Structured Text and XML in Medicine This is the home page for Structured Text and XML in Medicine (BIOINF 2991, 1 or 3 credits), a directed study in text markup taught as part of the University of Pittsburgh Center for Biomedical Informatics medical informatics training program. The course description, goals and grading policies are outlined below. Resources for the course including the schedule and assignments are listed in the sidebar to the right. Course description This course is an introduction to text markup, expecially XML markup, and applications of markup in medical informatics. Students will learn to create and work with well-formed and valid XML documents and to develop new XML vocabularies using document type descriptions and XML Schema. The course will review the use of XML in both data-centric and document-centric applications, including communications and native XML databases, and will survey the current status of XML development in areas related to biomedical science. Students may elect to take the course for one hour or three hours. There is 60 minute lecture per week. The three hour version of the course includes additional online tutorials and a more extensive project. Instructor: James H. Harrison, Jr., M.D., Ph.D. Days/Times: Fridays, 9:00 to 10:00 am Location: The CBMI Conference Room (inside FT 8084) Prerequisites: One course or experience with text markup such as HTML Recitations: None Expected class size: 4-12 students The course is usually offered in the spring term. ĘSpecial permission from the instructor is required to register for this course. Goals, expectations and grading The goals of this course are to introduce students to the key concepts of text markup and the family of standards associated with the Extensable Markup Language (XML), including Document Type Descriptions (DTD), XML Schema, Extensable Style Language (XSL), XSL Transformations and document navigation using XPath expressions. Students completing this course will be able to: - Write valid XML documents based on existing DTDs? or schemas using text editors and specialized XML editors - Create new XML DTDs and schemas - Display and transform XML documents using CSS and XSLT - Access specific sections of XML documents using Xpath and Xpointer - Understand the use of XML in modeling information in document- or data-centric settings - Understand and use the special characteristics of native XML databases - Describe the current status of existing XML development related to biomedical science, including HL7 v.3 messaging, the Clinical Document Architecture and BioML In addition, students will be equipped to discuss markup-related topics with web and software developers or vendors. This is a directed study that may be taken for 1 or 3 hours. Students taking the course for 3 hours will have additional assignments consisting of online tutorials and a more extensive class project. Students' responsibilities All students should attend the weekly lecture at 10 am on Fridays, participate actively in the class discussions and complete the assigned readings (see ClassSchedule). Students should also participate actively in the online class discussion using individual session pages, including posting questions and responding to others' questions, and they should make sure they understand each week's material thoroughly. Class projects should be carried out during the second half of the term (see ClassSchedule) and presented during the last two weeks of class. Students taking the class for three hours credit should also complete the assigned online tutorial each week and send any required work to Dr. Harrison. Project All students should select a standard document of some type as a basis for their project. Medical documents are good candidates, but any type of document can be used. A document that is relatively structured, such as a clinical consultant's report or a prescription, is best. The project should consist of a set of XML tags appropriate for the chosen document, a DTD in correct format specifying the tags, their attributes and their relationships, and an example document marked up with the tags. Students taking the course for three hours should also include an XML Schema in correct format that can be used as an alternative to the DTD, and an XSLT stylesheet that can be used to transform the example document into XHTML for display. Projects should be presented and demonstrated at the assigned times during the last two class periods. Presentations should include an overview, rationale and demonstration of project components. Grading Eighty percent of the grade is based on the quality of the class project 20% is based on class and online discussion participation. With respect to the latter, all students should plan to post questions and comments regularly to the online discussion; the number and quality of these postings will affect the grade.