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Wed 21 Nov 2018
10:00 - 15:00

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Ontologies and ontology-based data analysis

Wed 21 Nov 2018


Ontologies have long provided a core foundation in the organization of biomedical entities, their attributes, and their relationships. With over 500 biomedical ontologies currently available there are a number of new and exciting opportunities emerging in using ontologies for large scale data sharing and data analysis.

This tutorial will help you understand what ontologies are and how they are being used in computational biology and bioinformatics. It will include hands-on examples and exercises and an introduction to Onto2Vec and OPA2Vec, two methods that can be used to learn semantic similarity measures in a data- and application-driven way.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • The tutorial will be of interest to computational biologists who use, produce or analyse large structured datasets.
  • The tutorial will be at an introductory level, but will also describe current research directions and challenges that will be of broad interest to researchers in computational biology.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

Suggested background reading:


Number of sessions: 1

# Date Time Venue Trainers
1 Wed 21 Nov 2018   10:00 - 15:00 10:00 - 15:00 Bioinformatics Training Room, Craik-Marshall Building map PAUL SCHOFIELD,  Robert Hoehndorf
Topics covered

Bioinformatics, Biology, Ontologies, nomenclature and classification


After this course you should be able to:

  • find ontologies in the biomedical domain and analyze their content
  • understand different types of associations between biological data and classes in ontologies
  • apply semantic similarity measures to biomedical data, specifically to analyze gene-disease relations based on phenotype similarity
  • apply neuro-symbolic (deep) machine learning methods to ontologies for clustering and prediction of biological relations

During this course you will learn about:

  • what ontologies are and where to find them
  • how to understand and use ontology semantics through automated reasoning
  • how to measure semantic similarity
  • how to incorporate ontologies and semantic similarity measures in bioinformatics analyses
  • recent developments in bio-ontologies

Presentations, demonstrations and practicals


Time Topics
10:00 - 10:40 Introduction: ontologies and their role in computational biology
10:40 - 11:20 Semantic Web: basic technologies underlying ontologies; understanding ontologies through OWL
11:20 - 12:20 Ontology-based analysis: semantic similarity and unsupervised machine learning methods
12:20 - 13:30 Lunch (not provided)
13:30 - 15:00 Hands-on: demonstration of some basic concepts
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



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