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JohnMoehrkeJohnMoehrke
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fixup PALM, and attempt (commented out) to add the dicom code.
1 parent fd6ea03 commit 08820d7

4 files changed

Lines changed: 133 additions & 55 deletions

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‎input/ignoreWarnings.txt‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,11 @@
11
== Suppressed Messages ==
22

33
# The following code systems are external and not supported by terminology server
4-
Error from server: Unable to provide support for code system http://profiles.ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode
4+
Error from server: Unable to provide support for code system http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode
55

66
# The following code system should eventually show up in the terminology server
7-
Code System URI "http://terminology.hl7.org/CodeSystem/hl7-document-format-codes" is unknown so the code cannot be validated
7+
Code System URI "http://terminology.hl7.org/CodeSystem/hl7-document-format-codes" is unknown so the code cannot be validated
8+
9+
# The valueset tries to import from dicom the SOP id for KOS which is identified as the FormatCode for XDS-I. But I get a warning from the IG build tool
10+
#The code 1.2.840.10008.5.1.4.1.1.88.59 is not valid in the system http://dicom.nema.org/resources/ontology/DCM
11+
# no need for this ignoreWarning as this warning causes the build to fail to expand, so I removed this from the ValueSet

‎input/resources/Bundle-history-IHE-formatcode.codesystem.xml‎

Lines changed: 54 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,13 +4,64 @@
44
<id value="history-IHE-formatcode.codesystem"/>
55
<type value="collection"/>
66
<!-- includes Provenance record for each revision of the IHE FormatCodes -->
7+
<entry xmlns="http://hl7.org/fhir">
8+
<fullUrl value="http://profiles.ihe.net/fhir/ihe.formatcode.fhir/Provenance/20200724"/>
9+
<resource>
10+
<Provenance>
11+
<id value="formatcode-provenance-20200724"/>
12+
<target>
13+
<reference value="http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
14+
<type value="CodeSystem"/>
15+
</target>
16+
<occurredPeriod>
17+
<end value="2020-07-24"/>
18+
</occurredPeriod>
19+
<recorded value="2020-07-24T13:00:00.0000Z"/>
20+
<reason>
21+
<coding>
22+
<system value="http://terminology.hl7.org/CodeSystem/v3-ActReason"/>
23+
<code value="METAMGT"/>
24+
</coding>
25+
<text value="Remove PAT domain, as PALM is right. Remove 2010 FormatCodes not used in favor of urn:ihe.palm:apsr:2016."/>
26+
</reason>
27+
<activity>
28+
<coding>
29+
<system value="http://terminology.hl7.org/CodeSystem/v3-DataOperation"/>
30+
<code value="UPDATE"/>
31+
</coding>
32+
</activity>
33+
<agent>
34+
<type>
35+
<coding>
36+
<system value="http://terminology.hl7.org/CodeSystem/provenance-participant-type"/>
37+
<code value="author"/>
38+
</coding>
39+
</type>
40+
<who>
41+
<display value="John Moehrke"/>
42+
</who>
43+
</agent>
44+
<agent>
45+
<type>
46+
<coding>
47+
<system value="http://terminology.hl7.org/CodeSystem/provenance-participant-type"/>
48+
<code value="custodian"/>
49+
</coding>
50+
</type>
51+
<who>
52+
<display value="IHE PaLM Domain"/>
53+
</who>
54+
</agent>
55+
</Provenance>
56+
</resource>
57+
</entry>
758
<entry xmlns="http://hl7.org/fhir">
859
<fullUrl value="http://profiles.ihe.net/fhir/ihe.formatcode.fhir/Provenance/20200723"/>
960
<resource>
1061
<Provenance>
1162
<id value="formatcode-provenance-20200723"/>
1263
<target>
13-
<reference value="http://profiles.ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
64+
<reference value="http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
1465
<type value="CodeSystem"/>
1566
</target>
1667
<occurredPeriod>
@@ -61,7 +112,7 @@
61112
<Provenance>
62113
<id value="formatcode-provenance-20200703"/>
63114
<target>
64-
<reference value="http://profiles.ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
115+
<reference value="http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
65116
<type value="CodeSystem"/>
66117
</target>
67118
<occurredPeriod>
@@ -112,7 +163,7 @@
112163
<Provenance>
113164
<id value="formatcode-provenance-20200701"/>
114165
<target>
115-
<reference value="http://profiles.ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
166+
<reference value="http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode"/>
116167
<type value="CodeSystem"/>
117168
</target>
118169
<occurredPeriod>

‎input/resources/codesystem-formatcode.xml‎

Lines changed: 60 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ The actual list of codes is intended to be extensible.
4343
</telecom>
4444
</contact>
4545

