1 Letter Ballot Status 2 2020/03/09 Date of Last Update 3 David Clunie 4 mailto:[email protected]Person Assigned 5 David Clunie 6 mailto:[email protected]Submitter Name 7 2018/07/04 Submission Date 8 Correction Number CP-1962 9 Log Summary: Changes to Abdomen-related anatomy concepts in SNOMED CT 10 Name of Standard 11 PS3.16 12 - Letter Ballot - 13 Page 1 CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT
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1 Letter BallotStatus2 2020/03/09Date of Last Update3 David Clunie
2 Page 2CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT
1 Rationale for Correction:
2 During its anatomy remodelling, SNOMED inactivated 416949008 "abdomen and/or pelvis structure", transiently redefined 113345001 "abdominal3 structure" to mean "abdominalpelvic" then inactivated it.
4 New specific imaging-specific concepts that relate to cross-sectional regions that do not necessarily have traditional clinical anatomical correlates,5 e.g., strcutures related to the"cross-sectional segment of trunk" have been added to account for the various different anatomical, clinical and6 radiological variants of the colloquial concept "abdomen". Details of the discussion can be found in the paper at7 http://docs.google.com/document/d/14900YhOBn63g3-zL_0lcP8BwSjRbhE4vKzOwFGt_8tk. See also the SNOMED CT Release Notes for the8 J A N 2 0 2 0 I N T R e l e a s e 9 (https://confluence.ihtsdotools.org/display/RMT/SNOMED+CT+January+2020+International+Edition+-+SNOMED+International+Release+notes).10 The cross-sectional variants are also applicable to projection radiography, and arguably ultrasound. since they involve the full thickness of the body11 and do not exclude the back.
12 Proposed changes:
13 • replace all 113345001 (inactive) with 818981001 "Structure of abdominal cross-sectional segment of trunk (body structure)" (new)
14 continue with DICOM synonym "Abdomen" mapped to BodyPartExamined "ABDOMEN"
15 • replace all 416949008 "Abdomen and/or pelvis structure (body structure)" (inactive) with 818982008 "Structure of abdominopelvic cross-sectional16 segment of trunk (body structure)" (new)
17 continue with DICOM synonym "Abdomen and Pelvis" mapped to BodyPartExamined "ABDOMENPELVIS"
18 (we use the cross-sectional concept, rather than using 818983003 "Structure of abdominopelvic cavity and/or content of abdominopelvic cavity19 and/or anterior abdominal wall (body structure)", which is not full thickness)
20 • replace all 12921003 "Structure of pelvis (body structure)" with 816092008 "Structure of pelvic cross-sectional segment of trunk (body structure)"21 (new)
22 continue with DICOM synonym "Pelvis" mapped to BodyPartExamined "PELVIS"
23 (even though 12921003 is still active in SNOMED CT, "in contrast to the 'pelvic segment of trunk' excludes the perineum, external genitalia")
24 • replace most 51185008 "Thoracic structure (body structure)" with 816094009 "Structure of thoracic cross-sectional segment of trunk (body25 structure)"
26 continue with DICOM synonyms "Chest" and "Thorax" mapped to BodyPartExamined "CHEST" and "THORAX"
27 (even though 51185008 is still active in SNOMED CT, we replace it with the cross-sectional concept that is full thickness)
28 • rather than 51185008 "Thoracic structure (body structure)" use 43799004 "Thoracic cavity structure (body structure)"
29 for DICOM synonym "Intra-thoracic" (for endoscopy site)
30 make consistent between common anatomic regions and endoscopy specific context group and Annex I
31 • replace 52731004 "Abdominopelvic cavity structure (body structure)" (inactive) with 818987002 "Structure of abdominopelvic cavity (body32 structure)" (new)
33 used with DICOM synonym "Intra-abdominal" (for endoscopy site) and "Abdominal cavity" add replace DICOM code meaning with34 "Intra-abdominopelvic" (since laparoscopy includes the pelvic cavity) and "Abdominopelvic cavity" to reduce ambiguity
35 make consistent between common anatomic regions and endoscopy specific context group and Annex I
36 • replace 21844003 "Pelvic cavity structure (body structure)" (inactive) with 816989007 "Structure of cavity of false and/or true pelvis (body37 structure)"
38 used with DICOM synonym "Intra-pelvic" (for endoscopy site)
39 use concept that includes both false and true pelvis since pelvic laparoscopy involves both
40 - Letter Ballot -
41 Page 3CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT
1 make consistent between common anatomic regions and endoscopy specific context group and Annex I - add to CID 4040
2 Subdivisions (e.g., upper abdomen) and surfaces (e.g., skin of abdomen) are not changed since these concepts remain active in SNOMED and3 their interpretaion has not changed.
