Data collections tagging

Here are the data collections associated to the following tag:

  • ontology (Data collections tagged with 'ontology' reference those ontologies that are used in the life sciences.)
NameDefinition
BioPortal BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.
Brenda Tissue Ontology The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
Cell Cycle Ontology The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.
Cell Type Ontology The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.
ChEBI Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
EDAM Ontology EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).
Experimental Factor Ontology The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.
FMA The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.
Gene Ontology The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
GOA The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.
Gramene Growth Stage Ontology Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.
Human Disease Ontology The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
MGED Ontology The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.
Molecular Interactions Ontology The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.
Mouse Adult Gross Anatomy A structured controlled vocabulary of the adult anatomy of the mouse (Mus)
NCIm NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.
NCIt NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.
NeuroLex The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).
Ontology of Physics for Biology The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
Pathway Ontology The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.
PATO PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.
Plant Ontology The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
Protein Modification Ontology The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.
Protein Ontology The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.
Relation Ontology The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.
Sequence Ontology The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.
Systems Biology Ontology The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.
TEDDY The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
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.
Unit Ontology Ontology of standardized units
VariO The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.

31 items returned.