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DICOM Amalgam v1.0 -- Overall DICOM RDF serialization plan #148

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ebremer opened this issue Jul 26, 2024 · 1 comment
Open

DICOM Amalgam v1.0 -- Overall DICOM RDF serialization plan #148

ebremer opened this issue Jul 26, 2024 · 1 comment
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Turtle FHIR specification Turtle examples

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@ebremer
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ebremer commented Jul 26, 2024 •
edited by dbooth-boston
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I've created an updated version of what I generate to reflect what I believe puts everything together to date.

  1. [ a dcm:null ] when nulls are needed in literal lists (see dcm:00080008)
  2. Removal of VR types when unambiguous. VR is kept in the binary types and BulkDataURIs.
  3. Removal of RDF List when Value Multiplicity is always 1.
  4. How to handle lists with missing elements. See How best to represent DICOM lists with missing elements, in FHIR RDF? #141
  5. All VR mapped to xsd data types
  6. DICOM sequence (SQ) are handled with RDF Lists and use nested blank nodes with any needed dcm tags ( see tag dcm:00291000) See DICOM Sequence Tags (SQ) handling #146
  7. DICOM Private Data Elements. See DICOM Private Data Elements in DICOM RDF #145
  8. DICOM InlineBinary and BulkDataURI. See DICOM: How to handle InlineBinary and BulkDataURI? #144
  9. What should the primary subject of the file be? See DICOM: What should a DICOM RDF file use as a primary subject? #142
PREFIX bib: <http://id.loc.gov/ontologies/bibframe/>
PREFIX cry: <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions/>
PREFIX dcm: <http://dicom.nema.org/resources/ontology/DCM/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

<urn:sha256:ee1fcf71fecb6a8aee3b1219388cc7ded40a804056a7647674ba1a77b797ae8e>
        rdf:type      dcm:DicomFile;
        dcm:00020001  [ dcm:InlineBinary  "AAE="^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00020002  "1.2.840.10008.5.1.4.1.1.12.1";
        dcm:00020003  "1.3.12.2.1107.5.4.3.321890.19960124.162922.29";
        dcm:00020010  "1.2.840.10008.1.2.4.50";
        dcm:00020012  "999.999";
        dcm:00080008  ( "DERIVED" "PRIMARY" [ dcm:null ] "SINGLE A" );
        dcm:00080016  "1.2.840.10008.5.1.4.1.1.12.1";
        dcm:00080018  "1.3.12.2.1107.5.4.3.321890.19960124.162922.29";
        dcm:00080020  "1994-10-13"^^xsd:date;
        dcm:00080030  "14:19:17"^^xsd:time;
        dcm:00080060  "XA";
        dcm:00082110  "01";
        dcm:00082112  [ dcm:00081150  "1.2.840.10008.5.1.4.1.1.12.1";
                        dcm:00081155  "1.3.12.2.1107.5.4.3.321890.19960124.162922.28"
                      ];
        dcm:00090010  ( "CARDIO-SMS 1.0" );
