Healthc Inform Res.  2012 Dec;18(4):272-278. 10.4258/hir.2012.18.4.272.

Development of Korean Rare Disease Knowledge Base

• Seo H
• Kim D
• Chae JH
• Kang HG
• Lim BC
• Cheong HI
• Kim JH

• KMID: 2284562
• DOI: http://doi.org/10.4258/hir.2012.18.4.272

Abstract

OBJECTIVES
Rare disease research requires a broad range of disease-related information for the discovery of causes of genetic disorders that are maladies caused by abnormalities in genes or chromosomes. A rarity in cases makes it difficult for researchers to elucidate definite inception. This knowledge base will be a major resource not only for clinicians, but also for the general public, who are unable to find consistent information on rare diseases in a single location.
METHODS
We design a compact database schema for faster querying; its structure is optimized to store heterogeneous data sources. Then, clinicians at Seoul National University Hospital (SNUH) review and revise those resources. Additionally, we integrated other sources to capture genomic resources and clinical trials in detail on the Korean Rare Disease Knowledge base (KRDK).
RESULTS
As a result, we have developed a Web-based knowledge base, KRDK, suitable for study of Mendelian diseases that commonly occur among Koreans. This knowledge base is comprised of disease summary and review, causal gene list, laboratory and clinic directory, patient registry, and so on. Furthermore, database for analyzing and giving access to human biological information and the clinical trial management system are integrated on KRDK.
CONCLUSIONS
We expect that KRDK, the first rare disease knowledge base in Korea, may contribute to collaborative research and be a reliable reference for application to clinical trials. Additionally, this knowledge base is ready for querying of drug information so that visitors can search a list of rare diseases that is relative to specific drugs. Visitors can have access to KRDK via http://www.snubi.org/software/raredisease/.

Keyword

Rare Diseases; Knowledge Bases; Korean; Genetic Databases; Online Systems

MeSH Terms

Databases, Genetic
Humans
Information Storage and Retrieval
Knowledge Bases
Korea
Online Systems
Rare Diseases

Figure

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  Figure 1 An optimized database schema for Korean Rare Disease Knowledge base (KRDK). Well-structured database keeps data integrity, avoiding data redundancy problem, and appropriately organized data structure helps searching effectively.

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  Figure 2 The search result page of disease and additional information. Summary section shows overall disease information briefly. With clicking gene symbol, it directly connects to Genome Research Information Pipeline (GRIP) for more information that relates to a specific gene such as: protein, protein family, pathway and so on. Moreover, Mendelian Inheritance in Man (MIM) number have hyperlink to online MIM (OMIM) so that user may browse on Website instantly.

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  Figure 3 An example of laboratory and clinic directory pages. Search result for laboratory and clinic directory pages. (A) All laboratories are list with available testing method with target gene. Additionally, by clicking laboratory name, visitors may get its information in detail such location, contact. (B) Clinic directory shows a name of practitioner that is a specialist of a specific disease and other information like clinic name and contact.

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  Figure 4 The summary of patient's registry and its original Web page link. Patient's registry shows a summary of records due to privacy policy. Summary is comprised of the number of registered patient and gene, director, contact, references and so on. Additionally, patient's registry URL directly links and visitors can fully have access to permission from Research Center for Rare Diseases (RCRD).

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  Figure 5 Drug information that is highly connected to rare disease and genetic information database. We are ready for storing drug information on Korean Rare Disease Knowledge base (KRDK). Drugs are highly connected to target genes and specific diseases. With this relationship, physician can perform several possible queries; What are drugs relative to Wilson disease? What target genes do Penicillamine have? What are genes that affect Wilson disease? By answering those queries, clinician can analyze research efficiently with this integrative database scheme.

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