Ontobee
A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for user-friendly web browsing and navigation, and to (ii) RDF source code for Semantic Web applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies.
Description
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A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for user-friendly web browsing and navigation, and to (ii) RDF source code for Semantic Web applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies.
metasource: Fairsharing.orgversion: FAIRsharing.org: Ontobee; Ontobee; DOI: https://doi.org/10.25504/FAIRsharing.q8fx1b; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.ontobee.org/Webpage
More detailed information about this field from each metasource.
http://www.ontobee.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Ontobee; Ontobee; DOI: https://doi.org/10.25504/FAIRsharing.q8fx1b; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
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Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
PMID: 27733503
metasource: Fairsharing.org
version: FAIRsharing.org: Ontobee; Ontobee; DOI: https://doi.org/10.25504/FAIRsharing.q8fx1b; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/1938
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
PMID: 27733503
metasource: Fairsharing.org
version: FAIRsharing.org: Ontobee; Ontobee; DOI: https://doi.org/10.25504/FAIRsharing.q8fx1b; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/1938
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
PubMed citations: 39.
39 articles citing: Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
Differential COVID-19 Symptoms Given Pandemic Locations, Time, and Comorbidities During the Early Pandemic. PMID:35155491
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. PMID:34986596
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties. PMID:34603473
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. PMID:34454610
X-CNV: genome-wide prediction of the pathogenicity of copy number variations. PMID:34407882
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). PMID:33981708
VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms. PMID:33777032
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. PMID:33722159
Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. PMID:33441564
Effects of Peptide Thanatin on the Growth and Transcriptome of Penicillium digitatum. PMID:33381100
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
A realism-based approach to an ontological representation of symbiotic interactions. PMID:33032576
SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation. PMID:33029585
ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. PMID:32047873
OHMI: the ontology of host-microbiome interactions. PMID:31888755
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. PMID:31865910
Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PMID:31626635
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
ROBOT: A Tool for Automating Ontology Workflows. PMID:31357927
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. PMID:31272389
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. PMID:30815206
Identifying Principles for the Construction of an Ontology-Based Knowledge Base: A Case Study Approach. PMID:30578220
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes. PMID:30400805
Knowledge-based biomedical Data Science. PMID:30294517
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. PMID:30034908
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. PMID:29854250
ONS: an ontology for a standardized description of interventions and observational studies in nutrition. PMID:29736190
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. PMID:29061976
Dietary and health biomarkers-time for an update. PMID:28974991 - http://dx.doi.org/10.1093/nar/1938
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genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genomics genome annotation terms, ontologies and nomenclature
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