        dcm:00091002  [ dcm:InlineBinary  "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"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00091003  [ dcm:InlineBinary  "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"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00091005  [ dcm:InlineBinary  "AAAPAAAAAGAAAAACAAAEsAAAACgAAAAD"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00100010  [ dcm:Alphabetic  "Rubo DEMO" ];
        dcm:00100020  "556342B";
        dcm:00100030  "1995-10-25"^^xsd:date;
        dcm:00100040  "M";
        dcm:00181063  "33"^^xsd:decimal;
        dcm:00181155  "GR";
        dcm:00181510  "-32"^^xsd:decimal;
        dcm:00181511  "2"^^xsd:decimal;
        dcm:00190010  ( "CARDIO-D.R. 1.0" );
        dcm:00191030  ( "262144"^^xsd:unsignedInt );
        dcm:0020000D  "1.3.12.2.1107.5.4.3.123456789012345.19950922.121803.6";
        dcm:0020000E  "1.3.12.2.1107.5.4.3.123456789012345.19950922.121803.8";
        dcm:00200011  1;
        dcm:00210010  ( "CARDIO-D.R. 1.0" );
        dcm:00211013  ( 15 );
        dcm:00280002  1;
        dcm:00280004  "MONOCHROME2";
        dcm:00280008  96;
        dcm:00280009  ( "00181063" );
        dcm:00280010  512;
        dcm:00280011  512;
        dcm:00280100  8;
        dcm:00280101  8;
        dcm:00280102  7;
        dcm:00280103  0;
        dcm:00281040  "LIN";
        dcm:00281090  "NAT";
        dcm:00286040  ( 20 53 77 );
        dcm:00286100  [ dcm:00286101  "NONE";
                        dcm:00286110  ( 0 )
                      ];
        dcm:00290010  ( "CARDIO-D.R. 1.0" );
        dcm:00291000  ( [ dcm:00290010  ( "CARDIO-D.R. 1.0" );
                          dcm:00291001  ( 5 5 );
                          dcm:00291002  ( 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 );
                          dcm:00291003  ( "0.5"^^xsd:float )
                        ]
                      );
        dcm:50000005  ( 2 );
        dcm:50000010  ( 3840 );
        dcm:50000020  ( "ECG" );
        dcm:50000030  ( "DPPS" "NONE" );
        dcm:50000103  ( 0 );
        dcm:50000110  ( 0 1 );
        dcm:50000112  ( 0 );
        dcm:50000114  ( 40 );
        dcm:50003000  [ dcm:BulkDataURI  <urn:sha256:ee1fcf71fecb6a8aee3b1219388cc7ded40a804056a7647674ba1a77b797ae8e?offset=0&length=7680>;
                        dcm:vr           "OW"
                      ];
        bib:FileSize  "1702398"^^xsd:int;
        cry:sha256    "ee1fcf71fecb6a8aee3b1219388cc7ded40a804056a7647674ba1a77b797ae8e";
        owl:sameAs    <file:///D:/dicom/sample/0002.DCM> .
@ebremer ebremer added the Turtle FHIR specification Turtle examples label Jul 26, 2024
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ebremer commented Aug 22, 2024 •
edited
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Here is a new version that changes the file name to the SOP Instance UID, and uses 0008,1190 for alternate locations for the SOP Instance (#142). Also changed, that the VR is kept for private (odd) tags (#145)

