bioregistry 0.13.17__py3-none-any.whl → 0.13.19__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bioregistry/analysis/paper_ranking.py +2 -0
- bioregistry/data/bioregistry.json +413 -199
- bioregistry/data/curated_papers.tsv +2 -0
- bioregistry/external/aberowl/processed.json +182 -66
- bioregistry/external/bartoc/processed.json +61 -28
- bioregistry/external/biolink/processed.json +3 -0
- bioregistry/external/bioportal/agroportal.json +106 -169
- bioregistry/external/bioportal/bioportal.json +251 -60
- bioregistry/external/bioportal/ecoportal.json +47 -0
- bioregistry/external/fairsharing/processed.json +37 -30
- bioregistry/external/go/processed.json +1 -0
- bioregistry/external/integbio/__init__.py +3 -3
- bioregistry/external/integbio/processed.json +28 -27
- bioregistry/external/lov/processed.json +26 -2
- bioregistry/external/obofoundry/processed.json +5 -3
- bioregistry/external/ols/processed.json +102 -57
- bioregistry/external/re3data/processed.json +142 -48
- bioregistry/external/uniprot/processed.json +54 -54
- bioregistry/version.py +1 -1
- {bioregistry-0.13.17.dist-info → bioregistry-0.13.19.dist-info}/METADATA +7 -7
- {bioregistry-0.13.17.dist-info → bioregistry-0.13.19.dist-info}/RECORD +23 -23
- {bioregistry-0.13.17.dist-info → bioregistry-0.13.19.dist-info}/WHEEL +2 -2
- {bioregistry-0.13.17.dist-info → bioregistry-0.13.19.dist-info}/entry_points.txt +0 -0
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},
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"AEO": {
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"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
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"download_owl": "http://aber-owl.net/media/ontologies/AEO/
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"download_owl": "http://aber-owl.net/media/ontologies/AEO/9/aeo.owl",
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"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
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"name": "Anatomical Entity Ontology",
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"prefix": "AEO"
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},
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"AIDENTIFYAGE": {
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"description": "The AIdentifyAGE ontology provides a comprehensive vocabulary description for forensic age assessment using dental biological markers, promoting the transparent assessment processes in forensic odontology and age diagnostics. It formalizes expert knowledge according to IOFOS, AGFAD, ABFO, ADA and ISO standards, ensuring semantic interoperability and ethical AI integration. This ontology is a work in progress developed under the AIdentifyAGE project (FCT Grant 2024.07444.IACDC), within the national investment RE-C05-i08 – More Digital Science, measure RE-C05-i08.M04 – Support to R&D projects for advanced cybersecurity, artificial intelligence and data science systems in public administration. This work is being developed in collaboration with researchers from the University of Lisbon (Portugal), the University of Münster (Germany), and the University of Zagreb (Croatia), within the framework of the AIdentifyAGE international consortium., Base Ontology for use in AIdentifyAGE Project",
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"download_owl": "http://aber-owl.net/media/ontologies/AIDENTIFYAGE/
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"download_owl": "http://aber-owl.net/media/ontologies/AIDENTIFYAGE/10/aidentifyage.owl",
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"name": "AIdentifyAGE",
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"prefix": "AIDENTIFYAGE",
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"version": "v1.0.
