In computer science and information science, an ontology encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities that substantiate one, many or all domains of discourse.
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
The Rat Genome Database (RGD) is the premiere location for rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. RGD is working with groups such as the Programs for Genomic Applications at MCW and the National BioResource Project for the Rat (NBPR-Rat) in Japan to collect and make available comprehensive physiologic data for a variety of rat strains. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse and human.
Phenomics is the systematic study of phenotypes. As such, it is a transdisciplinary area of research that involves biology, data sciences, engineering and other fields. Phenomics is concerned with the measurement of phenomes where a phenome is the set of phenotypes that can be produced by a given organism over the course of development and in response to genetic mutation and environmental influences. Phenomics concepts are used in functional genomics, pharmaceutical research, metabolic engineering, agricultural research, and increasingly in phylogenetics.
Ontology alignment, or ontology matching, is the process of determining correspondences between concepts in ontologies. A set of correspondences is also called an alignment. The phrase takes on a slightly different meaning, in computer science, cognitive science or philosophy.
The ISO 15926 is a standard for data integration, sharing, exchange, and hand-over between computer systems.
The Open Biomedical and Biological Ontologies is an effort to create ontologies for use across biological and medical domains. OBO forms part of the resources of the U.S. National Center for Biomedical Ontology and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of developers of ontologies related to the life sciences containing more than a hundred different ontologies. It is the group behind the Open Biomedical Ontologies effort. It establishes a set of principles for ontology development with the goal of creating a suite of interoperable reference ontologies in the biomedical domain. The Foundry approach has been adopted by other initiatives, such as the Monarch, the Neuroscience Information Framework (NIF) Standard and the cROP initiatives.
In philosophy, the term formal ontology is used to refer to an ontology defined by axioms in a formal language with the goal to provide an unbiased view on reality, which can help the modeler of domain- or application-specific ontologies to avoid possibly erroneous ontological assumptions encountered in modeling large-scale ontologies.
The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
Integrative bioinformatics is a discipline of bioinformatics that focuses on problems of data integration for the life sciences.
The Foundational Model of Anatomy Ontology (FMA) is a reference ontology for the domain of Human anatomy. It is a symbolic representation of the canonical, phenotypic structure of an organism; a spatial-structural ontology of anatomical entities and relations which form the physical organization of an organism at all salient levels of granularity.
The Zebrafish Information Network is an online biological database of information about the zebrafish. The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data generated by this research. To facilitate use of the zebrafish as a model of human biology, ZFIN links these data to corresponding information about other model organisms and to human disease databases. Abundant links to external sequence databases and to genome browsers are included. Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the University of Oregon in the United States, with funding provided by the National Institutes of Health (NIH).
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.
Virtual Fly Brain, or VFB, is an interactive, web-based tool that allows neurobiologists to explore the detailed neuroanatomy, transgene expression and associated phenotypes of the Drosophila melanogaster brain. Users can browse painted 3D image stacks of the Drosophila brain, choosing any plane of section they want and clicking on painted regions to find names' definitions, references and synonyms for the chosen region. For each region, they can run queries to find neurons, transgene expression and phenotypes. For each neuron found, users can browse definitions, references and synonyms.
Uberon is a comparative anatomy ontology representing a variety of structures found in animals, such as lungs, muscles, bones, feathers and fins. These structures are connected to other structures via relationships such as part-of and develops-from. One of the uses of this ontology is to integrate data from different biological databases, and other species-specific ontologies such as the Foundational Model of Anatomy.
The Human Phenotype Ontology (HPO) is a formal ontology of human phenotypes. Developed in collaboration with members of the Open Biomedical Ontologies Foundry, HPO currently contains over 13,000 terms and over 156,000 annotations to hereditary diseases. Data from Online Mendelian Inheritance in Man and medical literature were used to generate the terms currently in the HPO. The ontology contains over 50,000 annotations between phenotypes and hereditary disease.
Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas.
The Monarch Initiative is a large scale bioinformatics web resource focused on leveraging existing biomedical knowledge to connect genotypes with phenotypes in an effort to aid research that combats genetic diseases. Monarch does this by integrating multi-species genotype, phenotype, genetic variant and disease knowledge from various existing biomedical data resources into a centralized and structured database. While this integration process has been traditionally done manually by basic researchers and clinicians on a case by case basis, The Monarch Initiative provides an aggregated and structured collection of data and tools that make biomedical knowledge exploration more efficient and effective.
Canto is a web-based tool that encourages community curation of genes. The tool allows professional curators and published authors alike to collaborate and increase inclusion in public biological database. Canto is developed as part of the PomBase project, which looked at Schizosaccharomyces pombe, and funded by the Wellcome Trust. Currently, Canto is used for Schizosaccharomyces pombe, Komagataella pastoris, and Generic Gene Ontology Implementation. However, it can be configured to use gene identifiers for any species or ontology, making it a diverse program.
