Gene Ontology (GO)

Gene Ontology (GO) provides structured, controlled vocabularies to annotate genes, gene products, and sequences and to represent biological functions across ontology domains.

Key Features:

• Controlled vocabularies: Structured, controlled vocabularies for annotating genes, gene products, and sequences across molecular function, biological process, and cellular component domains.
• Relationship types: Introduction of new relationship types alongside existing ones to enhance connectivity within and between ontology domains.
• Consistency checking: Systematic checks for inconsistencies within the ontology to improve biological representation.
• Annotation growth: Expanded total annotations and increased species coverage derived from GOC curation activities.
• Ontology editing: OBO-Edit serves as an ontology-editing tool for creating and modifying ontology terms and relationships.
• Ontology browsing: AmiGO serves as the primary ontology browser for accessing GO terms and annotations.
• Curation methods: Literature-based annotation and ortholog-based functional inference performed by GOC groups to generate GO annotations.
• Computable definitions and term addition: Targeted ontology development introducing computable logical definitions and tools for adding terms to the ontology.
• Query support: Structured ontologies and relationships that enable ontology-based querying of gene product functions.

Scientific Applications:

• Gene and protein annotation: Functional annotation of genes and gene products using GO terms derived from literature-based curation and ortholog inference.
• Functional representation: Representation of molecular functions, biological processes, and cellular components across species for comparative analyses.
• Ontology validation: Detection and resolution of inconsistencies in ontology structure and relationships to refine biological models.
• Cross-species inference: Transfer of functional annotations across species via ortholog-based functional inference to increase species coverage.
• Computable reasoning: Use of computable logical definitions to support automated reasoning and ontology-driven analyses.

Methodology:

Methods explicitly include use of OBO-Edit and AmiGO, introduction of new relationship types, systematic inconsistency checks, literature-based annotation, ortholog-based functional inference, computable logical definitions, and tools for adding ontology terms.