It's all GO for plant scientists

Abstract

The Gene Ontology project (http://www.geneontology.org/) produces structured, controlled vocabularies and gene product annotations. Gene products are classified according to the cellular locations and biological process in which they act, and the molecular functions that they carry out. We annotate gene products from a broad range of model species and provide support for those groups that wish to contribute annotation of further model species. The Gene Ontology facilitates the exchange of information between groups of scientists studying similar processes in different model organisms, and so provides a broad range of opportunities for plant scientists.

Figure 1.

The ontologies. Here, sections of the three ontologies are represented schematically with only term names shown. The biological process ontology is shown on the left side (dark blue background), the molecular function ontology is shown in the center (light blue background), and the cellular component ontology is shown on the right side (yellow background). More general concepts are at the top and the more specific ones are at the bottom. The is_a relationships (continuous black lines) indicate that a child concept is a type of the parent concept, and the part_of relationships (dashed black lines) indicate that the child concept is a part of the parent concept. A term may have multiple parent terms, as in the case of adaxial/abaxial axis specification. Separately and in parallel with the development of the GO, gene products are annotated (red lines) to the terms. Annotation indicates that the gene product (gray background, black outline) is involved in the process described, or that it has the function, or acts in the location described.

Figure 2.

Annotation. A wide variety of gene products (gray background, black outline) may be annotated (red lines) to a single GO function term (light blue background). The annotations are made by curators in a range of bioinformatics database resources, for example MGI, TAIR, and Wormbase (text in yellow circles). The annotation of multiple gene products to a single GO function term (as shown here) indicates that they mediate the same single step reaction. The database resource acronyms are expanded as follows: Saccharomyces Genome Database (SGD), UniProt Knowledgebase (UniProt), The Arabidopsis Information Resource (TAIR), Mouse Genome Informatics (MGI), and Plasmodium falciparum GeneDB (GeneDB).

Figure 3.

The gene_association file format. The gene_association file format is used for submission of annotations to the GO Consortium. An excerpt from a gene_association file format is shown, with eight individual annotations taking up one line each. The file is split half way along its horizontal length to allow it to fit in the page (break indicated by zigzag line). The content of the columns are explained in Table III and the evidence codes are explained in Table IV.

Figure 4.

AmiGO. AmiGO is a free online tool for searching the ontologies and manual annotations (http://www.godatabase.org/). A term is displayed, with its name, definition, unique identifier and synonyms (A). Following this, the position in the ontology is displayed (B) with the relationships marked as i for is_a and p for part_of. The gene product association search may be refined by database, evidence code or species (C), and the search results are displayed at the bottom of the page (D). Each row begins with the gene product symbol for a gene product that has been associated with the GO term displayed above (E). Following this is a link to the entry for the gene product in the submitting database resource (F). Primary papers providing evidence for the association of the gene product to the particular GO term may be found on the submitting database resource Web site. The evidence codes (G) and the full gene or gene product names follow (H).