dictyBase Help: Gene Ontology (GO)

dictyBase Help: Gene Ontology (GO)



The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. The use of a consistent vocabulary allows genes from different species to be compared based on their GO annotations.

Using the Gene Ontology (GO)

What is GO?

For each of three categories of biological information - molecular function, biological process, and cellular component - a set of terms has been selected and organized. Each set of terms uses a controlled vocabulary, and parent-child relationships between terms are defined. This combination of a controlled vocabulary with defined relationships between items is referred to as an ontology. Within an ontology, a child may be a "part of" or an example ("instance") of its parent. For example, the nucleolus is part of the nucleus, whereas histidine biosynthesis is an example ("instance") of amino acid metabolism.

There are three independently organized controlled vocabularies, or gene ontologies, one for molecular function, one for biological process, and one for cellular component. The distinction between molecular function and biological process is a key feature of GO: function refers to specific activities or tasks carried out by individual gene products, while process refers to broad biological goals that encompass more than one function.

Many-to-many parent-child relationships are allowed in all of the ontologies. In the following example (kindly provided by SGD, Stanford), pheromone processing is a child of both protein modification and mating in the biological process ontology.

A gene may be annotated to any level in an ontology, and to more than one item within an ontology. dictyBase curators are annotating D. discoideum genes to the most detailed level in each ontology for which there is support in the literature, and will revise annotations to reflect new data.

The Gene Ontology (GO) project started as a collaboration between three model organism databases, the Saccharomyces Genome Database (SGD), FlyBase (Drosophila), and Mouse Genome Informatics (MGI). The GO Consortium has expanded since considerably, and now includes dictyBase and many other model organism databases.

GO Annotations in dictyBase

Each locus page lists the GO terms that have been annotated temporarily (electronically) or by a dictyBase curator. It also links to a page that lists all of the GO terms, with references and evidence codes, that have been used to annoatate a particular gene, e.g. ndkC GO evidence and references.

GO terms displayed on dictyBase locus pages link to a page describing that GO term itself. The GO page includes a unique identifier (the GO number), which of the three ontologies the item is contained within, any synonyms that have been entered into the ontology, a definition if one has been entered, and a list of all of the genes in dictyBase that have been associated with the term. The AmiGO icon links to the page for the same term in the AmiGO browser, where one can view associations between the GO term and the genes of many species. A link to AmiGO is also located next to the GO term on the locus page.

In the table of genes annotated to the GO node, gene names are listed in the "Locus" column, and each gene name links to the locus page for the gene. Each association between a locus and a GO item is attributed to at least one source, listed in the "Reference(s)" column. In case of a curator annotation this is usually a published paper, in case of electronic annotation this source is cited as "dictybase (2003) Unpublished". All electronic annotations will eventually be replaced by curated annotations. The citation links to the dictyBase Paper object for the reference cited. The "Evidence" column lists the kind of evidence that supports the assignment of a GO item to a locus. There are several possible types of evidence:

Code Definition
IDA Inferred from Direct Assay
IEA Inferred from Electronic Annotation
IEP Inferred from Expression Pattern
IGI Inferred from Genetic Interaction
IMP Inferred from Mutant Phenotype
IPI Inferred from Physical Interaction
ISS Inferred from Sequence or structural Similarity
NAS Non-traceable Author Statement
ND No biological Data available
NR Not Recorded
TAS Traceable Author Statement

The evidence codes used on a particular GO term page or on the GO annotations page for a given locus are hyperlinked to a page that lists all of the Evidence Codes for the Gene Ontology (GO) with examples, and links to the relevant documentation on the GO Consortium web site.

Please note that the reference given for a GO annotation is what a curator used to make the annotation. The evidence code indicates what type of evidence is found in that particular reference. Thus if a curator uses a review to make a GO annotation, the review will be cited and the evidence code will be "TAS (Traceable Author Statement", even if the author of the review states explicitly in the text of the paper that the authors of the original source performed a genetic experiment. Also please note, that the use of a given paper for a GO annotation is not an endorsement of the particular paper, nor does it make any judgement about lack of quality of any other paper not used. It is merely a statement of which paper was used to make the annotation.

NOT Annotations:

Prefixing a GO term with the string NOT means that a particular gene product is annotated to the negated form (NOT) of the particular GO term. Note: This field is used when a cited reference explicitly says the gene product is NOT a Gene Ontology (GO) term (e.g. "our favorite protein is not found in the nucleus"). It was introduced to allow curators to document conflicting claims in the literature. NOT can also be used in cases where associating a GO term with a gene product should be avoided (but might otherwise be made, especially by an automated method). For example, if a protein has sequence similarity to an enzyme (whose activity is GO:nnnnnnn), but has been shown experimentally not to have the enzymatic activity, it can be annotated as NOT GO:nnnnnnn. (This text is excerpted from the Gene OntologyTM Consortium's GO Annotation Guide; more information about the GO project is available from the GO home page.)

Accessing the Gene Ontology (GO)

GO terms used to annotate genes are listed on the Locus page for each gene, and link to the GO items in the database. Click on the text of the GO term to see a list of all Dictyostelium genes that have been annotated to that term.

Other Relevant Links

Associated Glossary Terms

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