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HPO / Human Phenotype Ontology
Provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO is developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. HPO also provides a large set of HPO annotations to approximately 4000 common diseases. HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things.
Uberon
Represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates. Uberon is an integrated cross-species ontology covering anatomical structures in animals. It has been constructed to integrate seamlessly with other ontologies, such as the OBO Cell Ontology, the Gene Ontology, Trait and Phenotype ontologies, as well as other anatomical ontologies. It includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
FMA / Foundational Model of Anatomy
Provides an ontology for the symbolic representation of the phenotypic structure of the human body. FMA is initially based on the anatomical content of Unified Medical Language System (UMLS). This ontology is organized through four interrelated components: anatomy taxonomy (At), anatomical structural abstraction (ASA), anatomical transformation abstraction (ATA) and metaknowledge (Mk). It includes approximately 75 000 and up to 120 000 terms for over 2.1 million relationship instances.
CELDA / Cell: Expression, Localization, Development, Anatomy
An ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms. CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages.
CMPO / Cellular Microscopy Phenotype Ontology
Provides about 360 phenotype terms. CMPO can be used to annotate mitotic phenotypes observed in live human cells, as well as cellular phenotypes from tissue microarrays of diseased tissues from both human patients and mouse models. It describes a cell population phenotype as a collection of qualities that inhere in a population of cells. The database follows many standard conventions from the open biological and biomedical ontologies (OBO) foundry for ontology term metadata.
PORO / Prolifera Ontology
New
Displays an anatomy ontology dealing with Porifera. PORO is a terminology that principally leans on the Thesaurus of Sponge Morphology, with the aim of extending its usabilty for character matrices construction for both modern and fossil taxa. This controlled vocabulary intends to link data about structural, functional, genetic, and gene expression data in sponges to improve researches about their morphological features as well as for further applications in molecular approaches.
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CL / Cell Ontology
An OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. CL, since its inception in 2005, has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CL is mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library.
CellFinder
Maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.
Limbform / Limb formalization
A database based on a functional ontology system that unambiguously centralize the knowledge of limb regeneration experiments in a diverse set of model organisms, enabling the unambiguous description, centralize storage and manual and automated mining of this vast dataset. In contrast to natural language or text-based ontologies, Limbform is based on a functional ontology using mathematical graphs to represent unambiguously limb phenotypes and manipulation procedures. The centralized database currently contains >800 published limb regeneration experiments comprising many model organisms, including salamanders, frogs, insects, crustaceans and arachnids. The Limbform database of limb regeneration experiment represents an invaluable resource for the community and establishes the first necessary steps of a new bioinformatics of shape.
CLO / Cell Line Ontology
A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. CLO includes more than 36000 cell lines derived from over 200 in vivo cell types from various organisms. Collaboration among the CLO, Cell Ontology (CL) and the Ontology for Biomedical Investigation (OBI) has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The CLO hierarchical structure makes it easy to browse, query, and perform automated classification.
Cellosaurus
Provides information about cell lines. Cellosaurus is composed of immortalized cell lines, naturally immortal cell lines, finite life cell lines when those are distributed and used widely, vertebrate cell line with an emphasis on human, mouse and rat cell lines, and invertebrate cell lines. It contains more than 100 000 cell lines, representing over 550 species. The database furnishes data such as synonyms, cross-references and references to publications, databases or ontologies.
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