RF1 data file
Page 299 and 300:
VersionDate refers to the official,
Page 301 and 302:
Example: Excluding the Fully Specif
Page 303 and 304:
4.2.1.3. Pre-processing of distribu
Page 305 and 306:
• Reject, highlight or apply othe
Page 307 and 308:
Table 236: Essential concept Identi
Page 309 and 310:
The purpose of this section of the
Page 311 and 312:
Table 240: Example results for a Se
Page 313 and 314:
• For each dual key, add rows to
Page 315 and 316:
• Description104951019 is elimina
Page 317 and 318:
4.4.1.4.1. Avoiding multiple hits o
Page 319 and 320:
Table 248: Relationship Example Con
Page 321 and 322:
• Since the depth of the hierarch
Page 323 and 324:
4.4.2.5. Using navigation Subsets t
Page 325 and 326:
Table 253: Concepts used in the Exa
Page 327 and 328:
SubsetId Mem
Page 329 and 330:
• 302402006 | radius and/or ulna
Page 331 and 332:
Now we have tree nodes and their ch
Page 333 and 334:
Subsets may be used to derive table
Page 335 and 336:
• One Subset can be used as the b
Page 337 and 338:
• A Context Concept Subset only r
Page 339 and 340:
• A Navigation Subset specifies a
Page 341 and 342:
• A RealmID identifies the specia
Page 343 and 344:
4.5. Testing and traversing subtype
Page 345 and 346:
This approach removes the need for
Page 347 and 348:
4.5.5.2.4. Using the transitive clo
Page 349 and 350:
Figure 55: Terminology server provi
Page 351 and 352:
A field in the Component History Ta
Page 353 and 354:
Cross maps table A data table consi
Page 355 and 356:
• References Table Inactive compo
Page 357 and 358:
A field in the Cross Maps Table tha
Page 359 and 360:
A Subset that specifies sets of Nav
Page 361 and 362:
A field in the Concepts Table that
Page 363 and 364:
TargetId A SNOMED CT Identifier tha
Page 365:
WordText A field in the Word Equiva
show all

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

Create successful ePaper yourself

Delete template?

Save as template?