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"version": "v1.0.8-beta"
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},
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"AIDSCLIN": {
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"description": "This new ontology will cover the knowledge on AIDS and the relevant clinic activities, which imports the HIV ontology at the site https://bioportal.bioontology.org/ontologies/HIVO004 as its main or basic concept system. The new ontology is named AIDSClinic001.owl",
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},
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"AISM": {
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"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
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"download_owl": "http://aber-owl.net/media/ontologies/AISM/
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"download_owl": "http://aber-owl.net/media/ontologies/AISM/21/aism.owl",
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"homepage": "https://github.com/insect-morphology/aism",
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"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)",
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"prefix": "AISM"
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"prefix": "ANCESTRO",
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"version": "1.0"
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"ANCO": {
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"description": "Ontology for Antenatal Care data capture, visits, services, risks, and outcomes.",
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"download_owl": "http://aber-owl.net/media/ontologies/ANCO/1/anco.owl",
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"name": "ANC Ontology",
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"prefix": "ANCO",
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"version": "1.0.0"
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},
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"AO": {
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"description": "Asthma ontology",
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"download_owl": "http://aber-owl.net/media/ontologies/AO/2/ao.owl",
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},
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"APO": {
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"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
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"download_owl": "http://aber-owl.net/media/ontologies/APO/
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"download_owl": "http://aber-owl.net/media/ontologies/APO/66/apo.owl",
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"homepage": "http://www.yeastgenome.org/",
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"name": "Ascomycete phenotype ontology",
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"prefix": "APO"
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"prefix": "BIOMODELS",
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"version": "21"
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"BIOPAX": {
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"description": "The goal of the BioPAX group is to develop a common exchange format for biological pathway data. More information is available at http://www.biopax.org. This ontology is freely available under the LGPL license",
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"download_owl": "http://aber-owl.net/media/ontologies/BIOPAX/1/biopax.owl",
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"name": "BioPAX Level 3 ontology",
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"prefix": "BIOPAX",
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"version": "v1.0"
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},
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"BIOTOP": {
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"description": "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network, and the UMLS Semantic Network (mapping files available), BioTop Website: http://purl.org/biotop See related articles at: http://www.google.com/search?q=Schulz+BioTop+site:www.ncbi.nlm.nih.gov/pmc/articles+ontology+OR+ontologies",
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"download_owl": "http://aber-owl.net/media/ontologies/BIOTOP/4/biotop.owl",
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"homepage": "http://purl.org/biotop",
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"name": "BioTop",
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"prefix": "BIOTOP",
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"version": "v2012-04-24"
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},
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"BIPOM": {
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"description": "BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are treated as instances. BiPOm, 1) contains biological knowledge as instances and 2) uses automatic reasoning through Semantic Web Rule Language (SWRL) in order to automatically infer, formalize and refine properties of molecules.",
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"download_owl": "http://aber-owl.net/media/ontologies/BIPOM/3/bipom.owl",
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"prefix": "CARELEX",
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"version": "1.02"
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"CARESSES": {
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"description": "The CARESSES Ontology encodes guidelines defined by experts in Transcultural Nursing, with the aim of offering a specific tool for endowing social assistive robots (assisting older adults) with cultural competence.",
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"download_owl": "http://aber-owl.net/media/ontologies/CARESSES/1/caresses.owl",
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"name": "CARESSES Ontology",
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"prefix": "CARESSES",
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"version": "1.0"
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"CARO": {
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"description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species",
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"download_owl": "http://aber-owl.net/media/ontologies/CARO/17/caro.owl",
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"CHEBI": {
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"description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
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"download_owl": "http://aber-owl.net/media/ontologies/CHEBI/210/chebi.owl",
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"homepage": "http://www.ebi.ac.uk/chebi",
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"name": "Chemical Entities of Biological Interest",
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"prefix": "CHEBI"
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"CMO": {
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"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
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"download_owl": "http://aber-owl.net/media/ontologies/CMO/
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"download_owl": "http://aber-owl.net/media/ontologies/CMO/170/cmo.owl",
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"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
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"name": "Clinical measurement ontology",
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"prefix": "CMO"
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"name": "Core Ontology for Biology and Biomedicine",
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"prefix": "COB"
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"COCHRANE": {
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"description": "The Cochrane Core ontology describes the entities and concepts that exist in the domain of evidence based healthcare. It is used for the construction of the Cochrane Linked Data Vocabulary containing some 400k terms including Interventions (Drugs, Procedures etc), Populations (Age, Sex, Condition), and clinical Outcomes., The Cochrane Core ontology describes the entities and concepts that exist in the domain of evidence based healthcare.",
