Reaction Ontology Outline

This outline will attempt to describe what the IntEnz Reaction Ontology project is. After reading this document you should understand what the project entails, its deliverables, who is involved and what timescales are expected.

The project can be subdivided into two parts, namely, specification and implementation. The implementation will largely depend on what is determined during the specification process and hence the implementation will not be discussed in great detail here.

Reaction Ontology Specification

This deliverable is a technical document which will investigate various Reaction ontologies, determine the use cases for our reaction ontology both internal and external. Then it should come to a conclusion regarding what would be the best IntEnz scenario.

Below is an outline of what the specification should contain and the questions it should answer.

  1. Introduction
  2. Background - mostly for your own benefit but very important for anyone with no background info into the project
    • What is an ontology?
    • What types of ontologies/graphs are there .e.g. DAG, Cyclic, hierarchical?
    • Why is an ontology useful?
    • What types of ontology formats are available e.g. OWL, OBO, DAML-OIL, RDF? Compare all the benefits pros and cons?
    • What is IntEnz?
    • How would an reaction ontology fit into IntEnz data, give examples?
  3. User Requirements - you need to determine what users both internal and external expect from the project. For this part Use Cases diagrams (UML) should be used to describe the user requirements.
    • External users - all users outside of the biobabel group which might have a potential interest including the following: In all cases you should give a description of what the database is about? How their data could link into IntEnz? How they could make use of a reaction ontology if they wanted to?
    • Internal Users - all users within our group namely curators and developers.
  4. Available Reaction Ontologies - you need to determine what other ontologies are available and then compare them. This comparison will consist of a spread sheet with benchmarks setup which will depend on our user requirements. Useful websites: In addition you should determine what API's are available, what components of these ontologies can be reused in IntEnz and how many users actually use these ontologies.
  5. Conclusion - you should conclude all your results with comparisons over whether our requirements fit into existing ontologies. What further functionality would be required etc...

People Involved and their roles

Name Role Description in context of project Location
Kirill Degtyarenko IntEnz and ChEBI curator Primary source for biological background to the project. EBI - A239
Rafael Alcantara IntEnz developer Primary IntEnz developer and can provide technical know-how for the project. EBI - A239
Paula de Matos ChEBI developer Primary ChEBI developer and can provide techical ontology experience from ChEBI ontology. EBI - A239
Marcus Ennis ChEBI curator ChEBI curator and can provide chemical knowledge in the project. EBI - A239
Kristian Axelsen IntEnz curator IntEnz curator and can provide enzyme background to the project. SIB but based in Denmark
Anne Morgat IntEnz curator IntEnz curator and can provide pathways knowledge to the project. SIB but based in Grenoble