General questions about the Gene Ontology.

How do I browse the GO?

The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Entering a search term into the quick search menu and choosing an auto-completed choice from the drop-down will return the summary page for that gene product or term. Alternatively terms can be entered by free text and the user will be allowed to choose whether the search will return genes, terms or annotations.

Sometimes the number of GO annotations changes significantly over a short period of time. Why?

Most annotations in association files are electronically inferred (IEA). As with all types of annotations, IEAs change over time, with an overall increasing trend. However, in the specific case of IEAs, significant fluctuations in numbers may sometimes be observed over a short period of time. Nearly always, these are not due to bugs, but rather to the following reasons and/or to a combination thereof:

    What is beyond the scope of the GO project?

    Almost as important as understanding the scope of the GO project is understanding what the GO project is not. The most common misapprehensions are (1) that the GO is a system for naming genes and proteins and (2) that the GO attempts to describe all of biology. The GO neither names genes or gene products, nor does it attempt to provide structured vocabularies beyond its three domains: molecular function, biological process and cellular component.

    Can I reason over GO?

    It is possible to do some reasoning over GO now, and we expect to do much more in the future. We provide logical definitions or 'cross-products' for some terms as part of the extended GO file, which can be reasoned over. The OWL version of GO is described in a conference paper Use of OWL within the Gene Ontology.

    Which biological domains are supported by GO?

    The current ontologies of the GO project are molecular function, biological process, and cellular component. The ontologies are developed to include all terms falling into these domains without consideration of whether the biological attribute is restricted to certain taxonomic groups. Therefore, biological processes that occur only in plants (e.g. photosynthesis) or mammals (e.g. lactation) are included. Other biological ontologies are discussed in the OBO web site .

    Why do we need GO?

    To ask meaningful questions, biologists often need to retrieve and analyse data from disparate sources. For example, if you were searching for new targets for antibiotics, you might want to find all the gene products that are involved in bacterial protein synthesis, but that have significantly different sequences or structures from those in humans. But if one database describes these molecules as being involved in 'translation', whereas another uses the phrase 'protein synthesis', it will be difficult for you - and even harder for a computer - to find functionally equivalent terms.