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Protocols

Ontobee specifications

Information


Unique identifier OMICS_09874
Name Ontobee
Restrictions to use None
Maintained Yes

Documentation


Publications for Ontobee

Ontobee citations

 (19)
call_split

ONS: an ontology for a standardized description of interventions and observational studies in nutrition

2018
PMCID: 5928560
PMID: 29736190
DOI: 10.1186/s12263-018-0601-y
call_split See protocol

[…] y (BFO) [] as upper ontology.Additional relevant ontologies were used orthogonally in the ONS as discussed in the results. To ensure and enhance orthogonality, all terms were first searched using the ONTOBEE [] web service and catalogued with their URIs. ONTOFOX [] was then used to import all terms with related annotations and axioms (option includeAllAnnotations). Newly defined terms, specific to […]

library_books

Unique extrication structure in a new megaspilid, Dendrocerus scutellaris Trietsch and Mikó (Hymenoptera: Megaspilidae)

2018
Biodivers Data J
PMCID: 5804289
PMID: 29434488
DOI: 10.3897/BDJ.6.e22676

[…] logy (PATO), Biospatial Ontology (BSPO), OBO Relation Ontology (RO), Ontology for Biomedical Investigations (OBI) and Information Artifact Ontology (IAO); these ontologies are available at http://www.ontobee.org (). By standardising taxonomic data through ontology-based semantic representation, we aim to facilitate future systematic work by facilitating the integration of taxonomic data sets from […]

library_books

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

2018
J Biomed Semantics
PMCID: 5765662
PMID: 29329592
DOI: 10.1186/s13326-017-0169-2

[…] us and inefficient, especially when the structure of ontology is enormous. Over the years, we have developed a collection of web-based “Ontoanimal” tools including Ontofox [], Ontodog [], Ontorat [], Ontobee [], Ontobeep [], Ontobull [], Ontokiwi [], and Ontobat []. Each Ontoanimal tool has its specific functions, and the collective use of these tools enables users to cover the full development of […]

library_books

Comparison, alignment, and synchronization of cell line information between CLO and EFO

2017
BMC Bioinformatics
PMCID: 5763470
PMID: 29322915
DOI: 10.1186/s12859-017-1979-z

[…] d import into EFO replacing locally identified terms. Permanent URLs (PURL) of both ontologies are also resolved on the EMBL-EBI Ontology Lookup Service (OLS) [], the EMBL-EBI RDF Platform [] and the Ontobee []. All information can be queried using SPARQL in Ontobee SPARQL endpoint (http://www.ontobee.org/sparql). […]

library_books

Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses

2017
BMC Bioinformatics
PMCID: 5763302
PMID: 29322930
DOI: 10.1186/s12859-017-1981-5

[…] the availability of LINCS-CLOview, we were able to analyze LINCS cell lines from different aspects. The tools used in our analyses include SPARQL-based queries, Protégé OWL editor visualization, and Ontobee statistics display and queries. Below we describe our analyzed results from three main aspects: related diseases, cell types, and tissues/organs.Our study found that LINCS cell lines are assoc […]

library_books

Ontology based systematic representation and analysis of traditional Chinese drugs against rheumatism

2017
BMC Syst Biol
PMCID: 5763303
PMID: 29322929
DOI: 10.1186/s12918-017-0510-5

[…] The Ontobee SPARQL query web page (http://www.ontobee.org/sparql) was used to query OCMR to address specific questions. The knowledge stored in the OCMR ontology was also analyzed under the Protégé OWL ed […]

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Ontobee institution(s)
University of Michigan Medical School, Ann Arbor, MI, USA
Ontobee funding source(s)
This project is supported by NIH grant 1R01AI081062.

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