Here we list all the ontologies used to create VFB.

Most we also actively contribute to and actively maintain but are all open source projects so feel free to review and follow the guidance provided to contribute.

Virtual Fly Brain Images (VFB)

The VFB query system relies on representation of data/knowledge in OWL. Central to this a representation of Drosophila neuro-anatomy in the Drosophila anatomy ontology. The anatomical structures depicted in images displayed on VFB are represented as a KnowledgeBase of OWL individuals, which are classified (typed) using OWL class expressions referencing the anatomy ontology. When this KnowledgeBase of individuals is combined with the ontology, a reasoner can be used to classify and query for anatomical structures depicted in the images on VFB.

Drosophila Anatomy Ontology (DAO)

An ontology of Drosophila melanogaster anatomy.

FlyBase (FB)

FlyBase: a database for drosophila genetics and molecular biology.

FlyBase Developmental Ontology (FBdv)

An ontology of Drosophila melanogaster developmental stages.

FlyBase Controlled Vocabulary (FBcv)

A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.

Gene Ontology (GO)

The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.

Sequence types and features ontology (SO)

A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.

GENO ontology

GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.

Information Artifact Ontology (IAO)

The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.

Phenotype And Trait Ontology (PATO)

An ontology of phenotypic qualities (properties, attributes or characteristics).

Basic Formal Ontology (BFO)

The upper level ontology upon which OBO Foundry ontologies are built.

Common Anatomy Reference Ontology (CARO)

An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species.

Ontology for Biomedical Investigations (OBI)

The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.

Population and Community Ontology (PCO)

The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.

OBO Relations Ontology (RO)

The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.

Uber-anatomy Ontology (UBERON)

Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.

NCBI organismal classification (NCBITaxon)

An ontology representation of the NCBI organismal taxonomy.

Biological Imaging Methods Ontology

A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.

Drosophila Phenotype Ontology (DPO)

An ontology for the description of Drosophila melanogaster phenotypes.

C elegans Phenotype Ontology (WBPhenotype)

Ontology about C. elegans and other nematode phenotypes.

Zebrafish Phenotype Ontology (ZP)

The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.

Last modified December 29, 2021: Update _index.md (bbfd8e2)