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http://purl.bioontology.org/ontology/CPTAC

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

Proper citation: CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) Copy   

•   Source: SciCrunch Registry

http://www.ncbcs.org/biositemaps/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO).

Proper citation: Biomedical Resource Ontology (RRID:SCR_004443) Copy   

•   Source: SciCrunch Registry

http://hymao.org

A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)

Proper citation: Hymenoptera Anatomy Ontology (RRID:SCR_003340) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NIFCELL

Ontology for cell types from NIFSTD

Proper citation: NIF Cell Ontology (RRID:SCR_003977) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MS

A structured controlled vocabulary for the annotation of mass spectrometry experiments.

Proper citation: Mass Spectrometry Ontology (RRID:SCR_003579) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/opl-ontology/

A reference ontology that models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.

Proper citation: Ontology for Parasite LifeCycle (RRID:SCR_003427) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/ontology-for-genetic-interval/

An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.

Proper citation: Ontology for Genetic Interval (RRID:SCR_003423) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OPE

Ontology that provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.

Proper citation: Ontology of Physical Exercises (RRID:SCR_003836) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/REXO

An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.

Proper citation: Regulation of Gene Expression Ontolology (RRID:SCR_006124) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/REPO

Ontology for livestock reproductive traits and phenotypes

Proper citation: Reproductive Trait and Phenotype Ontology (RRID:SCR_006245) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/sbo/

A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services.

Proper citation: SBO (RRID:SCR_006753) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/SHR

Ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .

Proper citation: Student Health Record Ontology (RRID:SCR_005854) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/behavior-ontology

An ontology consisting of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending the GO process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. The prime application of NBO is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes. The main ontology is available in both the OBO Flatfile Format and the Web Ontology Language (OWL).

Proper citation: Neurobehavior Ontology (RRID:SCR_006201) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/PCL/

Collection of ontology of provisional cells determined by experimental methods.

Proper citation: Provisional Cell Ontology (RRID:SCR_018332) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MAMO

Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.

Proper citation: Mathematical Modelling Ontology (RRID:SCR_000910) Copy   

•   Source: SciCrunch Registry

http://www.biopax.org/

Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.

Proper citation: Biological Pathways Exchange (RRID:SCR_001681) Copy   

•   Source: SciCrunch Registry

https://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology

A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase.

Proper citation: Teleost Anatomy Ontology (RRID:SCR_001610) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/obophenotype/porifera-ontology

An ontology covering the anatomy of Porifera (sponges).

Proper citation: Porifera Ontology (RRID:SCR_000134) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TEO

Ontology for representing events, time, and their relationships.

Proper citation: Time Event Ontology (RRID:SCR_000310) Copy   

•   Source: SciCrunch Registry