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An Object-Oriented Programming System for the Integration of Internet-Based Bioinformatics Resources

  • Bioinformatics Software Engineering
  • Published:
Applied Bioinformatics

Abstract

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java™, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java™ code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

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Notes

  1. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  2. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  3. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  4. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  5. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  6. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  7. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  8. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

  9. Supplementary figures to this article can be found with the electronic version of this article on AdisOnline (http://www.AdisOnline.com/). The supplementary material is listed as ‘ArticlePlus’.

References

  1. Servant F, Bru C, Carrère S, et al. Automated clustering of homologous domains. Brief Bioinform 2002; 3: 246–51

    Article  PubMed  CAS  Google Scholar 

  2. Bateman A, Coin L, Durbin R, et al. The Pfam protein families database. Nucleic Acids Res 2004; 32: 138–41

    Article  Google Scholar 

  3. Attwood TK, Bradley P, Flower DR, et al. PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 2003; 31: 400–2

    Article  PubMed  CAS  Google Scholar 

  4. Henikoff S, Henikoff JG. Protein family classification based on searching a database of blocks. Genomics 1994; 19: 97–107

    Article  PubMed  CAS  Google Scholar 

  5. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990; 215: 403–10

    PubMed  CAS  Google Scholar 

  6. Murray-Rust P, Rzepa HS. Chemical markup, XML, and the Worldwide Web. I: basic principles. J Chem Inf Comput Sci 1999; 39: 928–42

    Article  CAS  Google Scholar 

  7. Murray-Rust P, Rzepa HS. Chemical markup, XML, and the World Wide Web. 4: CML schema. J Chem Inf Comput Sci 2003; 43(3): 757–72

    Article  PubMed  CAS  Google Scholar 

  8. Araki K, Ohashi K, Yamazaki S, et al. Medical markup language (MML) for XML-based hospital information interchange. J Med Syst 2000; 24: 195–211

    Article  PubMed  CAS  Google Scholar 

  9. Hucka M, Finney A, Sauro HM, et al. The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003; 19: 524–31

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

The software described in this paper was developed by the author in the department of Professor Hans Lehrach, Max Planck Institute for Molecular Genetics, Berlin, Germany.

The author has no conflicts of interest that are directly relevant to the content of this article.

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Authors and Affiliations

  1. Max Planck Institute for Molecular Genetics, Berlin, Germany

    Allan Beveridge

Authors
  1. Allan Beveridge
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Correspondence to Allan Beveridge.

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Appendix

Appendix

Refer to figure A1, Java™ code for the GenericInternetQuery class. This is a typical example of a derived InternetQuery class.

Fig. A1
figure A1

Class definition of GenericInternetQuery.

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Beveridge, A. An Object-Oriented Programming System for the Integration of Internet-Based Bioinformatics Resources. Appl-Bioinformatics 5, 29–39 (2006). https://doi.org/10.2165/00822942-200605010-00004

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