CaCORE Version 3: Implementation of a Model Driven, Service-oriented Architecture for Semantic Interoperability

Overview

Journal J Biomed Inform

Publisher Elsevier

Specialty Medical Informatics

Date 2007 May 22

PMID 17512259

Citations 41

Authors

George A Komatsoulis

Denise B Warzel

Francis W Hartel

Krishnakant Shanbhag

Ram Chilukuri

Gilberto Fragoso

Sherri de Coronado

Dianne M Reeves

Jillaine B Hadfield

Christophe Ludet

Peter A Covitz

Affiliations

Soon will be listed here.

Abstract

One of the requirements for a federated information system is interoperability, the ability of one computer system to access and use the resources of another system. This feature is particularly important in biomedical research systems, which need to coordinate a variety of disparate types of data. In order to meet this need, the National Cancer Institute Center for Bioinformatics (NCICB) has created the cancer Common Ontologic Representation Environment (caCORE), an interoperability infrastructure based on Model Driven Architecture. The caCORE infrastructure provides a mechanism to create interoperable biomedical information systems. Systems built using the caCORE paradigm address both aspects of interoperability: the ability to access data (syntactic interoperability) and understand the data once retrieved (semantic interoperability). This infrastructure consists of an integrated set of three major components: a controlled terminology service (Enterprise Vocabulary Services), a standards-based metadata repository (the cancer Data Standards Repository) and an information system with an Application Programming Interface (API) based on Domain Model Driven Architecture. This infrastructure is being leveraged to create a Semantic Service-Oriented Architecture (SSOA) for cancer research by the National Cancer Institute's cancer Biomedical Informatics Grid (caBIG).

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References

Kudla K, Rallins M . SNOMED: a controlled vocabulary for computer-based patient records. J AHIMA. 1998; 69(5):40-4; quiz 45-6. View

Tuttle M, Olson N, Erlbaum M, Sherertz D, Lipow S, Cole W . MEME-II supports the cooperative management of terminology. Proc AMIA Annu Fall Symp. 1996; :84-8. PMC: 2233169. View

Fragoso G, de Coronado S, Haber M, Hartel F, Wright L . Overview and utilization of the NCI thesaurus. Comp Funct Genomics. 2008; 5(8):648-54. PMC: 2447470. DOI: 10.1002/cfg.445. View

Bodenreider O, Hayamizu T, Ringwald M, de Coronado S, Zhang S . Of mice and men: aligning mouse and human anatomies. AMIA Annu Symp Proc. 2006; :61-5. PMC: 1560846. View

Saltz J, Oster S, Hastings S, Langella S, Kurc T, Sanchez W . caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics. 2006; 22(15):1910-6. DOI: 10.1093/bioinformatics/btl272. View

Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View

Ceusters W, Smith B, Goldberg L . A terminological and ontological analysis of the NCI Thesaurus. Methods Inf Med. 2005; 44(4):498-507. View

Strausberg R . The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer. J Pathol. 2001; 195(1):31-40. DOI: 10.1002/1096-9896(200109)195:1<31::AID-PATH920>3.0.CO;2-W. View

Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz P . The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services. BMC Med Inform Decis Mak. 2006; 6:2. PMC: 1379637. DOI: 10.1186/1472-6947-6-2. View

10.

Covitz P, Hartel F, Schaefer C, de Coronado S, Fragoso G, Sahni H . caCORE: a common infrastructure for cancer informatics. Bioinformatics. 2003; 19(18):2404-12. DOI: 10.1093/bioinformatics/btg335. View

11.

de Coronado S, Haber M, Sioutos N, Tuttle M, Wright L . NCI Thesaurus: using science-based terminology to integrate cancer research results. Stud Health Technol Inform. 2004; 107(Pt 1):33-7. View

12.

Strausberg R, Greenhut S, Grouse L, Schaefer C, Buetow K . In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol. 2001; 11(11):S66-71. DOI: 10.1016/s0962-8924(01)02104-3. View

13.

Zhang S, Bodenreider O . Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2006; :864-8. PMC: 1560629. View

14.

Buetow K, Klausner R, Fine H, Kaplan R, Singer D, Strausberg R . Cancer Molecular Analysis Project: weaving a rich cancer research tapestry. Cancer Cell. 2002; 1(4):315-8. DOI: 10.1016/s1535-6108(02)00065-x. View

15.

Whetzel P, Parkinson H, Causton H, Fan L, Fostel J, Fragoso G . The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006; 22(7):866-73. DOI: 10.1093/bioinformatics/btl005. View

16.

McDonald C, Huff S, Suico J, Hill G, Leavelle D, Aller R . LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem. 2003; 49(4):624-33. DOI: 10.1373/49.4.624. View

17.

Tuttle M, Sperzel W, Olson N, Erlbaum M, Sherertz D, Nelson S . The homogenization of the Metathesaurus schema and distribution format. Proc Annu Symp Comput Appl Med Care. 1992; :299-303. PMC: 2248004. View

18.

Sioutos N, de Coronado S, Haber M, Hartel F, Shaiu W, Wright L . NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform. 2006; 40(1):30-43. DOI: 10.1016/j.jbi.2006.02.013. View

19.

Hartel F, de Coronado S, Dionne R, Fragoso G, Golbeck J . Modeling a description logic vocabulary for cancer research. J Biomed Inform. 2005; 38(2):114-29. DOI: 10.1016/j.jbi.2004.09.001. View

20.

Wu C, Apweiler R, Bairoch A, Natale D, Barker W, Boeckmann B . The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2005; 34(Database issue):D187-91. PMC: 1347523. DOI: 10.1093/nar/gkj161. View