1. caCORE Software Development Kit George Komatsoulis 25-Feb-2005

2. caCORE SDK Project Team  Development – Sasikumar Thangaraj 1 – Michael Connolly 1 – Joshua Phillips 1 – Jennifer Zeng 1 – Sailaja Mashetty 1 – Shaziya Mushin 1 – Aruna Tibriwal 1 – Ye Wu 1 – Ying Long 1 – Andrew Shinohara 1 – Ram Chilukuri 2 – Christopher Ludet 2 – Gilberto Fragoso 3 1 Science Application International Corp (SAIC) 2 Oracle Corp 3 NCICB  Guide – Sasikumar Thangaraj 1 – Michael Connolly 1 – Elizabeth Lucchesi 1 – Joshua Phillips 1 – Jill Hadfield 3 – Denise Warzel 3 – Ram Chilukuri 2 – Krishnakant Shanbhag 3 – George Komatsoulis 3  Program Management – Tara Akhavan 1 – George Komatsoulis 3 – Denise Warzel 3 – Frank Hartel 3 – Krishnakant Shanbhag 3 – Peter Covitz 3

3. caCORE and the SDK  caCORE is designed around 4 principles: – Model Driven Architecture – Open APIs – Use of controlled vocabularies – Registered metadata  Systems that utilize these criteria are said to be ‘caCORE-like’  These principles correspond to the caBIG ‘Silver’ compatibility level.  The caCORE SDK is designed to allow a moderately experienced Java programmer to create a ‘Silver’ compatible software system.  Although helpful, UML Modeling experience is not required to use the toolkit.

4. What is (semantic) metadata Class or Attribute Name ValueNCI MetadataCIA Metadata AgentA chemical compound administered to a human being to treat an existing disease or condition, or prevent the onset of a disease or condition A sworn intelligence agent; a spy nSCNumber007Identifier given to a chemical compound by the US Food and Drug Administration (FDA) Nomenclature Standards Committee (NSC) Identifier given to an intelligence agent by the National Security Council nameTaxolName of a chemical compound given by the NCI Cancer Therapeutics Evaluation Program (CTEP) Code name given to intelligence agents by the Central Intelligence Agency (CIA)

5. Components of the toolkit  UML Modeling Tool – Not supplied as part of the toolkit – We use Enterprise Architect (EA) at NCICB, but any modeling tool that supports XMI 1.3 will work (see the Developer’s Guide for details).  Semantic Connector – Assists with the semantic integration component by searching for concepts and annotating the XMI representation of a UML model. – Distributed with the toolkit, but will not be fully functional until the release of caCORE 3.0 in March. Until then, NCICB will run the semantic connector for groups with properly annotated UML models.  UML Loader – Takes the semantically annotated XMI file and loads it into the caDSR. – The UML loader is not included in this distribution; for now, all UML loading will be done at NCICB.  Code Generator – Input is an XMI representation of a UML model – Creates the ‘caCORE-like’ software system. – Distributed with the toolkit, fully functional.

7. Semantic Integration  UML Class = ISO Object Class – Example: Agent – ISO Object Classes are mapped to 1 or more concepts from EVS  UML Class Attribute = ISO Property – Example: nSCNumber – ISO Properties are mapped to 1 or more concepts from EVS  UML Class + UML Class Attribute = ISO Data Element Concept – Agent:nSCNumber – ISO DEC’s are mapped to 2 or more concepts (from OC + Property)  UML (Java) Datatype = ISO Value Domain (at least initially) – Example: java.lang.Integer – Enumerated value domains curated after initial UML loading  UML Class + UML Class Attribute + Datatype/Valid Values = ISO Common Data Element – Example: Agent:nSCNumber: java.lang.Integer Object Agent Property NSCNumber Data Element Concept Agent NSCNumber Data Element Agent NSCNumber Value Domain java.lang.Integer Representa tion Code Valid Values (where relevant)

8. Semantic Integration (II)  Some Concepts: – C1708: An active power or cause (as principle, substance, physical or biological factor, etc.) that produces a specific effect. – C41243: A unique drug identifier issued by the Nomenclature Standards Committee of the U.S. Food and Drug Administration. – C99999: A spy – C99998: Identification Number given to a spy by the National Security Agency  Some Applications: – A: caBIO: Agent.nSCNumber Agent = C1708 nSCNumber = C41243 Value Domain = java.lang.Integer – B: Another application: Drug.nomenclatureStandardsCommitteeCode Drug = C1708 nomenclatureStandardsCommitteeCode = C41243 Value Domain = java.lang.Integer – C: CIA Agent Information System: Agent:nSCNumber Agent = C99999 nSCNumber = C99998 Value Domain = java.lang.String  Semantic Integration is based on concept codes, not name.

9. UML loaded CDEs are self-harmonizing  At loading time, the UML loader searches for other CDEs that are described by the same set of concept codes.  If a matching CDE is found, the loader ‘designates’ the existing CDE, and puts the existing CDE into an additional classification scheme corresponding to the new project.  New versions of a software project work in a similar fashion, ‘designating’ existing CDEs where relevant and placing the CDE in an additional classification scheme.

10. http://ncicb.nci.nih.gov/core/SDK