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National Cancer Imaging Archive (NCIA) DICOM Object Model Changes

National Cancer Imaging Archive (NCIA) DICOM Object Model Changes. https://imaging.nci.nih.gov NCIA Interim Report Review Team NCICB CDE Curator: Dianne Reeves, Janice Chilli VCDE Mentor: Stuart Turner NCIA: Jennifer Zeng, Larry Holeman. NCIA response to workspace comments.

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National Cancer Imaging Archive (NCIA) DICOM Object Model Changes

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  1. National Cancer Imaging Archive (NCIA) DICOM Object Model Changes https://imaging.nci.nih.gov NCIA Interim Report Review Team NCICB CDE Curator: Dianne Reeves, Janice Chilli VCDE Mentor: Stuart Turner NCIA: Jennifer Zeng, Larry Holeman

  2. NCIA response to workspace comments • Present NCIA response to IVI workspace comments • General Comments • NCIA Object Model Changes - Specific Class/Attribute changes • Proposed New Class – PatientStudy • Use of Alternate Names and Definitions in NCIA • Issues Bigger than NCIA • Next Steps

  3. Motivation behind NCIA Object Model Changes • Current NCIA Object model tightly adheres to DICOM. • DICOM is an external standard in imaging community. • DICOM has not been reviewed under caBIG process. • Many of the attributes, concepts, and definitions based on DICOM do not meet caBIG criteria, as stated in the March 2008 NCIA Silver Interim Review. • Complete NCIA Silver Review Interim Report document • https://gforge.nci.nih.gov/frs/download.php/3500/VCDE_SilverLevelReview_NCIA_InterimReport_Jan2008_v1.0.doc • NCIA Silver Review Interim Report presentation, Architecture Workspace • https://gforge.nci.nih.gov/frs/download.php/3296/NCIA_Silver_Level_Architecture_Review_20080125.ppt • NCIA Silver Review Interim Report presentation, VCDE Workspace • https://gforge.nci.nih.gov/frs/download.php/3167/NCIA_VCDE_SilverLevelReview_InterimReport_Jan2008_Turner.pdf • Imaging workspace and CBIIT leadership got involved to resolve issues…

  4. Decisions made by Imaging Workspace & CBIIT Leadership NCIA DICOM Object Model Resolution Meeting, May 30th 2008 • Attendees: Eliot Siegel, Paul Mulhern, Frank Hartel, Brian Davis, George Komatsoulis, Michael Keller, Carl Blake, Janice Chilli • DICOM should be for syntactic and structural purposes only • Not for semantic annotations • DICOM is not automatically to be used as a vocabulary for annotating • Furthermore, we can only use DICOM for the vocabulary and definitions when there is no ambiguity. • Many of the attributes in the DICOM IE's are not clear and do not meet caBIG standards for semantic interoperability. The corresponding properties in the NCIA model will be changed accordingly.

  5. General Comments from Workspace Review • Workspace Comments received from: • Tony Pan/Ohio State/Middleware, • Pat Mongkolwat/Northwestern/AIM, • Janice Chilli/NCI Curation Support • General Comments • Different attributes in AIM and Middleware • Changing the attribute names is not a big deal as the middleware can map model attributes to and from DICOM fields (TP/OSU) • Attribute names changes is also not a big deal for NCIA. • Concur. Proposed changes in attribute names to comply with caBIG and improve the underlying semantics which will improve searching on the grid.

  6. General Comments from Workspace Review General Comments continued: Current model remains CT centric Tony Pan/Middleware: Image class has CT specific attributes and therefore is difficult to extend. I would suggest that we make the model more modular, possibly following how DICOM groups attributes into modules, to allow for extensibility. During July 2007 review, it was determined to roll up all image attributes into a single image class. The workspace was to identify which attributes were modality specific and new child classes would then be created. NCIA concur. Future expansion of NCIA to address modality specific attributes Intent is to expand the model to support modality specific attributes when data is added to the NCIA database using the modality specific modules defined in the DICOM. Image class would contain common attributes. NCIA needs workspace to help identify which attributes are generic to all images and which attributes should be moved to a child class, such as CTImage, MRIImage, etc.

  7. NCIA Object Model Changes – Clinical Trial • Classes: ClinicalTrialSponsor, ClinicalTrialProtocol, ClinicalTrialSubject • Not currently used by NCIA application. No data in the database. • Will the proposed Clinical Trial Tools Integration (CTTI) project need them? • Are there any imaging use cases which utilize these classes/attributes?

  8. NCIA Object Model Changes – Image Class • Proposed Modeling Best Practice changes: • Remove the word image from imageComments, imageSize, imageLaterality, imageOrientationPatient, imagePositionPatient, and imageType • Add distinguishable definitions for acquisitionDate, acquisitionDateTime, acquisitionTime, and contentDate. • Modify DICOM attribute name for acquisitionDate to acquisitionStartDate. • Modify DICOM attribute name for columns to columnCount. • Modify DICOM attribute name for rows to rowCount. • Workspace feedback • Can we define “unpaired” in the value domain of imageLaterality to be “not matched by a corresponding part on the opposite side”? • Vote: Does the workspace agree with these changes?

