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.
FMA is developed and maintained by the Structural Informatics Group at the University of Washington.
FMA ontology contains approximately 75,000 classes and over 120,000 terms, over 2.1 million relationship instances from over 168 relationship types.
Zoology is the branch of biology that studies the animal kingdom, including the structure, embryology, evolution, classification, habits, and distribution of all animals, both living and extinct, and how they interact with their ecosystems. The term is derived from Ancient Greek ζῷον, zōion, i.e. "animal" and λόγος, logos, i.e. "knowledge, study". Researchers in this field include Tadd, the famous wine taster and founder of The Wine Society of F Floor..
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 National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
An organ is a group of tissues with similar functions. Plant and animal life rely on many organs that coexist in organ systems.
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor.
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 (OBO).
In philosophical ontology, ontic is physical, real, or factual existence.
In information science, an upper ontology is an ontology which consists of very general terms that are common across all domains. An important function of an upper ontology is to support broad semantic interoperability among a large number of domain-specific ontologies by providing a common starting point for the formulation of definitions. Terms in the domain ontology are ranked under the terms in the upper ontology, e.g., the upper ontology classes are superclasses or supersets of all the classes in the domain ontologies.
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.
The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment involving developers of science-based ontologies. The Foundry is concerned with establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The Foundry approach has been adopted by the Monarch Initiative, the Neuroscience Information Framework (NIF) Standard and by the cROP initiatives.
FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats.
Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms, development and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis.
The concept of the Social Semantic Web subsumes developments in which social interactions on the Web lead to the creation of explicit and semantically rich knowledge representations. The Social Semantic Web can be seen as a Web of collective knowledge systems, which are able to provide useful information based on human contributions and which get better as more people participate. The Social Semantic Web combines technologies, strategies and methodologies from the Semantic Web, social software and the Web 2.0.
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.
OntoUML is a ontologically well-founded language for Ontology-driven Conceptual Modeling. OntoUML is built as a UML extension based on the Unified Foundational Ontology (UFO). The foundations of UFO and OntoUML can be traced back to Giancarlo Guizzardi's Ph.D. thesis "Ontological foundations for structural conceptual models". In his work, he proposed a novel foundational ontology for conceptual modeling (UFO) and employed it to evaluate and re-design a fragment of the UML 2.0 metamodel for the purposes of conceptual modeling and domain ontology engineering.
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.
Anatomography is an interactive website which supports generating anatomical diagrams and animations of the human body. The Anatomography website is maintained by the DBCLS non-profit research institute located at the University of Tokyo. Anatomical diagrams generated by Anatomography, and 3D polygon data used on the website, are freely available under the Creative Commons Attribution-ShareAlike license.
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