46-
<description value="The [IHE](http://www.ihe.net) FormatCode code set is defined to be the set of [FormatCode(s) define by IHE] (http://wiki.ihe.net/index.php?title=IHE_Format_Codes), for use with [Document Sharing](https://wiki.ihe.net/index.php/Category:DocShare). This code set additionally includes, as deprecated, format codes defined by [HL7 for some Implementation Guides](http://wiki.hl7.org/index.php?title=CDA_Format_Codes_for_IHE_XDS). The HL7 codes are now managed by HL7. The set of IHE FormatCode codes was listed in HITSP C80 Table 2-153 Format Code Value Set Definition, but since has been updated. The use of the FormatCode specifies the technical format of the document. The FormatCode tends to reference the IHE Content Profile (Implementation Guide) that defines the use-case and constraints. The FormatCode is a further specialization more detailed than the mime-type. The FormatCode provides sufficient metadata information to allow any potential document content consumer to know if it can process and/or display by identifying a document encoding, structure and template. The set of codes is intended to be extensible."/>
46+
<description value="The [IHE](http://www.ihe.net) FormatCode code system with cannical URI of http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode is defined to be the set of [FormatCode(s) define by IHE] (http://wiki.ihe.net/index.php?title=IHE_Format_Codes), for use with [Document Sharing](https://wiki.ihe.net/index.php/Category:DocShare). This code set additionally includes, as deprecated, format codes defined by [HL7 for some Implementation Guides](http://wiki.hl7.org/index.php?title=CDA_Format_Codes_for_IHE_XDS). The HL7 codes are now managed by HL7. The set of IHE FormatCode codes was listed in HITSP C80 Table 2-153 Format Code Value Set Definition, but since has been updated. The use of the FormatCode specifies the technical format of the document. The FormatCode tends to reference the IHE Content Profile (Implementation Guide) that defines the use-case and constraints. The FormatCode is a further specialization more detailed than the mime-type. The FormatCode provides sufficient metadata information to allow any potential document content consumer to know if it can process and/or display by identifying a document encoding, structure and template. The set of codes is intended to be extensible."/>
4747
<copyright value="Some content from IHE® Copyright © 2015 [IHE International, Inc](http://www.ihe.net/Governance/#Intellectual_Property)."/>
4848
<caseSensitive value="true"/>
4949
<content value="complete"/>
@@ -73,7 +73,7 @@ The actual list of codes is intended to be extensible.
7373
<!-- could define our own property as we are actually including the cda-template ID as a comment, it is really not a comment
7474
<property>
7575
<code value="CDA-Template" />
76-
<uri value="http://ihe.net/fhir/formatcode#CDA-Template"/>
76+
<uri value="http://profiles.ihe.net/fhir/formatcode#CDA-Template"/>
7777
<description value="Indicates the CDA-Template to use with the given formatCode, when CDA mime-type is used."/>
7878
<type value="string" />
7979
</property>
@@ -189,8 +189,8 @@ The actual list of codes is intended to be extensible.
189189
<display value="Care Management (CM)"/>
190190
</concept>
191191
<concept>
192-
<code value="urn:ihe:pcc:ic:2008"/>
193-
<display value="Immunization Content (IC)"/>
192+
<code value="urn:ihe:pcc:irc:2008"/>
193+
<display value="Immunization Registry Content (IRC)"/>
194194
<property>
195195
<code value="comment"/>
196196
<valueString value="1.3.6.1.4.1.19376.1.5.3.1.1.18.1.2" />
@@ -475,123 +475,134 @@ The actual list of codes is intended to be extensible.
475475
</concept>
476476
<!--Anatomic Pathology-->
477477
<concept>
478-
<code value="urn:ihe:pat" />
478+
<code value="urn:ihe.palm" />
479479
<display value="Pathology Domain" />
480480
<definition value="Ontology group for all Pathology defined FormatCodes" />
481481
<property>
482482
<code value="notSelectable" />
483483
<valueBoolean value="true" />
484484
</property>
485485
<concept>
486-
<code value="urn:ihe:pat:apsr:all:2010"/>
