1. MMHCC Informatics Providing Innovative and Integrative Informatics Solutions Johnita Beasley (SAIC) Dana Zhang (SAIC) Sharon Settnek (SAIC)

2. 2 Cancer Models Database (caMDB) The Cancer Models Database allows both intramural and extramural researchers to search and submit mouse models –All models submitted by extramural researchers are curated to ensure data integrity

3. 3 Model Search A simple search is available to allow researchers to search by model name, tumor, organ system, tissue, or species An advanced search includes genetic descriptions, carcinogenic agents, the model phenotype, cell lines, and therapeutic approaches

4. 4 Search Results Model search results are displayed in table format –Model details can be displayed by selecting the model descriptor link –Specific Model components can be viewed by selecting each component Tab

5. 5 Image Constructs Search results include any associated image constructs and annotations –Full image views with zoom and pan capabilities are available

6. 6 Model Submission Users can submit new models via the Add new model link Users can edit previously submitted models by selecting the model descriptor Users can clone or delete a model that they previously submitted

7. 7 Model Components Submitting a new model involves entering model information including: –General Information –Genetic Descriptions –Carcinogenic Agents –Publications –Histopathology –Therapeutic Approaches –Cell Lines –Images –Microarray Data Required fields appear in bold red text Data is saved throughout the submission process

8. 8 Model Curation The Cancer Models review process is automated in the CMD Admin Function –A model coordinator assigns users to review specific models –Reviewers inform the coordinator of any recommendations and modify the status of the model –The coordinator contacts the model originator concerning any modifications

9. 9 New Features In recent months we’ve added or enhanced several caMDB features to include: –Updating the delete and clone capabilities. –Adding the Model Vocabulary –Adding the ability to interface with the GEDP –Adding the Comment capability To stay abreast of all new features, visit our “What’s New” link on the caMDB home page.

10. 10 Model Vocabulary The Enterprise Vocabulary System (EVS) is a set of services and resources that address NCI’s needs for controlled vocabulary The CMD utilizes EVS to access controlled vocabulary –Organ/Tissue –Diagnosis

11. 11 GEDP Interface User’s can now connect to the Gene Expression Data Portal (GEDP) to submit Microarray Data they’d like to be associated with a model.

12. 12 Comments This newly added feature will allow users of the database to comment on models and to enter additional data to models previously entered by other labs.

13. 13 caMDB Object Model The caMDB object model is represented with Unified Modeling Language (UML). The object model evolved through a use-case driven, architecture-centric, iterative, and incremental process. The object model establishes a standard set of genomic components related to an animal model. The object model is extensible and employs reuse (i.e. the caBIO API is used to provide access to other data sources).

14. 14 caMDB Object Model

15. 15 caMDB API The caMDB API provides a means of accessing animal model data submitted via the Cancer Models Database (caMDB) application. The API is based on the caMDB Object Model The caMDB objects, through their relationships, simulate the behaviors of an animal model. The model components include: –Cell Lines –Histopathologies –Images –Genetic Descriptions (Transgenes, Genomic Segments, Targeted Modifications, and Induced Mutations) –CarcinogenicInterventions –Theraputic Approaches –Microarray Data –Publications

16. 16 caMDB API The caMDB objects can simulate the behavior of actual genomic components, link to an animal model, such as genes, organs, diseases, etc. by accessing other genomic data sources like: - caBIO - Enterprise Vocabulary Services (EVS)

17. 17 caMDB API Architecture External Java Apps ClientsPresentation LayerObject Layer Data Sources Browsers Other Apps HTML /HTTP XML/ HTTP Internal Java Apps Web Server Servlet Container JSPs Servlets UI Bean XML Builder XSLT Engine SOAP Engine XML Docs DTDs XSL Style Sheet RMI URLs Flat Files Databases Histopathologies Phenotypes Publications CellLines InducedMutations Object Managers JDBC HTTP FTP SOAP Data Access Objects Transgenes Therapies Other Domain Objects

18. 18 caMDB API Architecture The caMDB API models the n-tiered architecture of caBIO with client interfaces, server components, back- end objects and data sources Clients (browsers, applications) can receive information (HTML and XML) from back-end objects over HTTP –Client applications can also communicate with back- end objects via Java RMI (Java applications) –Non-Java based applications will communicate via SOAP Server components communicate with back-end objects via Java RMI Back-end objects communicate directly with data sources (database, URLs, flat files)

19. 19 Image Portal The NCICB has developed an image portal to allow researchers to search and submit rodent and human images with annotations

20. 20 Image Portal Image annotations may include a detailed description, species, organ, diagnosis, strain, and image dimensions

21. 21 Imaging Technologies The NCICB is investigating imaging technologies to facilitate efficient image retrieval and annotation integration Imaging technologies include JPEG 2000, DICOM 3, and Image Content Servers –JPEG 2000 is a standard currently under development that defines a set of lossless (bit-preserving) and lossy compression methods for coding continuous-tone, bi-level, gray-scale, or color digital still images –DICOM 3 (Digital Imaging and Communications in Medicine) is the industry standard for the transferal of radiology images and other medical information between computers DICOM- SR (Structured Reporting) is a UML and XML representation of the DICOM specification –Image Content Servers provide a mechanism to speed image transmission and improve image quality NCICB is exploring interfacing with the MIRC Project (RSNA)

22. 22 Image Annotation Standards To facilitate image sharing, a “minimal” set of image annotations are necessary Image annotations should leverage existing standards and may be derived from use cases for image retrieval and analysis Annotations should include parent-child relationships

23. 23 Image Object Model

24. 24 caIMAGE Architecture Browser Client caIMAGE Web Application Server LizardTech Image Content Server Network File System CaIMAGE Database Lizard Image Converter Images Image Annotations Images Sid Files Images

25. 25 MMHCC Links EMICE Website http://emice.nci.nih.gov Cancer Models Database (caMDB) http://cancermodels.nci.nih.gov Cancer Image Portal (caImage) http://cancerimages.nci.nih.gov caMDB API (including JavaDocs and Object Model) http://emice.nci.nih.gov/MMHCC/mmhcc_organization/members/bioinformatics