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

Ontology as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.

Proper citation: Human Physiology Simulation Ontology (RRID:SCR_010340) Copy   

•   Source: SciCrunch Registry

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

Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009

Proper citation: Logical Observation Identifier Names and Codes (RRID:SCR_010341) Copy   

•   Source: SciCrunch Registry

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

DICOM Controlled Terminology (PS3.16 2013 Annex D)

Proper citation: DICOM Controlled Terminology (RRID:SCR_010302) Copy   

•   Source: SciCrunch Registry

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

A computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. They also report high percentage of agreement among five observers as a result of the inter-observer agreement that they conducted among them to tag 13 articles using the diagnostic ontology. Moreover, they extend their existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.

Proper citation: Diagnostic Ontology (RRID:SCR_010307) Copy   

•   Source: SciCrunch Registry

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

A high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.

Proper citation: Translational Medicine Ontology (RRID:SCR_010439) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/BP-METADATA

Ontology that represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)

Proper citation: BioPortal Metadata Ontology (RRID:SCR_010167) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites.

Proper citation: Biositemaps (RRID:SCR_001976) Copy   

•   Source: SciCrunch Registry

http://www.rightfield.org.uk/

An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Proper citation: RightField (RRID:SCR_002649) Copy   

•   Source: SciCrunch Registry

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

Ontology of clinical trial terminology.

Proper citation: Epoch Clinical Trial Ontology (RRID:SCR_000366) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.

Proper citation: Vertebrate Skeletal Anatomy Ontology (RRID:SCR_000313) Copy   

•   Source: SciCrunch Registry

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

Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries

Proper citation: Research Network and Patient Registry Inventory Ontology (RRID:SCR_000308) Copy   

•   Source: SciCrunch Registry

https://github.com/information-artifact-ontology/IAO

An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.

Proper citation: Information Artifact Ontology (RRID:SCR_000477) Copy   

•   Source: SciCrunch Registry

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

Ontology of nursing interventions classification.

Proper citation: Nursing Interventions Classification (RRID:SCR_000911) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ICPC2P

Ontology of the international classification of primary care -2 PLUS

Proper citation: International Classification of Primary Care - 2 PLUS (RRID:SCR_000909) Copy   

•   Source: SciCrunch Registry

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

Ontology to represent standardized graphical notation for synthetic biology.

Proper citation: Synthetic Biology Open Language Visual Ontology (RRID:SCR_001261) Copy   

•   Source: SciCrunch Registry

http://aclame.ulb.ac.be/Classification/mego.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.

Proper citation: MeGO (RRID:SCR_000110) Copy   

•   Source: SciCrunch Registry

http://environmentontology.org/

Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.

Proper citation: EnvO (RRID:SCR_000182) Copy   

•   Source: SciCrunch Registry

https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

•   Source: SciCrunch Registry

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

Ontology of the international classification for nursing practice.

Proper citation: International Classification for Nursing Practice (RRID:SCR_003099) Copy   

•   Source: SciCrunch Registry

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

An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).

Proper citation: Spider Ontology (RRID:SCR_003117) Copy   

•   Source: SciCrunch Registry