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First published February 5, 2004 as JAMIA PrePrint; doi:10.1197/jamia.M1453
Journal of the American Medical Informatics Association 2004;11(3):174-178
© 2004 American Medical Informatics Association

A more recent version of this article appeared on May 1, 2004
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Submitted on September 8, 2003
Accepted on January 11, 2004

A Simple and Practical Dictionary-Based Approach for Identification of Proteins in MEDLINE Abstracts

Sergei Egorov PhD1, Anton Yuryev PhD1, and Nikolai Daraselia PhD1*

Affiliation of the authors: 1 Ariadne Genomics, Inc., Rockville, MD

* To whom correspondence should be addressed.

Objective Develop the practical and efficient protein identification system for biomedical corpora.

Design The developed system, called ProtScan, utilizes a carefully constructed dictionary of mammalian proteins in conjunction with a specialized tokenization algorithm to identify and tag protein name occurrences in biomedical texts and also takes advantage of MEDLINE Name-of-Substance(NOS) annotation. The dictionaries for ProtScan were constructed in a semi-automatic way from various public-domain sequence databases followed by an intensive expert curation step.

Measurements The recall and precision of the system has been determined using 1,000 randomly selected and hand-tagged MEDLINE abstracts.

Results The developed system is capable of identifying protein occurrences in MEDLINE abstracts with a 98% precision and 88% recall. It was also found to be capable of processing approximately 300 abstracts per second. Without utilization of NOS annotation, precision and recall were found to be 98.5% and 84% respectively.

Conclusion The developed system appears to be well-suited for protein-based MEDLINE indexing and can help to improve biomedical information retrieval. Further approaches to ProtScan's recall improvement are also discussed. The authors claim to have a financial interest in the ProtScan system (see Acknowledgements).




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