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Method of accessing PubMed MEDLINE data from IBM DB2 UDB Using a DiscoveryLink Wrapper Disclosure Number: IPCOM000016146D
Original Publication Date: 2002-Nov-09
Included in the Prior Art Database: 2003-Jun-21
Document File: 2 page(s) / 74K

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  Method of accessing PubMed MEDLINE data from IBM DB2 UDB Using a DiscoveryLink Wrapper


     Disclosed is a solution to access and integrate data into RDBMS from web based databases, using a federated system. The solution covers web based databases having the following characteristics.

They are accessible via Internet using an URL and have one or more predefined native formats for data representation. They are large in size and frequently updated, so that, downloading the data is not feasible.

Data source and RDBMS

     1One such database with the above mentioned characteristics is PubMed (a service of National 1Library of Medicine). PubMed represents it's data in several native formats including MEDLINE. The 2solution uses IBM DiscoveryLink, a federated system, which is an IBM offering that uses IBM DB2 UDB to provide integrated access to data sources used in the life sciences industry. The solution is implemented as a wrapper in IBM DiscoveryLink which is dynamically integrated to IBM DB2 UDB.

Existing access methods of PubMed

     1The existing method of accessing data from PubMed is via NCBI Entrez Retrieval system. Users can access PubMed using web browser and make use of various Entrez utilities to query the data source by

Providing key words for search criteria. Formulating an URL string corresponding to the query and executing the query by accessing the URL using a web browser.

Problems with the existing access methods

Data Integration: They do not provide the capability for merging and analyzing large sets of diverse data residing in data sources external to NCBI.

Scalability: When an user designs an application to access PubMed and other related data sources, it would be difficult to scale this application to add new data sources.

Usability: User should be skilled in Entrez retrieval system and the querying methods provided by the same.

Advantages of the solution

Data Integration: User can integrate the PubMed data with data from other RDBMS and non-RDBMS data sources participating in the IBM DB2 UDB federated database system. This would help the user greatly to compare and analyze data from these diverse data sources. Scalability: Scalability is handled by IBM DiscoveryLink as the solution forms a part of it....