Computer Laboratory

Course pages 2012–13

Biomedical Informatics

Principal lecturers: Dr Anna Korhonen, Dr Pietro Lio
Taken by: MPhil ACS, Part III
Code: R211
Hours: 8
Prerequisites: Introduction to Natural Language Processing (L100) and R07 Introductory Logic recommended as matching half-module


Biomedical informatics is a growing, interdisciplinary field that studies effective uses of biomedical data and information for scientific inquiry, problem solving, and decision making, motivated by efforts to improve human health. This course provides an introduction to biomedical informatics. It has a specific emphasis on computational techniques used in this field. A variety of data and text mining techniques are introduced and applied to study practical problems in biological sciences, clinical medicine and public health. The course provides also an overview of applications in the field.


  • Introduction to biomedical informatics: bioinformatics;, clinical informatics, public health informatics [1 lecture]
  • Computational resources and techniques in biomedical informatics: biomedical literature, databases, ontologies and associated tools, techniques for data, sequence, string and text mining, biomedical information visualisation [1 lecture]
  • Biology: identifying, relating and analysing information related to genes, drugs, diseases and nutraceuticals [2 lectures]
  • Clinical medicine: comparing, sharing and using different types of clinical health data among patients and health professionals [2 lectures]
  • Public health: gathering public health data from expert and non-expert resources (e.g. scientific publications vs. social media) and using these for epidemiology and health surveillance [1 lecture]
  • Student presentations of literature surveys of topics in biomedical informatics. [1 lecture]

Note that some content may vary, and the number of lectures per topic is provisional; the final plan will depend on the students' background and the number of students taking the course.


On completion of this module, students should:

  • have a general understanding of the field of biomedical informatics and an in-depth understanding of selected techniques and topics;
  • understand the main advantages and limitations of the techniques covered during the course;
  • be able to locate, read, understand, and present a research paper from the field;
  • be familiar with current research in a number of aspects of the field.


Practical work

Coursework will consist of two practical exercises. First, students will select one of a list of topics in biomedical informatics and carry out a literature survey of state-of-the-art research on this topic. The literature survey should be about 10 pages long and be based on approximately 8-10 papers. Second, students will give a short presentation about their literature survey to the rest of the class.


It will be mandatory for students to give a presentation, but the presentation will not be marked. The module will be assessed by a 10 page literature survey, marked by the lecturers using a percentage score. The survey will be due two weeks after the end of the module (subject to timetabling).

Recommended reading

Biomedical Informatics: Computer Applications in Health Care and Biomedicine. Shortliffe, E. H. and Cimino, J. J. (Eds.) 3rd edition, 2006, Springer New York. Available on-line from:


R211 Biomedical Informatics cannot be taken in conjunction with P33 Building an Internet Router in 2012-13.