Tools to curate, browse, search and visualize GO

Gene Ontology provides a variety of tools to help users curate, browse, search, visualize and download both the GO ontology and GO annotations.

Curate

Noctua is the curation platform developed by the Gene Ontology Consortium and allows to create both GO annotations and GO Causal Activity Models or GO-CAMs. The Noctua curation platform includes both a simple form editor and a more advanced and expressive graph editor for finer details on knowledge modeling.

Noctua Curation Platform

Documentation and guidelines for curators are available at wiki.geneontology.org.

Browse

Drill-down browsing of the GO ontology is pissible via an interactive tree.

Browse GO ontology example

To browse curated and inferred GO annotations, visit AmiGO.

Ontology and standard GO Annotations

AmiGO can be used to search both the GO ontology, the GO annotations and details about Gene Products described in our Knowledgebase.

Powered by the Solr search engine, AmiGO allows for advanced faceted searching to refine your query by restricting, for instance, to a specific species, a specific aspect (Biological Process, Molecular Function or Cellular Component), a specific evidence (e.g. only curated annotations), etc.

AmiGO faceted search example

GO-CAM

GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple standard GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.

GO-CAMs can be browsed and searched in the http://geneontology.org/go-cam section of this site. For example, you can limit your search results to GO-CAMs having a certain GO term, a certain gene, or created by a specific curation group or curator.

GO-CAM example

Visualize

GO ribbon: a configurable tool for visualizing GO annotations

Many genes have large numbers of annotations, making it difficult to get a quick overview of a gene function, or the functions of gene sets. The GO ribbon is specifically designed to help users visualize and explore the functions of a gene and was developed as a lightweight, reusable widget that can be embedded in any website, and retrieves data directly from the GO resource via API.

GO Ribbon example of SOX9

The GO Ribbon is currently integrated in the Alliance of Genome Resources and work is underway for further integration in several projects.