Biomedical Informatics

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Written for healthcare workers, students, and biomedical researchers who wish to use informatics technologies in their own clinics and laboratories, Biomedical Informatics discusses and reviews the many types of biomedical data resources and the open source software tools needed to fully utilize biomedical data. It teaches the reader how the Perl language is used in biomedical informatics and provides examples of short Perl scripts that can be applied in the biological research and healthcare settings. The text also provides a review of the ethical, legal, and social aspects of biomedical informatics and covers the legal and regulatory issues related to the acquisition and use of confidential medical data. Key features Explains how biomedical data are acquired, organized, annotated, and analyzed. Provides in-depth discussions of data representation including XML metadata, RDF, and ontologies. An extensive Appendix describes free, open source tools that will facilitate software interoperability and greatly reduce the cost of information technology. Contains over 240 lists that can be downloaded and used in Power Point TM presentations. Includes Perl source code to be used in your Perl applications. Provides guidance in employing data organizations and data sharing technologies in research grant applications. About The Author Jules Berman, PhD, MD is a pathologist with an eclectic technical background that includes a bachelor’s degree in mathematics from MIT. He was Program Director for Pathology Informatics in the Cancer Diagnosis Program in the US National Cancer Institute for a period that spanned two millennia (1998-2005). He has first- authored more than 100 scientific articles. Currently, he is President of the Association for Pathology Informatics. Table of Contents What are biomedical data and what do we do with them? The Data of Biomedical Informatics Confidential Biomedical data Standards for Biomedical Data Just Enough Programming Programming Common Biomedical Informatics Tasks Biomedical Nomenclatures Misbehaving Text: Dealing with Poorly Written Medical Text Autocoding Unstructured Data (Narrative Text) Computational Methods for De-identification and Data Scrubbing Cryptography in Biomedical Informatics Describing Data with Metadata Simplifying Complex Data with Classifications and Ontologies Clinical Trials: The Informatician Lives in a Statistical World Distributed Computing A Practical Approach to Ethics for Biomedical Informaticians Grantsmanship for Biomedical Informaticians