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https://github.com/obophenotype/porifera-ontology
An ontology covering the anatomy of Porifera (sponges).
Proper citation: Porifera Ontology (RRID:SCR_000134) Copy
http://purl.bioontology.org/ontology/TEO
Ontology for representing events, time, and their relationships.
Proper citation: Time Event Ontology (RRID:SCR_000310) Copy
http://purl.bioontology.org/ontology/VARIO
An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Proper citation: Variation Ontology (RRID:SCR_000311) Copy
http://purl.bioontology.org/ontology/SEDI
An ontology for DICOM as used in the SeDI project.
Proper citation: Semantic DICOM Ontology (RRID:SCR_000309) Copy
http://purl.bioontology.org/ontology/DOID
Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.
Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy
http://purl.bioontology.org/ontology/GAZ
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.
Proper citation: Gazetteer (RRID:SCR_000473) Copy
http://www.xenbase.org/anatomy/xao.do?method=display
A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology.
Proper citation: Xenopus Anatomy Ontology (RRID:SCR_004337) Copy
http://purl.bioontology.org/ontology/JERM
An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/
Proper citation: SysMO JERM Ontology of Systems Biology for Micro-Organisms (RRID:SCR_004569) Copy
http://www.proconsortium.org/pro/
An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).
Proper citation: PR (RRID:SCR_004964) Copy
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
Proper citation: Gene Ontology (RRID:SCR_002811) Copy
http://purl.bioontology.org/ontology/APO
A structured controlled vocabulary for the phenotypes of Ascomycete fungi.
Proper citation: Ascomycete Phenotype Ontology (RRID:SCR_003254) Copy
http://code.google.com/p/bcgo-ontology/
An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.
Proper citation: Beta Cell Genomics Ontology (RRID:SCR_003259) Copy
Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.
Proper citation: Biological Collections Ontology (RRID:SCR_003262) Copy
http://purl.bioontology.org/ontology/LIPRO
An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.
Proper citation: Lipid Ontology (RRID:SCR_003349) Copy
http://purl.bioontology.org/ontology/MMO
An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.
Proper citation: Measurement Method Ontology (RRID:SCR_003373) Copy
http://sig.biostr.washington.edu/projects/fm/
A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. 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 in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.
Proper citation: FMA (RRID:SCR_003379) Copy
http://purl.bioontology.org/ontology/IDOMAL
An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO).
Proper citation: Malaria Ontology (RRID:SCR_003369) Copy
http://purl.bioontology.org/ontology/DDANAT
A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.
Proper citation: Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) Copy
http://purl.bioontology.org/ontology/MAT
An ontology of minimal set of terms for anatomy.
Proper citation: Minimal Anatomical Terminology (RRID:SCR_003385) Copy
http://www.bioontology.org/wiki/index.php/CARO:Main_Page
An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies.
Proper citation: Common Anatomy Reference Ontology (RRID:SCR_003296) Copy
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