GO Tutorial: Build Your Own Ontology I

Exercise I

Definitions for biological concepts

Download exI.ontology (you may need to right-click on it and choose Save as...) and load the file into DAG-Edit.

The file contains the top nodes of the three GO ontologies. Create new terms with the following strings and try to come up with some definitions for them. Try to make your answers as non-species-specific as possible.

Which ontology should these terms go in?

In addition to text books and your own knowledge, there are various web resources you can use to find definitions:

Using definitions from GO is cheating!

GO uses sensu [species name] to distinguish identical words which have different meanings in different species; a plant biologist talking about a bud would be referring to something completely different to a yeast biologist (try a Google Images search for "plant bud" and "yeast bud" to see). GO would distinguish these concepts by calling them bud (sensu Plantae) and bud (sensu Fungi).

Are there any terms above which need clarification using sensu?

Gene Ontology function terms representing reactions have the suffix activity, whilst cellular component terms representing an enzyme complex are given the suffix complex. Thus 6-phosphofructokinase activity refers to the reaction ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate, and 6-phosphofructokinase complex represents the physical protein you would put in a test tube.

Could any of the terms above be split into a term representing activity and a term representing the protein complex?