PREFIX dcm: <https://halcyon.is/dicom/ns/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

<urn:oid:1.3.12.2.1107.5.4.3.321890.19960124.162922.29>
        rdf:type      dcm:SOPInstance;
        dcm:00020001  [ dcm:InlineBinary  "AAE="^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00020002  "1.2.840.10008.5.1.4.1.1.12.1";
        dcm:00020003  "1.3.12.2.1107.5.4.3.321890.19960124.162922.29";
        dcm:00020010  "1.2.840.10008.1.2.4.50";
        dcm:00020012  "999.999";
        dcm:00080008  ( "DERIVED" "PRIMARY" "SINGLE PLANE" "SINGLE A" );
        dcm:00080016  "1.2.840.10008.5.1.4.1.1.12.1";
        dcm:00080018  "1.3.12.2.1107.5.4.3.321890.19960124.162922.29";
        dcm:00080020  "1994-10-13"^^xsd:date;
        dcm:00080030  "14:19:17"^^xsd:time;
        dcm:00080060  "XA";
        dcm:00081190  "file:///D:/dicom/sample/0002.DCM";
        dcm:00082110  "01";
        dcm:00082112  [ dcm:00081150  "1.2.840.10008.5.1.4.1.1.12.1";
                        dcm:00081155  "1.3.12.2.1107.5.4.3.321890.19960124.162922.28"
                      ];
        dcm:00090010  [ dcm:Value  ( "CARDIO-SMS 1.0" );
                        dcm:vr     "LO"
                      ];
        dcm:00091002  [ dcm:InlineBinary  "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"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00091003  [ dcm:InlineBinary  "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"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00091005  [ dcm:InlineBinary  "AAAPAAAAAGAAAAACAAAEsAAAACgAAAAD"^^xsd:base64Binary;
                        dcm:vr            "OB"
                      ];
        dcm:00100010  [ dcm:Alphabetic  "Rubo DEMO" ];
        dcm:00100020  "556342B";
        dcm:00100030  "1995-10-25"^^xsd:date;
        dcm:00100040  "M";
        dcm:00181063  "33"^^xsd:decimal;
        dcm:00181155  "GR";
        dcm:00181510  "-32"^^xsd:decimal;
        dcm:00181511  "2"^^xsd:decimal;
        dcm:00190010  [ dcm:Value  ( "CARDIO-D.R. 1.0" );
                        dcm:vr     "LO"
                      ];
        dcm:00191030  [ dcm:Value  ( "262144"^^xsd:unsignedInt );
                        dcm:vr     "UL"
                      ];
        dcm:0020000D  [ dcm:Value  ( "1.3.12.2.1107.5.4.3.123456789012345.19950922.121803.6" );
                        dcm:vr     "UI"
                      ];
        dcm:0020000E  [ dcm:Value  ( "1.3.12.2.1107.5.4.3.123456789012345.19950922.121803.8" );
                        dcm:vr     "UI"
                      ];
        dcm:00200011  1;
        dcm:00210010  [ dcm:Value  ( "CARDIO-D.R. 1.0" );
                        dcm:vr     "LO"
                      ];
        dcm:00211013  [ dcm:Value  ( 15 );
                        dcm:vr     "IS"
                      ];
        dcm:00280002  1;
        dcm:00280004  "MONOCHROME2";
        dcm:00280008  96;
        dcm:00280009  ( "00181063" );
        dcm:00280010  512;
        dcm:00280011  512;
        dcm:00280100  8;
        dcm:00280101  8;
        dcm:00280102  7;
        dcm:00280103  0;
        dcm:00281040  "LIN";
        dcm:00281090  "NAT";
        dcm:00286040  ( 20 53 77 );
        dcm:00286100  [ dcm:00286101  "NONE";
                        dcm:00286110  ( 0 )
                      ];
        dcm:00290010  [ dcm:Value  ( "CARDIO-D.R. 1.0" );
                        dcm:vr     "LO"
                      ];
        dcm:00291000  [ dcm:Value  ( [ dcm:00290010  [ dcm:Value  ( "CARDIO-D.R. 1.0" );
                                                       dcm:vr     "LO"
                                                     ];
                                       dcm:00291001  [ dcm:Value  ( 5 5 );
                                                       dcm:vr     "US"
                                                     ];
                                       dcm:00291002  [ dcm:Value  ( 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 );
                                                       dcm:vr     "US"
                                                     ];
                                       dcm:00291003  [ dcm:Value  ( "0.5"^^xsd:float );
                                                       dcm:vr     "FL"
                                                     ]
                                     ]
                                   );
                        dcm:vr     "SQ"
                      ];
        dcm:50000005  ( 2 );
        dcm:50000010  ( 3840 );
        dcm:50000020  ( "ECG" );
        dcm:50000030  ( "DPPS" "NONE" );
        dcm:50000103  ( 0 );
        dcm:50000110  ( 0 1 );
        dcm:50000112  ( 0 );
        dcm:50000114  ( 40 );
        dcm:50003000  [ dcm:BulkDataURI  <file:/C:/Users/erich/AppData/Local/Temp/blk8069536285080632981.tmp?offset=0&length=7680>;
                        dcm:vr           "OW"
                      ] .

@dbooth-boston dbooth-boston mentioned this issue Sep 26, 2024
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@dbooth-boston dbooth-boston changed the title Amalgam v1.0 Amalgam v1.0 -- Overall DICOM RDF serialization plan Sep 26, 2024
@dbooth-boston dbooth-boston changed the title Amalgam v1.0 -- Overall DICOM RDF serialization plan DICOM Amalgam v1.0 -- Overall DICOM RDF serialization plan Jan 2, 2025
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