4 [Ed.Note: SNOMED Request ID 748359 includes 818981001, 818982008, 818983003, 816092008, 816094009, 818987002, 816989007, 43799004,5 816990003, 816991004]
6 Correction Wording:
7 - Letter Ballot -
8 Page 4CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT
1 Amend DICOM PS3.16 as follows (changes to existing text are bold and underlined for additions and struckthrough for removals):
2 CID 4 Anatomic Region3 Resources:4 HTML | FHIR JSON | FHIR XML | IHE SVS XML5 Type:6 Extensible7 Version:8 20170914yyyymmdd9 UID:10 1.2.840.10008.6.1.2
Designator4 218219218219C3696900R-FB504Skin of upper5 abdomen
699935000SCT
6 600601C3696900R-FB504Skin of upper7 abdomen
699935000SCT
8 232232Skin of upper9 paraspinal region
130302DCM
10 520XA4QH7C0222138T-02401Skin of upper11 trunk
54440003SCT
12 Note
13 1. It is desirable to use more general standard coding schemes such as SNOMED CT whenever possible, to support inter-14 operability across specialist domains, yet the numeric codes from the NYU and Mayo systems are well known to derma-15 tologists. Multiple codes may be encoded in the image by using the equivalent code mechansism. See ????. Standard16 Coding Scheme Designators (NYUMCCG and MAYOASRG) are defined.
17 2. SNOMED CT and FMA "skin of" or "mucosa of" specific concepts are used here when available, rather than the more18 generic underlying organ or part concepts; this sacrifices commonality with the anatomic regions used for more general19 applications, but is appropriate for dermatologic applications. E.g., (59112000, SCT, "Skin of anus") is used instead of20 (53505006, SCT, "Anal structure").
21 3. The DICOM convention is to use "structure of" concepts rather than "entire" concepts when both are defined, and that22 convention is followed here. E.g., (37671003, SCT, "Skin structure of lateral canthus") is used in preference to (368772009,23 SCT "Entire skin of lateral canthus").
24 4. .
25 5. .
26 6. .
27 7. .
28 8. Laterality is pre-coordinated in most of the NYU and Mayo codes, but by convention is factored out and encoded29 seperately in DICOM. The appropriate modifiers are listed in ???. The left and right modifiers correspond to the NYU/Mayo30 columns labelled "L" and "R" in this context group table. An entry in the "M" column of this table means that the NYU or31 Mayo code is for a midline or unpaired structure or refers to the median part of a structure that spans from left to right.
32 9. .
33 CID 4030 CT, MR and PET Anatomy Imaged34 Resources:35 HTML | FHIR JSON | FHIR XML | IHE SVS XML36 Type:37 Extensible38 Version:39 2017091440 UID:41 1.2.840.10008.6.1.307
18 CID 7483 Common Anatomic Regions for Animals19 Resources:20 HTML | FHIR JSON | FHIR XML | IHE SVS XML21 Type:22 Extensible23 Version:24 20170914yyyymmdd25 UID:26 1.2.840.10008.6.1.815
27 Table CID 7483. Common Anatomic Regions for Animals
7 E French Language Meanings of Selected Codes Used in the DCMR (Normative)
8 Table E-1. French Language Meanings of Selected Codes
9 Code Meaning French10 Language
Code Meaning EnglishLanguage
Code ValueCoding SchemeVersion
Coding SchemeDesignator
11 Abdomen supérieurUpper abdomen80581009SCT
12 I Relationship of Endoscopy Procedures to Anatomic Regions (Informative)13 Table I-1 provides examples of the common nomenclature for the type of endoscopy performed, and the code value suggested for14 use for anatomic region in CID 4040 “Endoscopy Anatomic Regions”.
