1. VCDE Silver Level Compatibility Review Digital Model Repository (DMR) 1.0 Mukesh Sharma VCDE WS Teleconference 01/08/2009

2. Agenda Review Team DMR Overview Summary of Review Review Process Vote

3. Review Team VCDE Mukesh Sharma (review lead) Mary J. Cooper Shantanu Deshpande Grace Stafford Baris Suzek (guide to mentor) Brian Davis (VCDE WS lead) Architecture Jyotishman Pathak Mike Keller (ARCH WS lead)

4. Digital Model Repository (DMR) Introduction To share tools and data throughout the nine Integrative Cancer Biology Program (ICBP) Centers, the ICBP relies on access to and integration/usage of relevant in vitro, in vivo and in silico tumor biology data from disparate sources. Usage includes storage, search and retrieval of heterogeneous data formats and qualities. A semantically enabled, preferably web-accessible knowledge warehouse platform is required - a platform that allows for data upload - and download to enable community-wide collaborations. Such a platform can be best described as a “semantic digital model repository”. This “semantic digital model repository” must prove its value for the community in a set of use cases that include a range of likely scenarios, such as data sharing, simulation-related workflow designs, and related aspects, such as parallelization, multi-resolution modeling and visualization. From DMR presentation from review submission package

5. Digital Model Repository (DMR) Objective The project aims to develop and deploy a semantic Digital Model Repository (DMR) and to achieve caBIG silver level compliance. This web- based digital repository is being designed for the purpose of archiving, retrieving and exchanging cancer modeling modules and the data that link to it. From DMR presentation from review submission package

6. Digital Model Repository (DMR) Development Team Thomas J. Taylor, Ray Bradley and Patrick Shironoshita INFOTECH Soft Inc. Jonathan Sagotsky, Zhihui Wang, Le Zhang, David Huynh and Thomas S. Deisboeck Complex Biosystems Modeling Laboratory Harvard-MIT (HST) Athinoula A. Martinos Center Massachusetts General Hospital

7. Summary of the Review The VCDE compatibility review team recommends “Digital Model repository (DMR) 1.0 information model and its associated metadata are meeting VCDE Silver Level Compatibility requirements” The notations in the main review document are highlighted to indicate degree of compliance: Red: Unresolved. Issues graded “absolute” that should be corrected Yellow: Points of concern. Issues graded “suggested” that should be corrected in the next phase of development The review team requests written responses to all issues categorized as either red or yellow VCDE and Architecture review was performed.

8. Project Metrics 16 Classes 90 Common Data Elements 1 Enumerated Value Domain

9. Review Process Pre-kickoff meeting- 10/15/2008 Kick off meeting- 11/06/2008 Interim review did not identify any “red flag” issues– 11/06/2008 Final review found no “red flag” issues – 12/15/2008 Review results presented to developers – 12/19/2008 Developers responded- 12/22/2008

10. Review Results Compatibility Review System (CRS) version 2.0 used Checklist used: https://gforge.nci.nih.gov/docman/view.php/233/12435/Silver- Checklist_VCDE_3.102.xlshttps://gforge.nci.nih.gov/docman/view.php/233/12435/Silver- Checklist_VCDE_3.102.xls Suggested criteria violations identified: Compatibility Guidelines QuoteOriginal PhrasingUpdated Meaning IM12 a. Use Package, Class and Attribute names that convey meaning clearly (definitions) (Concept Mapping for definitions should be clear to reviewer) This item is NOT about re-usability (see below). The names given to packages, classes, and attributes should accurately convey their meaning (as determined by the UML definition). In other words, the name should be consistent with the definition. CDE16 Reuse of existing validated CDEs in the caDSR must be considered before any new data elements are created. Existing CDEs are reused (the public ID of a reused CDE is recorded in the metadata). Existing CDEs are reused wherever possible before new CDEs are created.

11. Review Results CRS version 2.0 used Yellow flag criteria violations identified: Class: Algorithm, Attribute: source CDE:Algorithm Information Resource Uniform Resource Locator java.lang.String; 2787146 v1.0 Recommended - The two concepts mapped to this attribute are Information Resource URL. Perhaps instead of source, this attribute should be resourceURL or resourceURI. Silver Checklist item:IM12; suggested Class: DataClassification Recommended- Definition of Class is “Data files can be included in an entry by way of upload, http reference, or internal repository reference.” This sounds like categories as opposed to classification. Silver Checklist item:IM12; suggested

12. Review Results Class: Reference, Attribute: description CDE: Reference Description java.lang.String; 2787098 v1.0 Recommended - As modeled, there does not appear to be a reusable CDE; Reviewer’s suggestion: If the class "Scientific Publication" was reused, CDE Scientific Publication Description java.lang.String (2771618) could be reused. Class: Reference, Attribute: id CDE: Reference Identifier java.lang.String; 2787097 v1.0 Recommended - As modeled, there does not appear to be a reusable CDE; Reviewer’s suggestion: If the class "Source Reference" was reused, this attribute could reuse CDE Source Reference Identifier java.lang.Long (ID2228416). Or, if the class "Scientific Publication" was reused, CDE Scientific Publication Identifier java.lang.Long (2224323) could be reused. Note: Reviewer has comments for the class "reference", but also suggests that changing the DMR model vis a vis References would better await the effort with the Integrative Cancer Research Work Space to develop a Domain Analysis Model.

13. Developer Response to Review Developers responded all “yellow flag” issues and agreed to resolve them in DMR 2.0

14. Review Documents Original Submission Package: https://gforge.nci.nih.gov/frs/download.php/4913/MGH_DMR- SilverCompatibilitySubmission-1.0.2.ziphttps://gforge.nci.nih.gov/frs/download.php/4913/MGH_DMR- SilverCompatibilitySubmission-1.0.2.zip Final Review Reports: https://gforge.nci.nih.gov/frs/download.php/5669/DMR-ARCH-Final- Review.ziphttps://gforge.nci.nih.gov/frs/download.php/5669/DMR-ARCH-Final- Review.zip https://gforge.nci.nih.gov/frs/download.php/5682/DMR_VCDE_Report.rtf

15. Acknowledgements Review Team Mukesh Sharma (review lead) Mary J. Cooper Shantanu Deshpande Grace Stafford Baris Suzek (guide to mentor) VCDE WS Brian Davis Developer Team Jonathan Sagotsky, Zhihui Wang, Le Zhang, David Huynh Thomas S. Deisboeck Thomas J. Taylor Ray Bradley Patrick Shironoshita

16. Vote “Digital Model Repository (DMR) information model and its associated metadata are meeting VCDE Silver Level Compatibility requirements”