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"download_owl": "http://aber-owl.net/media/ontologies/COCHRANE/1/cochrane.owl",
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"homepage": "https://data.cochrane.org/ontologies/core/index-en.html",
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"name": "Cochrane Core Vocabulary Ontology",
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"prefix": "COCHRANE",
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"version": "2.0.1"
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"CODO": {
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"description": "The initial version, CODO ontology v1.0 to v1.3, encompasses pivotal features such as classes like patients, clinical findings, symptoms, and properties like relationships between patients, travel history, and test results. It facilitates tracking specific pandemic cases, detailing how patients may have been infected, and identifying potential contacts at risk due to their connection with the infected individual. CODO also enables monitoring of clinical tests, travel history, available resources, and actual needs like ICU beds and invasive ventilators. With capabilities for advanced analytics, contact tracing, trend studies, and growth projections based on daily COVID-19 data, CODO supports the organization and representation of COVID-19 data on a daily basis. It allows semantic querying and data retrieval and aids in behavior analysis of the disease and transmission routes. In contrast, Version 1.4, also known as CODO_COVIDRO 1.4 or COVID-19 Drug and Risk Ontology (COViDRO), presents a formal model specifically designed to tackle the multifaceted challenges associated with COVID-19 treatment, risk factors, and drug interactions. The knowledge embedded in the COViDRO model is extracted from diverse medical literature and treatment guidelines provided by reputable organizations such as the World Health Organization (WHO), the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and the Centers for Disease Control and Prevention (CDC). The model incorporates information on therapeutics, adverse effects, and drug interactions from authoritative medical literature, making a significant contribution to patient care, research, and public health strategies. COViDRO, or COVID-19 Drug and Risk Ontology 1.4, seamlessly integrates into knowledge graph information systems or recommender systems. It assists healthcare professionals in suggesting appropriate treatments by considering a comprehensive set of factors, abbreviated as \"PRADiCT\" (Patient Risk factors, Adverse effects, Drug interaction, Clinical findings, and Treatment procedure). These factors encompass patient risk level, risk factors (such as underlying health conditions, age, immunocompromised state, and occupation), drug interactions, drug adverse effects, clinical findings (including diagnosis, signs, symptoms, and status), and treatment procedures. By offering a standardized framework for organizing and integrating data from diverse sources like clinical trials, medical literature, and real-world patient data, COViDRO enhances informed decision-making, thereby elevating the quality of patient care. It stands as a patient-centric solution, facilitating COVID-19 treatment options and personalized care based on individual patient characteristics. CODO V1.5 extends the previous CODO V1.4 with the focus on COVID-19 Virus Genomics for representation of genomic sequence data. VGO model comprises 261 classes, 55 object properties, and 14 data properties. Designed to streamline the use and dissemination of COVID-19 genomic sequence data, VGO serves as a robust resource for researchers and healthcare professionals. It incorporates data from the Global Initiative on Sharing All Influenza Data (GISAID), which facilitates efficient querying and visualization of genomic data, thereby improving both accessibility and usability. VGO includes a variety of classes that represent COVID-19-related data such as variants, mutations, amino acids, genes, proteins, genome sequencing, samples, hosts, sampling strategies, and assembly methods. Furthermore, VGO supports automated reasoning, enhancing its functionality for in-depth analysis and interpretation. By integrating GISAID data into the VGO knowledge graph, the model not only enriches its conceptual representation but also optimizes the querying and visualization processes, making genomic data more accessible and usable for the scientific and medical communities.",
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"download_owl": "http://aber-owl.net/media/ontologies/CODO/6/codo.owl",
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"prefix": "DATASET",
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"version": "1.0.0"
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"DBM": {
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"description": "An ontology for the Drug Bureau of Macedonia (DBM)., An ontology for describing brand-name drugs.",
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"download_owl": "http://aber-owl.net/media/ontologies/DBM/1/dbm.owl",
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"name": "DBM Ontology",
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"prefix": "DBM",
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"version": "1.1"
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"description": "The Dublin Core Schema is a small set of vocabulary terms that can be used to describe several kinds of resources. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations.",
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"download_owl": "http://aber-owl.net/media/ontologies/DC/3/dc.owl",
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"description": "The ontology has been developed in the framework of the Dem@Care project for representing the experimentation protocol towards diagnostic support and assessment of Dementia in a controlled environment. The aim of the protocol is to provide a brief overview of their health status of the participants during consultation (cognition, behaviours and function), and to correlate the system (sensor) data with the data collected using typical dementia care assessment tools., and to correlate the system (sensor) data with the data collected using typical dementia care assessment tools. The ontology describes the basic Steps of the experimentation protocol (Directed Activities, Semi-directed Activities and Free Discussion with the Clinician), the Tasks that are involved, as well as the measurement types relevant to each Task. The defined protocol can be reused and further extended, adding new steps, tasks and measured data. Documentation regarding the ontology vocabulary can be found at http://www.demcare.eu/ontologies/demlab.html",
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"homepage": "http://www.demcare.eu/ontologies/demlab.html",
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"name": "Dem@Care Lab Ontology for Dementia Assessment",
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"description": "This is a controlled vocabulary for Salmonella serotype",
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"description": "Ontology for healthcare metadata - especially metadata found in DICOM files (Digital Imaging and Communications in Medicine, see http://dicom.nema.org/). Author: Michael Brunnbauer, Bonubase GmbH (www.bonubase.com). The author's email address is brunni@netestate.de. See http://purl.org/healthcarevocab/v1help for explanations.",
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"name": "Healthcare metadata - DICOM ontology",
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"description": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology",
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"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.",
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"description": "An ontology for experimental and other evidence statements.",
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"homepage": "https://www.evidenceontology.org",
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"description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.",
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"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