  9. NCIA Object Model Changes – Series, Equipment and Data Provenance • Class: Series • Remove the word series from seriesDate, seriesDescription, seriesInstanceUID, and seriesNumber • Rename seriesDate to startDate • The definition for startDate will be modified to explain that it is the “start” of the series date. This attribute would become: Series:startDate • Need the workspace to provide a definition for the DICOM attribute SynchronizationFrameOfReferenceUID. • Is there a need for Frame of Reference ID to be in a separate class? • Class: TrialDataProvenance • Rename to DataCollectionProvenance to better capture the class content; content is related to data collection and not to a clinical trial. • Class does persist in the current model; it may be removed in a future release. • Class: Equipment • Rename softwareVersions to softwareVersion • Vote: Does the workspace agree with these changes?

  10. NCIA Object Model Changes - Study • Class: Study • Remove the word study from studyDate, studyDescription, studyId, and studyInstanceUID. • Rename patientSize to patientLength and clarify the definition. • Rename studyTime to startTime and clarify the definition. • Rename studyDate to startDate and clarify the definition. • The definition for admittingDiagnosisCodeSequence will note that the data is an unordered list. • Clarify the definition for additionalPatientHistory; issue is that there is no patientHistory attribute in DICOM or NCIA model. • Need workspace to provide better definition. • Is there a better name for this attribute? • Do we need to capture if this is patient or radiologist provided information? • Vote: Does the workspace agree with these changes?

  11. NCIA Object Model Changes – Patient Study Proposed Class: PatientStudy Proposed definition: Information about the Patient at the time the study was performed. (DICOM PS 3.3-2008)

  12. NCIA Object Model Changes – Patient Study • Current Model • Proposed Model

  13. NCIA Object Model Changes – Patient Study Class: PatientStudy Move patient attributes from Study class: Remove “patient” from patientOccupation, patientAge, patientWeight, etc. Attributes that are particular to a patient at the time of study will be moved into a new class, PatientStudy, a subclass of the DICOM Study class. We will specifically treat it as a collection of “Time Varying” patient attributes. Question to the Workspace: Is it a one-to-one relationship between PatientStudy and Study classes? Vote: Does the workspace agree with these changes?

  14. Use of Alternate Names and Definitions in NCIA model and DICOM CDE example

  15. Use of Alternate Names and Definitions in NCIA model and DICOM CDE example • Alternate Names: • DICOM tags; for example (0008,0060) • DICOM Attribute Name. If the DICOM Attribute Name needs to be changed to capture semantics included in the definition but not currently in the attribute name, then the DICOM Attribute Name will be preserved as a CDE alternate name. • Alternate Definitions: • Model definition is captured as an alternate definition if the model attribute is annotated with an existing CDE. • If the DICOM Definition needs to be changed, then the DICOM definition will be retained as an alternate definition in the CDE. • When changes are made to the DICOM attribute name and/or definition, they will be submitted to David Clunie as a change request to the DICOM committee.

  16. Issues Bigger than NCIA • Multiple “id” attribute presents in all classes • Three “id” use cases found in NCIA attributes are: • Class.id is an unique id as grid identifier  Class. caGridId • Class.*Id  Class.id • Class.*InstanceUID  Class.instanceUID • Workspace to develop a common naming convention and definition for grid ids used all in imaging application (use case 1); • DICOM definition to be used for ids in use cases 2 & 3. • The IDs in following classes are involved: • Patient.id, Patient.patientId • Study.id, Study.studyId, Study.studyInstanceUID • Series.id, Series.seriesInstanceUID • Image.id, Image.sopInstanceUID • ClinicalTrialSite.id, ClinicalTrialSite.siteId • ClinicalTrialSubject.id, ClinicalTrialSubject.subjectId • ClinicalTrialProtocal.id, ClinicalTialProtocol.protocolId

  17. Issues Bigger than NCIA Cases where the DICOM attribute name does not fully describe the data attribute definition. EXAMPLE: The definition of DICOM attribute acquisitionDate is “the date the acquisition of data that resulted in this image started”. Can we add “start” to the attribute name and the semantics? Can we change the attribute name to acquisitionStartDate? caGRID Date, Time, DateTime definition differs from DICOM value representation (VR) types. Should a date or date/time datatype be used to improve query across the grid? NCIA object model currently uses a “date” type, not DICOM VD character type. DICOM “date” is 8 bytes fixed defined as “A string of characters of the format yyyymmdd.“ DICOM “datetime” VR is a 26 bytes maximum value defined as “A concatenated date-time character string in the format:YYYYMMDDHHMMSS.FFFFFF&ZZXX” DICOM “time” VR is a 16 byte value defined as “A string of characters of the format HHMMSS.FFFFFF.“

  18. Issues Bigger than NCIA • Inherent redundancy in DICOM attributes • There is inherent redundancy in the concept of date in Image.acquisitionDate, Image.acquisitionTime and Image.acquisitionDatetime. Will it create query problems on the grid? • There is currently no submitted data for the datatime attribute. Recommend deleting datatime attribute and keeping the date and time attributes for which there is data in the NCIA database.

  19. Next Steps • NCIA team to implement changes approved by the workspace today. • NCIA team and VCDE Silver Compatibility Review team to prepare a consolidated change request for submission to DICOM committee. • All IVI imaging applications and models going through a Silver Review can benefit from these NCIA lessons learned.

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