OGSA-WebDB/Repository

Outline †

Web database registration/installation involves difficult tasks such as Web database field mapping and file downloads. This tasks become more difficult for those that are not the creators of Web database wrappers. To alleviate this problem, current release of OGSA-WebDB (version 2.0) provides a fully automatic Web database registration function that uses an installation configuration file written in an XML format. The configuration file includes the following information.

• Web database (search) fields and its proxy relation columns mapping
• The name of an (implemented) wrapper class and its location (for download)
• The location of a wrapper script (in case the wrapper class use it)
• The name of a proxy relation of the newly registered Web database and the logical schema definition
• The URL of the Web database (optional)
• Whether the Web database needs an authentication

Writing a Registration Configuration File †

The easiest way to write a registration configuration file is by updating an existing one. Please find the configuration files below and see comments in the files (especially in dblp-mapping.xml). The configuration file must be based on resource-config.xsd XML schema.

How to Contribute †

If you have wrapper implementations and want to let OGSA-WebDB users use your wrappers, please provide us links of the configuration files or send us all related files including the wrapper implementation class and configuration file. We will place your wrappers in this repository so that users can get benefits from using your wrappers.

Current Available Web Databases †

Note: see the tutorial for easy installation of Web databases using OGSA-WebDB client

Bibliographic Web Databases †

• DBLP (DataBase systems and Logic Programming)
  • Config file: dblp-mapping.xml
  • Wrapper author: OGSA-WebDB team
  • Wrapper implementation: Java & WebL script
  • Description: Provides bibliographic information on major computer science journals and proceedings. The server indexes more than 765000 articles and contains several thousand links to home pages of computer scientists (June 2006).

• CiteSeer
  • Config file: citeseer-mapping.xml
  • Wrapper author: OGSA-WebDB team
  • Wrapper implementation: Java & WebL script
  • Description: It is a scientific literature digital library that aims to improve the dissemination and feedback of scientific literature, and to provide improvements in functionality, usability, availability, cost, comprehensiveness, efficiency, and timeliness. It indexes Postscript and PDF research articles on the Web, and provides many notable features.

• CSB (The Collection of Computer Science Bibliographies)
  • Config file: csb-mapping.xml
  • Wrapper author: OGSA-WebDB team
  • Wrapper implementation: Java & WebL script
  • Description: Contains bibliographies covering most aspects of computer science. The collection currently contains more than 2 millions of references (mostly to journal articles, conference papers and technical reports), clustered in about 1500 bibliographies, and consists of more than 2.3 GBytes (530MB gzipped) of BibTeX entries.

• PubMed (due to substantial changes in PubMed web pages this wrapper currently does not work properly)
  • Config file: pubmed-mapping.xml
  • Wrapper author: OGSA-WebDB team
  • Wrapper implementation: Java & WebL script
  • Description: It is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.

Drug Web Database †

• RxList (The Internet Drug Index)
  • Config file: rxlist-mapping.xml
  • Wrapper author: OGSA-WebDB team
  • Wrapper implementation: Java & WebL script
  • Description: Providing fast, realible information to both the consumer and the medical professional.

Wrappers Developed by Bussiness Search Technology Corp(BST) †

• OMIM
  • Config file: omim-mapping.xml
  • Wrapper author: BST Corp.
  • Wrapper implementation: Java
  • Description: OMIM(Online Mendelian Inheritance in Man) database is a catalog of human genes and genetic disorders.

• JSNPS (A database of Japanese Single Nucleotide Polymorphisms)
  • Config file: jsnps-mapping.xml
  • Wrapper author: BST Corp.
  • Wrapper implementation: Java
  • Description:

• PharmGKB
  • Config file: pharmgkb-mapping.xml
  • Wrapper author: BST Corp.
  • Wrapper implementation: Java
  • Description: PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products.

• PubMed
  • Config file: Wrapper is in Development
  • Wrapper author: BST Corp.
  • Wrapper implementation: Java
  • Description: Yet another Pubmed Wrapper