487-
<display value="PAT APSR"/>
486+
<code value="urn:ihe.palm:apsr:2016"/>
487+
<display value="PALM APSR"/>
488+
<definition value="Anatomic Pathology Structured Report"/>
489+
<property>
490+
<code value="comment"/>
491+
<valueString value="1.3.6.1.4.1.19376.1.8.1.1.1" />
492+
</property>
493+
</concept>
494+
<!-- all old ones from 2010 that are not to be recognized as the supplement was updated in 2016 and cleaned
495+
<concept>
496+
<code value="urn:ihe.palm:apsr:all:2010"/>
497+
<display value="PALM APSR"/>
488498
<definition value="Anatomic Pathology Structured Report All"/>
489499
</concept>
490500
<concept>
491-
<code value="urn:ihe:pat:apsr:cancer:all:2010"/>
492-
<display value="PAT APSR Cancer"/>
501+
<code value="urn:ihe.palm:apsr:cancer:all:2010"/>
502+
<display value="PALM APSR Cancer"/>
493503
<definition value="Anatomic Pathology Structured Report Cancer All"/>
494504
</concept>
495505
<concept>
496-
<code value="urn:ihe:pat:apsr:cancer:breast:2010"/>
497-
<display value="PAT APSR Cancer Breast"/>
506+
<code value="urn:ihe.palm:apsr:cancer:breast:2010"/>
507+
<display value="PALM APSR Cancer Breast"/>
498508
<definition value="Anatomic Pathology Structured Report Cancer Breast"/>
499509
</concept>
500510
<concept>
501-
<code value="urn:ihe:pat:apsr:cancer:colon:2010"/>
502-
<display value="PAT APSR Cancer Colon"/>
511+
<code value="urn:ihe.palm:apsr:cancer:colon:2010"/>
512+
<display value="PALM APSR Cancer Colon"/>
503513
<definition value="Anatomic Pathology Structured Report Cancer Colon"/>
504514
</concept>
505515
<concept>
506-
<code value="urn:ihe:pat:apsr:cancer:prostate:2010"/>
507-
<display value="PAT Cancer Prostate"/>
516+
<code value="urn:ihe.palm:apsr:cancer:prostate:2010"/>
517+
<display value="PALM Cancer Prostate"/>
508518
<definition value="Anatomic Pathology Structured Report Cancer Prostate"/>
509519
</concept>
510520
<concept>
511-
<code value="urn:ihe:pat:apsr:cancer:thyroid:2010"/>
512-
<display value="PAT APSR Cancer Thyroid"/>
521+
<code value="urn:ihe.palm:apsr:cancer:thyroid:2010"/>
522+
<display value="PALM APSR Cancer Thyroid"/>
513523
<definition value="Anatomic Pathology Structured Report Cancer Thyroid"/>
514524
</concept>
515525
<concept>
516-
<code value="urn:ihe:pat:apsr:cancer:lung:2010"/>
517-
<display value="PAT APSR Cancer Lung"/>
526+
<code value="urn:ihe.palm:apsr:cancer:lung:2010"/>
527+
<display value="PALM APSR Cancer Lung"/>
518528
<definition value="Anatomic Pathology Structured Report Cancer Lung"/>
519529
</concept>
520530
<concept>
521-
<code value="urn:ihe:pat:apsr:cancer:skin:2010"/>
522-
<display value="PAT Cancer Skin"/>
531+
<code value="urn:ihe.palm:apsr:cancer:skin:2010"/>
532+
<display value="PALM Cancer Skin"/>
523533
<definition value="Anatomic Pathology Structured Report Cancer Skin"/>
524534
</concept>
525535
<concept>
526-
<code value="urn:ihe:pat:apsr:cancer:kidney:2010"/>
527-
<display value="PAT Cancer Kidney"/>
536+
<code value="urn:ihe.palm:apsr:cancer:kidney:2010"/>
537+
<display value="PALM Cancer Kidney"/>
528538
<definition value="Anatomic Pathology Structured Report Cancer Kidney"/>
529539
</concept>
530540
<concept>
531-
<code value="urn:ihe:pat:apsr:cancer:cervix:2010"/>
532-
<display value="PAT Cancer Cervix"/>
541+
<code value="urn:ihe.palm:apsr:cancer:cervix:2010"/>
542+
<display value="PALM Cancer Cervix"/>
533543
<definition value="Anatomic Pathology Structured Report Cancer Cervix"/>
534544
</concept>
535545
<concept>
536-
<code value="urn:ihe:pat:apsr:cancer:endometrium:2010"/>
537-
<display value="PAT Cancer Endometrium"/>
546+
<code value="urn:ihe.palm:apsr:cancer:endometrium:2010"/>
547+
<display value="PALM Cancer Endometrium"/>
538548
<definition value="Anatomic Pathology Structured Report Cancer Endometrium"/>
539549
</concept>
540550
<concept>
541-
<code value="urn:ihe:pat:apsr:cancer:ovary:2010"/>
542-
<display value="PAT Cancer Ovary"/>
551+
<code value="urn:ihe.palm:apsr:cancer:ovary:2010"/>
552+
<display value="PALM Cancer Ovary"/>
543553
<definition value="Anatomic Pathology Structured Report Cancer Ovary"/>
544554
</concept>