15 Table I-1. Examples of the Common Nomenclature for the Type of Endoscopy Performed
16 Example of the type of endoscopy for17 which this region is applicable18 (Informative)
27 Since the Adult Mouse Anatomy Ontology is not in the UMLS, the mapping of Mouse Anatomy codes described here is an28 extract of a mapping to the NCI Thesaurus described in Hayamizu TF, de Coronado S, Fragoso G, Sioutos N, Kadin JA,29 Ringwald M. The mouse-human anatomy ontology mapping project. Database: The Journal of Biological Databases and30 Curation 2012;2012:bar066. doi:10.1093/database/bar066. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308156/. The31 mapping files used can be found at ftp://ftp.informatics.jax.org/pub/reports/ma2ncit.obo.
32 The NCI Thesaurus codes were then used to look up corresponding concepts in UMLS, from which SNOMED and FMA33 codes were extracted automatically (and various conflicts and ambiguities resolved manually). The same correspondence34 to existing Body Part Examined values is used as in other tables in this Annex.
35 Another mapping project using the FMA as a reference ontology was not used, since the files were not available. See Zhang36 S, Bodenreider O. Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Ref-37 erence. AMIA Annual Symposium Proceedings 2005;2005:864-868 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560629/.
38 Table L-4. Correspondence between Animal-specific and Generic NCI Thesaurus Codes
39 Rat-specific UMLS40 Concept UniqueID
Rat-specificNCIt ID
Mouse-specificUMLS Concept
41 UniqueID
Mouse-specificNCIt ID
Generic UMLSConcept UniqueID
Generic NCItID
CodeMeaning
42 C23698C0030797C12767Pelvis
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44 Page 12CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT
2 For the mouse, NCIt contains some duplicate anatomical concepts, including those which have been marked inactive and3 appear to have been replaced with improved codes for the "Mouse Models of Human Cancers Consortium" (MMHCC).4 Whenever duplicates were found, the MMHCC concept has been used in this table.
5 This table was produced by searching NCIt for all concepts that had "mouse" or "rat" in their concept name or synonyms,6 and then using that synonym with the word "mouse" or "rat" removed, to match against generic concept names.
7 The NCI Thesaurus codes were then used to look up corresponding concepts in UMLS, though not all of the concepts are8 included in UMLS yet (especially the MMHCC concepts).
9 Table L-5. Pairedness of Anatomic Concepts
10 Paired StructureCode MeaningSNOMED Code Value11 NAbdomen113345001 81898100112 NAbdomen and Pelvis416949008 81898200813 NChest51185008 81609400914 NChest, Abdomen and Pelvis41677500415 NChest and Abdomen41655000016 NNeck, Chest, Abdomen and Pelvis41631900317 NNeck, Chest and Abdomen41615200118 NNeck and Chest41743700619 NPelvis12921003 81609200820 NPelvis and lower extremities41663100521 NThorax51185008 816094009
22 Amend DICOM PS3.16 to add the following retired code entries:
23 J SNOMED Retired Codes
24 Table J-1. SNOMED Codes Retired from DICOM Use
25 NotesReplacement CodeCode MeaningRetired Code Value26 Replacement code has meaning of "Structure of abdominal27 cross-sectional segment of trunk (body structure)".
28 Retired code is inactive in SNOMED CT.
818981001Abdomen113345001
29 Replacement code has meaning of "Structure of abdominopelvic30 cross-sectional segment of trunk (body structure)".
31 Retired code is inactive in SNOMED CT.
818982008Abdomen andPelvis
416949008
32 Replacement code has meaning of "Structure of thoracic33 cross-sectional segment of trunk (body structure)".
34 Retired code is still active in SNOMED CT.
35 Also used in DICOM with synonym "Thorax".
816094009Chest51185008
36 Replacement code has meaning of "Structure of pelvic cross-sectional37 segment of trunk (body structure)".
38 Retired code is still active in SNOMED CT.
816092008Pelvis12921003
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40 Page 13CP-1962 - Changes to Abdomen-related anatomy concepts in SNOMED CT