August 24-25, 2006, Cologne, Germany
| International HL7 Interoperability Conference IHIC 2006
August 24-25, 2006, Cologne, Germany |
|
||
To the IHIC 2006 conference program committee
Email: junnaka@med.kobe-u.ac.jp
Jun Nakaya,
Clinical Genome Informatics Center, Graduate School of Medicine, Kobe University,
Kusunokicho 7-5-2, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
Tel: +81-78-382-6559, FAX: +81-78-512-1612
email: junnaka@med.kobe-u.ac.jp
Kaei Hiroi (Kobe University), Keisuke Ido (Kobe University), Woosung Yang (Kobe University), Michio Kimura (Hamamatsu Medical SChool)
Jun Nakaya has received the B.S. and M.S. degrees in Mech. Eng. from Hokkaido Univ. in 1985 and 1987, respectively. After staying in IBM as a Systems Engineer until 1989, he received M.D. and Ph.D. degrees from graduate school of medicine, Hokkaido Univ. in 1995 and 1999, respectively. He stayed in M.I.T. Sloan School as a senior executive student, Institute of Medical Science, Univ. of Tokyo as a senior researcher, and Tokyo Medical and Dental Univ. as an associate professor. Now he is a Professor of Clinical Genome Informatics Center, graduate school of medicine, Kobe Univ.. He is a member of ISO, HL7, AMIA, ISMH, MIT-J, SSJ, and MSJ.
The Genomic Sequence Variation Markup Language (GSVML) and its Interface to the HL7 Information Models
research
research: short
The development of the data exchanging format for the genomic sequence variation data exchanging with focusing on human health application including researches is the demand. The GSVML with the interface to the HL7 information models was developed through eight steps having the use case analysis and the domain investigations. The GSVML is human health oriented and has three categories as variation data, direct annotation, and indirect annotation. The GSVML having HL7 interface has an ability to enhance the genomic sequence variation data utilization internationally by providing a standardized platform for both clinical and research applications.
Objective: Internationally accumulated genomic sequence variation data needs the development and the standardization of the interoperable data exchanging format without forcing to change any existing database schema. This demands are typical in the human health application domain such as the gene based medicine or the pharmacogenomics.
Design and Method: We developed the GSVML with considering on the interface to the HL7 Information Models. The development was through eight steps having the use case analysis and the domain investigations. Initially we intended to follow and to satisfy the requirements derived from the use case analysis of human based clinical genomic applications. By focusing on the design scope to human health application and genomic sequence variation, we eliminated the ambiguity and gave the practicability. Through the database investigations, we minimized the redundancy of the data format with maximizing the data covering range. We designed GSVML to have communication ability and interface ability to the Health Level Seven Information Models and the other markup languages with intention to exchange various omics data among different kinds of omics researchers or facilities.
Results: The Genomic Sequence Variation Markup Language (GSVML) and its interface to HL7 Information Models were developed. The GSVML is designed as human health oriented and has three categories as variation data, direct annotation, and indirect annotation. The variation data category is the required category, while the direct annotation category and the indirect annotation category are optional. The annotation categories contain the omics information, clinical information, and internal relations. Six use cases and three criteria in human health application were examined. Eleven data elements and three criteria are examined as the data format for genomic sequence variation data exchange. The data format of five international SNP databases and six markup languages were investigated. An interface to HL7 Genotype Information Models was designed and its interface ability to Health Level Seven Information Models was investigated in terms of 317 items.
Conclusion: The development of the data exchanging format for the genomic sequence variation data exchanging with focusing on human health application including researches is the demand. The international standardization of the GSVML and the development of its interface to the HL7 Information Models are the just answer for this demand and is in progress. The GSVML having HL7 Interface has an ability to enhance the genomic sequence variation data utilization internationally by providing a standardized platform for both clinical and research applications.