545555
<concept>
546-
<code value="urn:ihe:pat:apsr:cancer:esophagus: 2010"/>
547-
<display value="PAT Cancer Esophagus"/>
556+
<code value="urn:ihe.palm:apsr:cancer:esophagus: 2010"/>
557+
<display value="PALM Cancer Esophagus"/>
548558
<definition value="Anatomic Pathology Structured Report Cancer Esophagus"/>
549559
</concept>
550560
<concept>
551-
<code value="urn:ihe:pat:apsr:cancer:stomach: 2010"/>
552-
<display value="PAT Cancer Stomach"/>
561+
<code value="urn:ihe.palm:apsr:cancer:stomach: 2010"/>
562+
<display value="PALM Cancer Stomach"/>
553563
<definition value="Anatomic Pathology Structured Report Cancer Stomach"/>
554564
</concept>
555565
<concept>
556-
<code value="urn:ihe:pat:apsr:cancer:liver:2010"/>
557-
<display value="PAT Cancer Liver"/>
566+
<code value="urn:ihe.palm:apsr:cancer:liver:2010"/>
567+
<display value="PALM Cancer Liver"/>
558568
<definition value="Anatomic Pathology Structured Report Cancer Liver"/>
559569
</concept>
560570
<concept>
561-
<code value="urn:ihe:pat:apsr:cancer:pancreas: 2010"/>
562-
<display value="PAT Cancer Pancreas"/>
571+
<code value="urn:ihe.palm:apsr:cancer:pancreas: 2010"/>
572+
<display value="PALM Cancer Pancreas"/>
563573
<definition value="Anatomic Pathology Structured Report Cancer Pancreas"/>
564574
</concept>
565575
<concept>
566-
<code value="urn:ihe:pat:apsr:cancer:testis:2010"/>
567-
<display value="PAT Cancer Testis"/>
576+
<code value="urn:ihe.palm:apsr:cancer:testis:2010"/>
577+
<display value="PALM Cancer Testis"/>
568578
<definition value="Anatomic Pathology Structured Report Cancer Testis"/>
569579
</concept>
570580
<concept>
571-
<code value="urn:ihe:pat:apsr:cancer:urinary_bladder:2010"/>
572-
<display value="PAT Cancer Urinary"/>
581+
<code value="urn:ihe.palm:apsr:cancer:urinary_bladder:2010"/>
582+
<display value="PALM Cancer Urinary"/>
573583
<definition value="Anatomic Pathology Structured Report Cancer Urinary Bladder"/>
574584
</concept>
575585
<concept>
576-
<code value="urn:ihe:pat:apsr:cancer:lip_oral_cavity:2010"/>
577-
<display value="PAT Cancer Lip"/>
586+
<code value="urn:ihe.palm:apsr:cancer:lip_oral_cavity:2010"/>
587+
<display value="PALM Cancer Lip"/>
578588
<definition value="Anatomic Pathology Structured Report Cancer Lip Oral Cavity"/>
579589
</concept>
580590
<concept>
581-
<code value="urn:ihe:pat:apsr:cancer:pharynx:2010"/>
582-
<display value="PAT Cancer Pharynix"/>
591+
<code value="urn:ihe.palm:apsr:cancer:pharynx:2010"/>
592+
<display value="PALM Cancer Pharynix"/>
583593
<definition value="Anatomic Pathology Structured Report Cancer Pharynx"/>
584594
</concept>
585595
<concept>
586-
<code value="urn:ihe:pat:apsr:cancer:salivary_gland:2010"/>
587-
<display value="PAT Cancer Salivary"/>
596+
<code value="urn:ihe.palm:apsr:cancer:salivary_gland:2010"/>
597+
<display value="PALM Cancer Salivary"/>
588598
<definition value="Anatomic Pathology Structured Report Cancer Salivary Gland"/>
589599
</concept>
590600
<concept>
591-
<code value="urn:ihe:pat:apsr:cancer:larynx:2010"/>
592-
<display value="PAT Cancer Larynx"/>
601+
<code value="urn:ihe.palm:apsr:cancer:larynx:2010"/>
602+
<display value="PALM Cancer Larynx"/>
593603
<definition value="Anatomic Pathology Structured Report Cancer Larynx"/>
594604
</concept>
605+
-->
595606
</concept>
596607
<!--Pharmacy-->
597608
<concept>

‎input/resources/valueset-formatcode.xml‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,6 +56,18 @@
5656
<system value="http://terminology.hl7.org/CodeSystem/hl7-document-format-codes"/>
5757
</include>
5858
-->
59+
60+
<!-- This one concept is used as the FormatCode for XDS-I. It is the KOS document definition SOP. -->
61+
<!-- but the build tool complains and refuses to do any valueSet expansion (TODO fix at some point)
62+
<include>
63+
<system value="http://dicom.nema.org/resources/ontology/DCM" />
64+
<concept>
65+
<code value="1.2.840.10008.5.1.4.1.1.88.59" />
66+
<display value="Key Object Selection Document" />
67+
</concept>
68+
</include>
69+
-->
5970
</compose>
71+
6072

61-
</ValueSet>
73+
</ValueSet>

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