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Related Experiment Videos

Text processing through Web services: calling Whatizit.

Dietrich Rebholz-Schuhmann1, Miguel Arregui, Sylvain Gaudan

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. rebholz@ebi.ac.uk

Bioinformatics (Oxford, England)
|November 17, 2007
PubMed
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Text-mining tools are essential for biomedical research. The Whatizit system offers a scalable, server-based solution for analyzing scientific literature and extracting key information from large datasets.

Area of Science:

  • Biomedical Informatics
  • Bioinformatics
  • Computational Biology

Background:

  • Text-mining (TM) solutions are increasingly vital for biomedical researchers.
  • Existing TM tools face challenges in scalability due to growing literature and resource demands.
  • A robust, server-based solution is needed to meet these evolving research requirements.

Purpose of the Study:

  • To introduce Whatizit, a suite of modules for analyzing scientific text.
  • To demonstrate Whatizit's capability in identifying terms and linking them to bioinformatics databases.
  • To provide access to text analysis services for researchers, including handling large text volumes.

Main Methods:

  • Developed Whatizit as a modular, server-based text analysis suite.
  • Integrated modules for term identification and linking to databases like UniProtKb/Swiss-Prot and Gene Ontology.

Related Experiment Videos

  • Implemented functionality for identifying specific annotation types, similar to EBIMed.
  • Enabled access via PMID or term query for Medline abstracts and a streaming mode for large text datasets.

    • Main Results:

    • Whatizit effectively analyzes scientific publications and Medline abstracts.
    • The system successfully links identified terms to relevant bioinformatics entries.
    • It supports the identification of various annotation types, enhancing information extraction.
    • Scalable processing is achieved through a server-based architecture and streaming mode.

    Conclusions:

    • Whatizit provides an efficient and scalable text-mining service for the biomedical community.
    • The system facilitates the extraction and linking of critical information from scientific literature.
    • It addresses the growing needs for advanced text analysis in bioinformatics and related fields.