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

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J - J Biomed Semantics (2013)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. paola@ebi.ac.uk.

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.

No MeSH data available.


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].
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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].

Mentions: An example of a protein complex, the mouse-specific form of eukaryotic translation initiation factor 2 complex 1, is represented in PRO using the ID PR:000026828 (FigureĀ 4). Each species-specific translation initiation factor complex is composed of specific protein entities, which can be any combination of isoforms, processed forms, or post-translationally modified forms. In this example, the mouse complex is shown. The human complex would be defined using human proteins and would be restricted to the human taxon. Both human and mouse complexes are defined with an is_a relationship to the generic GO complex. At present, there are almost 500 protein complex terms in PRO [24].


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

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J - J Biomed Semantics (2013)

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].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852282&req=5

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].
Mentions: An example of a protein complex, the mouse-specific form of eukaryotic translation initiation factor 2 complex 1, is represented in PRO using the ID PR:000026828 (FigureĀ 4). Each species-specific translation initiation factor complex is composed of specific protein entities, which can be any combination of isoforms, processed forms, or post-translationally modified forms. In this example, the mouse complex is shown. The human complex would be defined using human proteins and would be restricted to the human taxon. Both human and mouse complexes are defined with an is_a relationship to the generic GO complex. At present, there are almost 500 protein complex terms in PRO [24].

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. paola@ebi.ac.uk.

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.

No MeSH data available.