ontoCAT statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

ontoCAT specifications

Information


Unique identifier OMICS_26394
Name ontoCAT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 1.29
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Natalja Kurbatova <>

Additional information


http://master.bioconductor.org/packages/release/bioc/html/ontoCAT.html https://sourceforge.net/projects/ontocat/

Publication for ontoCAT

ontoCAT in publications

 (4)
PMCID: 5763153
PMID: 28726811
DOI: 10.1038/gim.2017.108

[…] iembase (version 1.0.0) and the four vocabularies. for snomed ct, extraction was restricted to only the terms categorized under “clinical finding” and “substance,” to minimize false mapping. the ontocat r package was used to parse hpo terms. the standard string library and nokogiri gem in ruby programming language were used to parse all others. second, all extracted terms were normalized […]

PMCID: 5333373
PMID: 28240266
DOI: 10.1038/ncomms14519

[…] file). we considered snps associated with any of the child terms of ‘efo_0000408: disease' as disease-associated snps. information of child terms of ‘efo_0000408: disease' was collected by using the ontocat package of r. we evaluate whether there is enrichment of sqtl snps among associated loci by one-tailed fisher's exact test with the following 2 × 2 table: columns; sqtl snps and non-sqtl […]

PMCID: 3348561
PMID: 22474121
DOI: 10.1093/bioinformatics/bts148

[…] makes external services easily accessible. as a service, magecomet provides validation through the limpopo parsers. it provides data mining through whatizit and interacts with ontologies using the ontocat library ()., magecomet is a web application created for harmonization of large-scale experiment annotations. it is designed to reduce the repetitive aspects of re-annotation and curation […]

PMCID: 3129328
PMID: 21619703
DOI: 10.1186/1471-2105-12-218

[…] this makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups., ontocat provides a seamless programming interface to query heterogeneous ontology resources including ols and bioportal, as well as user-specified local owl and obo files. each resource is wrapped […]


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ontoCAT institution(s)
EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK; Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
ontoCAT funding source(s)
Supported by the European Community’s Seventh Framework Programme projects GEN2PHEN (grant number 200754); SYBARIS (grant number 242220); and NWO/Rubicon (grant number 825.09.008).

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