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Protocols

Ontorat specifications

Information


Unique identifier OMICS_25576
Name Ontorat
Interface Web user interface
Restrictions to use None
Input format txt, xlsx
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yongqun He

Publication for Ontorat

Ontorat citations

 (8)
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

[…] ically tedious 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 de […]

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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
call_split See protocol

[…] Based on the new design patterns, Ontorat [] was used to incorporate LINCS cell line data from different data sources to CLO. Two steps were performed. The first step was to add to existing CLO cell lines with new data obtained from L […]

call_split

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
call_split See protocol

[…] Web Ontology Language (OWL2) (https://www.w3.org/TR/owl-guide/). Ontofox (http://ontofox.hegroup.org/) [] was used to extract subsets of related terms from different ontologies. In addition, we used Ontorat (http://ontorat.hegroup.org/) [] to quickly add the annotations and relations between different entities. […]

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Ontology based systematical representation and drug class effect analysis of package insert reported adverse events associated with cardiovascular drugs used in China

2017
Sci Rep
PMCID: 5653862
PMID: 29061976
DOI: 10.1038/s41598-017-12580-4
call_split See protocol

[…] e drug products and drug ingredients are aligned under BFO:material entity branch, and the MoAs are aligned under the BFO:role branch. After the two ontology subsets are aligned under OCVDAE, we used Ontorat (http://ontorat.hegroup.org/) to automatically generate annotations (e.g., Chinese drug names) and axioms that link drugs with AEs in OCVDAE. The input files of the Ontorat operation were the […]

call_split

Ontology based collection, representation and analysis of drug associated neuropathy adverse events

2016
J Biomed Semantics
PMCID: 4875649
PMID: 27213033
DOI: 10.1186/s13326-016-0069-x
call_split See protocol

[…] ontology subsets under the ODNAE ontology hierarchical structure. Once the top level terms are aligned, the middle and bottom level ontology terms will be aligned automatically. In addition, we used Ontorat, another internally developed web-based program (http://ontorat.hegroup.org/) [], to assign RxNorm and NDF-RT identifiers to corresponding DrON drug terms using the annotation property rdfs:se […]

library_books

Webulous and the Webulous Google Add On a web service and application for ontology building from templates

2016
J Biomed Semantics
PMCID: 4818523
PMID: 27042287
DOI: 10.1186/s13326-016-0055-3

[…] []. Both OPPL and M2 are designed to support a form of Manchester OWL syntax that uses variables that can be assigned to values to form new OWL axioms.Dedicated applications like MappingMaster [] and OntoRat [] were developed to support the conversion of data from spreadsheets into OWL, but they don’t provide support for the management and creation of the data entry templates. Populous [] was deve […]

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Ontorat institution(s)
University of Michigan, Ann Arbor, MI, USA; University of Pennsylvania, Philadelphia, PA, USA
Ontorat funding source(s)
Supported by the National Institutes of Health (NIH) grants 1R01AI081062 from the National Institute of Allergy and Infectious Diseases (NIAID).

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