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"description": "EVORAO is an ontology for standardized metadata supporting the sharing of pathogens as biological materials, their derived products, and associated services, organized into collections. While initially focused on virology, it is designed for interoperability and is extensible to other pathogens. EVORAO is compatible with DCAT, making it well-suited for efficiently cataloguing pathogen collections and related resources.",
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"description": "A collection of curated and standardized values used in metadata specifications produced by ADAMS (Accelerating DAta and Metadata Standards \u000bin the Environmental Health Sciences Study of Emerging Water Contaminants) group. These values are designed to ensure uniformity in the description of the various metadata standards produced by the group.",
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"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
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"description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
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"download_owl": "http://aber-owl.net/media/ontologies/GAZ/15/gaz.owl",
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"GB": {
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"description": "GlycanBind is an ontology for representing glycan and pathogen binding interaction data in RDF. Many of the terms are based on the data originally contained in the SugarBind database.",
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"description": "An ontology for describing the function of genes and gene products",
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"homepage": "http://geneontology.org/",
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"HIFM": {
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"description": "An ontology for describing brand-name drugs.",
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"download_owl": "http://aber-owl.net/media/ontologies/HIFM/1/hifm.owl",
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"name": "HIFM Ontology",
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"HINO": {
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"description": "The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.",
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"description": "A RDF Schema that defines concepts and relationships used for Hospital data.",
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"download_owl": "http://aber-owl.net/media/ontologies/HOSP/1/hosp.owl",
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"name": "Hospital Vocabulary",
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"HP": {
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"description": "The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.",
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"HRAVS": {
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"description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
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"HRDO": {
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"description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). </ br> Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
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"MA": {
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"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
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"homepage": "https://github.com/obophenotype/adult-mouse-anatomy-ontology",
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"name": "Mouse adult gross anatomy",
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"MAXO": {
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"description": "The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.",
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"name": "MedRed ontology: clinical data acquisition model",
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"MEDRT": {
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"description": "MED-RT is a replacement and successor to NDF-RT. Both terminologies are formal ontological representations of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them. Description MED-RT includes native pharmacologic classification concepts (e.g. mechanisms of action (MoA), physiologic effects (PE), Established Pharmacologic Class (EPC)) and all relationships asserted between concepts in any namespace. MED-RT incorporates the following terminologies: RxNorm for prescribable medications, active ingredients, and relationships between them MeSH for indexing chemical structure and therapeutics using its concept hierarchies SNOMED CT International to aid in mapping between FDA pharmacologic classes and its product and substance hierarchies MED-RT will maintain the pharmacologic classification relationships from NDF-RT. It also maintains the National Committee on Vital and Health Statistics (NCVHS) standards for describing medication pharmacologic classification: MoA and PE hierarchy concepts. The concepts are components of the Federal Medication Terminologies (FMT) interagency collaboration.",
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"MI": {
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"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
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"description": "A representation of the variety of methods used to make clinical and phenotype measurements.",
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"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
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"description": "A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.",
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"homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
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"description": "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments",
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"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
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"description": "Managing patients with respiratory failure increasingly involves non-invasive respiratory support (NIRS) strategies as alternatives to traditional ventilation methods. However, despite the rapidly expanding use of NIRS, there is a significant challenge to its best use under all medical circumstances. It lacks a unified ontological structure, complicating guidance on NIRS modalities across healthcare systems. We introduced this NIRS ontology study to support knowledge representation in acute care settings by providing a unified framework that enhances data clarity, interoperability, and clinical decision-making. We developed this NIRS ontology using the Web Ontology Language (OWL) and Protégé to organize clinical concepts and relationships. To enable rule-based clinical reasoning beyond hierarchical structures, we added Semantic Web Rule Language (SWRL) rules. We evaluated logical reasoning by adding 17 hypothetical clinical scenarios. We used SPARQL queries to retrieve and test targeted inferences. The ontology has 129 classes, 11 object properties, and 17 data properties across 886 axioms that establish concept relationships. To standardize clinical concepts, we added 361 annotations, including descriptive definitions based on controlled vocabularies.",
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"description": "An ontology of neuron types based on the phenotypic dimensions of cells that can be measure experimentally.",
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"homepage": "https://github.com/SciCrunch/NIF-Ontology",
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"NRO": {
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"description": "The neural reprogramming ontology encompasses the domain of neural regenerative cell reprogramming knowledge. As research progresses, researchers and specialists in the field of reprogramming could continue to expand the bounds of this foundation, so adding to its depth.",
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"description": "An integrated ontology for the description of life-science and clinical investigations",
