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Cutting-Edge Web Wrapper Technology for Bioinformatics: Enabling Resource Detection and Automated Search

Explore how web wrappers automate input queries for bioinformatics searching, extract data, and offer practical solutions. Improve accuracy and efficiency in nucleotide sequence searches across diverse interfaces.

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Cutting-Edge Web Wrapper Technology for Bioinformatics: Enabling Resource Detection and Automated Search

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  1. Automatic Resource Detection Enabling Wrappers to Crawl the Web for Bioinformatics Searching Sites

  2. Wrapper Technology • As the Web grows, and forms become more prevalent, inputting queries in each site becomes too time consuming • Wrappers can crawl the Web for forms that require particular kinds of queries (i.e. nucleotide sequences), and automatically test each for function. • XML is most often used today, along with Java.

  3. Practicality of Wrappers • Many can be automatically generated once type of website has been detected • Extraction of data can also be automated and dumped into a database or given to a human for curation of results • As a technology that has been around for at least 6 years, Web wrappers are well-established ways of reconciling different parts of the Web (ShopBot)

  4. Example of BLAST • 160 different interfaces available for searching BLAST with different availability of options for each one • Wrapper can automatically search across all of these and identify that they are potential nucleotide sequence searchers • For those that have no intermediation or unruly processing, queries can be automated through the wrapper.

  5. Possible Applications of This • With so many different interfaces and more being formed every day, this is a way of controlling for possible errors introduced into some of these search engines. • If the results can be automatically compared for content (i.e. run a meta-BLAST search), then any outliers can be excluded and the most probable list presented.

  6. Interesting Current Applications • DiscoveryLink • Dbget • Biokleisli – can anyone find this? It’s referenced, but apparently is only a paper on Citeseer.

  7. Final Results of the Wrapper • 2/3rds of all resources were correctly identified as capable of BLAST nucleotide searches. • While a greater number would be desirable, this would all analysis across different search interfaces to determine ranking and function

  8. Another Possible Application • Ranking and function is another possible use of this wrapper. • Once the meta-BLAST search has been completed, the individual results could be compared to the meta-search to gain an idea of how accurate or in-depth each search is. • A tentative ranking scheme could be computed from this data for future searches.

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