ontology

Connecting annotations: LEGO Models

The Gene Ontology Consortium is moving towards a more expressive way of describing the function of gene products that allows annotations to be connected together to give a complete function of what each gene does in the context of a larger biological process. The new model is called LEGO, for "Logical Extension of the Gene Ontology".

Background

For example, with the current datamodel and Gene Association Files, it's possible to make two statements:
  • TEM1 enables GTPase activity
  • BFA1 enables GTPase inhibitor activity

TermGenie

TermGenie is a web-based tool for requesting new Gene Ontology classes. TermGenie also allows for an ontology developer to review all generated terms before they are committed to the ontology. The system makes extensive use of OWL axioms (logical definitions), but can be easily used without understanding these axioms.

Integration with SAO (Subcellular Anatomy Ontology)

The primary use of the GO Cellular Component Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.

Maintaining complete 'is_a' and 'part_of' trees in cellular component

The cellular component ontology is is_a complete, meaning that every term has a path to the root node which passes solely through is_a relationships. This should be preserved; the following guidelines should help maintain this structure.

GO Projects

The following areas of biology are the focus of ontology development and annotation in the Gene Ontology Consortium (GOC). Some of these projects are currently underway and we welcome your feedback and contributions. Please reach the GOC using our "Contact us" form.

Biological Process Ontology Guidelines

A biological process is a recognized series of events or molecular functions. A process is a collection of molecular events with a defined beginning and end. Mutant phenotypes often reflect disruptions in biological processes.

General Considerations

Beginning and end

Every process should have a discrete beginning and end, and these should be clearly stated in the process term definition.

Collections of processes