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"description": "The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.",
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"download_owl": "http://aber-owl.net/media/ontologies/OBO/2/obo.owl",
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"name": "Ontology for Biomedical Investigation",
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"version": "2019-08-06"
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"OBOE": {
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"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. The main concepts in OBOE include: - Observation: an event in which one or more measurements are taken - Measurement: the measured value of a property for a specific object or phenomenon (e.g., 3.2) - Entity: an object or phenomenon on which measurements are made (e.g., Quercus rubrum) - Characteristic: the property being measured (e.g., VolumetricDensity) - Standard: units and controlled vocabularies for interpreting measured values (e.g., g/cm^3) - Protocol: the procedures followed to obtain measurements (e.g., DensityProtocol2014) OBOE can characterize the context of an observation (e.g., space and time), as well as dependencies such as nested experimental observations. It includes an extensive set of unit definitions (e.g., grams of carbon per liter of seawater), and can facilitate automatic unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to create Entities and Characteristics for specific research domains, making it both broadly applicable and highly customizable. OBOE is being used to improve data interpretation, facilitate reuse, and create precise and effective systems for data search and discovery.",
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"OHMI": {
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"description": "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
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"OMRSE": {
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"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
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"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
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"version": "2015-11-27"
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"OSDI": {
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"description": "OSDi is an ontology designed to help the health technology assessment (HTA) community automate multiple stages in the development of economic evaluations. OSDi includes concepts and relationships that model the HTA domain, from characterizing diseases or affected populations to assessing interventions. OSDi serves as a supporting framework for the structured extraction of knowledge from literature and the automated generation of computational models using decision trees or discrete-event simulation., Ontología diseñada para recopilar e inferir los parámetros necesarios para crear una evaluación de tecnología sanitaria basada en simulación, Ontology designed for collecting and inferring the parameters required to create a simulation-based Health Technology Assesment",
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"download_owl": "http://aber-owl.net/media/ontologies/OSDI/2/osdi.owl",
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"name": "Ontology for the Simulation of Diseases",
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"OSM": {
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"description": "Esta ontologia foi desenvolvida para auxiliar na gestão da Rede de Atenção Psicossocial no contexto brasileiro, a fim de possibilitar a criação de ferramentas computacionais inteligentes, permitindo a integração e interoperabilidade entre bases de dados independentes e possibilitando a geração de indicadores para a saúde mental, visando melhorar a tomada de decisão, o planejamento e a eficiência e eficácia dos serviços prestados à comunidade.",
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"PHIPO": {
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"description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.",
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"homepage": "https://github.com/PHI-base/phipo",
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"name": "Pathogen Host Interaction Phenotype Ontology",
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"PLANTSO": {
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"description": "This ontology describes biotic and abiotic stresses that a plant may encounter., An ontology describing biotic and abiotic plant stresses.",
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"homepage": "https://github.com/Planteome/plant-stress-ontology",
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"PLIO": {
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"description": "The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references.",
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"PO": {
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"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
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"PREFER": {
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"description": "PREFER is an ontology designed to integrate high-throughput bioprocess data, covering operational, environmental and process parameters across different scales of a precision fermentation process, to accelerate the development and scaling of biosustainable production processes., An ontology for PREcision FERmentation.",
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"PREGONTO": {
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"description": "The pregnancy ontology is a biomedical ontology used for identifying pregnancies in routine health databases. The ontology was primarily developed for conducting surveillance of vaccine uptake in pregnant women in the UK.",
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"PSDO": {
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"description": "Ontology to reproducibly study visualizations of clinical performance",
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"homepage": "https://github.com/Display-Lab/psdo",
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"description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
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"PW": {
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"description": "A controlled vocabulary for annotating gene products to pathways.",
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"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
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"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
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"description": "Relationship types shared across multiple ontologies",
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"homepage": "https://oborel.github.io/",
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"ROS": {
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"description": "This ontology describes commonly contoured (anatomical and treatment planning) structures for radiation treatment planning. 22000 structures labels (created over a 16 years period in our radiation department) were extracted, classified and categorized to produce this ontology. Lymph nodes delineation international guidelines are provided. This ontology was created to ease and standardize the integration of radiation oncology data into clinical datawarehouses for multicentric studies. The high granularity of this ontology will allow precise dosimetric evaluations.",
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"description": "The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. SAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both: - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e. - Use case 1 ?elderly at home monitoring and support?, - Use case 2 ?monitoring and support of healthy lifestyles for citizens?, - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification. SAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology.  For semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure). For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service., i.e. - Use case 1 “elderly at home monitoring and support”, - Use case 2 “monitoring and support of healthy lifestyles for citizens”, - Use case 3 “Early Warning System (EWS) and Cardiovascular Accidents detection”. - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509",
