The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

Abstract

Background: The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this 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 to the GO-CCO 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.

Description: Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases.

Conclusions: In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

Figure 1

Diagram and ontology placement of 'nuclear inner membrane'. (A) Diagram of human cell nucleus, including the nuclear inner membrane. (Taken from Wikimedia commons, http://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Diagram_human_cell_nucleus.svg/2000px-Diagram_human_cell_nucleus.svg.png). (B) Placement of the Gene Ontology term GO:0005637 'nuclear inner membrane', drawn using the ontology editing tool OBO-Edit (see ‘Methods’). Due to space limitations, not all ancestor and descendant terms are shown. Is_a links are indicated by "I"; part_of links are indicated by "P" (see main text for explanation).

Figure 2

Image and ontology placement of ‘dendritic tree’. (A) Dendritic tree from a Purkinje neuron from mouse cerebellum injected with Lucifer Yellow and imaged using confocal microscopy. (Taken from the Cell Centered Database (CCDB), http://ccdb.ucsd.edu/sand/main?mpid=3&event=displayRecon). (B) Placement of the newly added Gene Ontology term GO:0097447 'dendritic tree', drawn using the ontology editing tool OBO-Edit (see ‘Methods’). Due to space limitations, not all ancestor and descendant terms are shown. Is_a links are indicated by "I"; part_of links are indicated by "P" (see main text for explanation). Has_part links are also discussed in the main text.

Figure 3

Representation of 'synapse part' in the Gene Ontology. Children of the GO term. GO:0044456 'synapse part' are shown using the ontology editing tool OBO-Edit (see ‘Methods’). Terms underlined in green were added as part of the SAO amalgamation. Due to space limitations, not all ancestor and descendant terms are shown. Is_a links are indicated by "I" (see main text for explanation).

Figure 4

Protein ontology report for entry PR:000026828. Ontology information for the Protein Ontology term 'eukaryotic translation initiation factor 2 complex 1 (mouse)', showing parent GO term and has_part links to other PR terms [25].

Figure 5

Refining GO annotations using Gene Ontology CC terms. The PomBase annotation for the ‘cut8’ gene to ‘proteasome localization’ (a GO biological process term) is further refined by specifying that this localization takes place in the ‘nuclear membrane’ (a GO-CCO term). (Taken from http://www.pombase.org/spombe/result/SPAC17C9.13c#go).