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

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86 | SNOMED CT Release Format 1 (RF1) Guide July 2012 An example execution command on a Windows machine, to produce the stated view of SNOMED CT according to OWL Functional syntax, would then look like the following: C:\> perl tls2_StatedRelationshipsToOwlKRSS_INT_20120131.pl OWLF sct2_Concept_Snapshot_INT_20120131.txt sct2_Description_Snapshot-en_INT_20120131.txt sct2_StatedRelationship_Snapshot_INT_20120131.txt res_StatedOWLF_INT_20120131.owl 2.3.5.2.5. Importing into an editor Once the output file has been successfully created (e.g. res_StatedOWLF_INT_20120131.owl), an ontology editor that uses the OWL API should be able to import the file, assuming that the editor can handle very large files and that it is configured to use large amounts of memory, and your system has adequate memory (see FAQ below). The current version of the transform script has been tested with Protege running the OWL API version 3.2.2 and the OWL 2 Profile is OWL 2 EL. Table 22: Metrics to Validate Import of SNOMED OWL, January 2012 International Release (20120131) Protege Ontology Metrics Class count Object property count DL expressivity SubClass axioms count Equivalent class axioms count Sub object property axioms count Object property chain subproperty axioms count Annotation Assertion axioms count 2.3.5.2.6. SNOMED CT OWL Distribution FAQ 2.3.5.2.6.1. Access Value 294469 62 ALER 227961 66507 11 1 294531 1. Where do I obtain a copy of the OWL version of SNOMED CT? • You can currently generate an OWL version of SNOMED CT using the Perl script and 'stated form' file in the standard distribution of SNOMED CT. • The Perl script and Stated Relationships files are distributed in the main release in different directories. The script is located in a folder called ‘Resources/StatedRelationshipsToOwlKRSS/ ’ and the RF2 snapshot files for concepts, Descriptions and stated Relationships are located in a folder called 'RF2Release/Snapshot/Terminology'. Prior to the January 2012 release, the transform was based on an RF1 format stated Relationships file - see documentation of prior releases for historical data and transform scripts. 2. What do you mean I need to ‘generate’ the OWL version of SNOMED CT? • The OWL version of SNOMED CT is currently not distributed with the core release. However you can generate a local OWL version of SNOMED CT by executing the Perl script mentioned above. The instructions for using the Perl script are included in the Stated Relationships Guide (part of the Technical Implementation Guide), and also as comments in the header of the file containing the Perl script, which can be viewed in your favorite text editor (e.g. Notepad, Wordpad, etc). 3. What do I need to generate the OWL version of SNOMED CT? © 2002-2012 International Health Terminology Standards Development Organisation CVR #: 30363434
• In order to generate the OWL version of SNOMED CT, you will need to have ‘Perl’ installed on your machine. • In addition to the Stated Relationships file and Perl script mentioned, you will also require the RF2 (Release Format 2) version of the concepts table and descriptions table, named ‘sct2_Concept_Snapshot_INT_yyyymmdd.txt’ , and ‘sct2_Description_Snapshot-en_INT_yyyymmdd.txt’ in the January 2012 International Release and subsequently. These are found in the ‘RF2Release/Snapshot/Terminology’ folder of the international release. 4. I get errors when I try to generate the OWL version using the Perl script. What can I do? • Please check the following, before you report errors in the build process: • Ensure you have Perl properly installed on your machine. • Ensure that you are using versions of the Perl script, Stated Relationships, Concepts, and Descriptions all from the same release date and same Release Format (i.e. RF2). You will definitely get errors if you try to use a script designed for RF2 on RF1 format files, and vice versa. There is no guarantee of backwards compatibility of the script - i.e. a version released for use with January 2012 RF2 files may not work with prior release RF2 files. • Errors may be reported on the IHTSDO Collaborative Space, under the Implementation SIG site (in the General Discussions Forum). 2.3.5.2.6.2. Licensing 1. What are the license restrictions on the OWL version of SNOMED CT? • There is a single world-wide license for SNOMED CT for all purposes, called the “affiliate license”. The same license applies to the OWL version of SNOMED CT. You can find it by following the highlighted link labelled "SNOMED CT Affiliate License Agreement" on the right hand side of the page at www.ihtsdo.org/join-us/use-snomed-ct-licenses 2.3.5.2.6.3. Importing and Visualization 1. How do I load and visualize SNOMED CT in OWL format? • Though the KRSS or OWL files generated by the perl script can be viewed in a text editor, in order to sensibly visualize the OWL release you require a tool like Protégé 4(http://protege.stanford.edu/). Please note that version 4 of Protégé is required to load and visualize SNOMED CT. 2. Protégé crashes (or becomes unresponsive) when I try to visualize the class hierarchy on my machine! • Protégé is known to take some time to generate the class hierarchy for display. It might be worthwhile increasing the memory allocation of Protégé before your start loading SNOMED CT. Please refer to the relevant Protégé documentation for exact details on increasing maximum memory available to Protégé. 3. Help, the hierarchies are rendered as concept IDs in Protégé! How can I change this into fully specified names? • You need change the rendering options in Protégé to render using ‘labels’. In order to do that in Protégé 4, select ‘Render using annotation values’ from ‘Preferences/Renderer/Entity rendering’. 2.3.5.2.6.4. Classification 1. What DL reasoners are currently supported for classifying OWL version of SNOMED CT? Structure and Content Guide | 87 • There are Protégé 4.1 plugins for several DL reasoners that can classify SNOMED CT provided the machine specifications listed below are met. These include Snorocket, ELK, and Fact++. © 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
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
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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
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Page 81 and 82: digitNonZero= %x31-39 The first cha
Page 83 and 84: excision of left fallopian tube. No
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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
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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
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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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