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"name": "SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain",
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"SALMON": {
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"description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.",
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"description": "A controlled vocabulary to describe phenotypic traits in plants.",
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"description": "The Unwarranted Clinical Variation Analysis ontology (UCVA) is an application ontology that standardizes the representation of local context factors of UCV analysis. It includes numerous instances designed to support the extraction of these factors as covariates in UCV analysis, making it practical and easy to use",
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"description": "A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.",
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"download_owl": "http://aber-owl.net/media/ontologies/UNITSONT/1/unitsont.owl",
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@@ -10260,7 +10369,7 @@
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},
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"UO": {
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"description": "Metrical units for use in conjunction with PATO",
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-
"download_owl": "http://aber-owl.net/media/ontologies/UO/
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+
"download_owl": "http://aber-owl.net/media/ontologies/UO/63/uo.owl",
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"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
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"name": "Units of measurement ontology",
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"prefix": "UO"
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@@ -10341,10 +10450,10 @@
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},
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"VFB_DRIVERS": {
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"description": "An ontology of Drosophila melanogaster drivers and expression patterns., An ontology of Drosophila melanogaster drivers and expression patterns. All genetic objects are created using data taken directly from FlyBase.",
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-
"download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/
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+
"download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/202/vfb_drivers.owl",
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"name": "vfb_drivers",
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"prefix": "VFB_DRIVERS",
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-
"version": "2026-01-
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+
"version": "2026-01-26"
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},
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"VHO": {
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"description": "Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.",
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@@ -10414,7 +10523,7 @@
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},
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"VO": {
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"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
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-
"download_owl": "http://aber-owl.net/media/ontologies/VO/
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+
"download_owl": "http://aber-owl.net/media/ontologies/VO/312/vo.owl",
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"homepage": "https://violinet.org/vaccineontology",
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"name": "Vaccine Ontology",
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"prefix": "VO"
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@@ -10554,7 +10663,7 @@
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},
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"VT": {
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"description": "An ontology of traits covering vertebrates",
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10557
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-
"download_owl": "http://aber-owl.net/media/ontologies/VT/
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|
10666
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+
"download_owl": "http://aber-owl.net/media/ontologies/VT/145/vt.owl",
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10558
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"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
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"name": "Vertebrate trait ontology",
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"prefix": "VT"
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@@ -10722,7 +10831,7 @@
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},
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10832
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"XCO": {
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10724
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"description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
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10725
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-
"download_owl": "http://aber-owl.net/media/ontologies/XCO/
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+
"download_owl": "http://aber-owl.net/media/ontologies/XCO/157/xco.owl",
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"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
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10727
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|
"name": "Experimental condition ontology",
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|
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|
"prefix": "XCO"
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@@ -10741,7 +10850,7 @@
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|
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},
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10851
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"XLMOD": {
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10743
10852
|
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
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|
10744
|
-
"download_owl": "http://aber-owl.net/media/ontologies/XLMOD/
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|
10853
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+
"download_owl": "http://aber-owl.net/media/ontologies/XLMOD/5/xlmod.owl",
|
|
10745
10854
|
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
|
|
10746
10855
|
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
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|
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|
"prefix": "XLMOD"
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@@ -10759,6 +10868,13 @@
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"name": "CrossRef Funder Registry",
|
|
10760
10869
|
"prefix": "XREF-FUNDER-REG"
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10761
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|
},
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|
10871
|
+
"YOGA": {
|
|
10872
|
+
"description": "Yoga Ontology is the list of vocabularies that define the yogic practice. Where Yoga is the union of the mind and body.",
|
|
10873
|
+
"download_owl": "http://aber-owl.net/media/ontologies/YOGA/1/yoga.owl",
|
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10874
|
+
"name": "Yoga Ontology",
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|
10875
|
+
"prefix": "YOGA",
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|
10876
|
+
"version": "0.1"
|
|
10877
|
+
},
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10762
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|
"YUNPING": {
|
|
10763
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|
"name": "yunping",
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|
10764
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|
"prefix": "YUNPING"
|