Tag: Ontology

CDAO 2019-06-26 – Comparative Data Analysis Ontology

CDAO 2019-06-26

:: DESCRIPTION

CDAO provides extensive conceptual coverage of commonly used concepts in evolutionary analyses in a single framework. It is developed in collaboration with a group of domain scientists specialising in phylogenetic analysis software, the EvoInfo working group (http://evoinfo.nescent.org) . CDAO is used in a number of projects, including nexML, Nexplorer3, TreeBASE, phyloXML.

::DEVELOPER

the Evolutionary Informatics working group of the National Evolutionary Synthesis Center (NESCent).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CDAO

:: MORE INFORMATION

Citation:

Evol Bioinform Online. 2009 Jul 3;5:47-66.
Initial implementation of a comparative data analysis ontology.
Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A.

Populous 1.2 beta – Populating Ontology Templates

Populous 1.2 beta

:: DESCRIPTION

Populous is a generic tool for building ontologies from simple spreadsheet like templates. The Populous approach is useful when a repeating ontology design pattern emerges that needs to be populated en-mass.

::DEVELOPER

Populous team

:: SCREENSHOTS

Populous

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Populous 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Jan 25;13 Suppl 1:S5. [Epub ahead of print]
Populous: a tool for building OWL ontologies from templates.
Jupp S1, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R.

Voronto – Mapping Gene Expression to Ontologies with Voronoi Tessellations

Voronto

:: DESCRIPTION

Voronto is a tool that integrates expression data and biological ontologies, allowing the analyst to explore the whole ontology and detect changes on expression patterns inside the ontology.

::DEVELOPER

RODRIGO SANTAMARÍA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/MacOS
  • Java

:: DOWNLOAD

 Voronto

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2281-2. doi: 10.1093/bioinformatics/bts428. Epub 2012 Jul 4.
Voronto: mapper for expression data to ontologies.
Santamaría R1, Pierre P.

OBO-Edit 2.3.1 – Ontology Editor for Biologists

OBO-Edit 2.3.1

:: DESCRIPTION

OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.

::DEVELOPER

OBO-Edit Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 OBO-Edit

:: MORE INFORMATION

Citation

OBO-Edit–an ontology editor for biologists.
Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group, Lewis S.
Bioinformatics. 2007 Aug 15;23(16):2198-200. Epub 2007 Jun 1.

OLS Dialog 3.4.14 – Java Front End to the Ontology Lookup service

OLS Dialog 3.4.14

:: DESCRIPTION

OLS Dialog is a Java front end to the Ontology Lookup Service allowing easy access to an extensive list of biomedical ontologies

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 OLS Dialog

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jan 17;11:34.
OLS dialog: an open-source front end to the ontology lookup service.
Barsnes H, Côté RG, Eidhammer I, Martens L.

SimTrek 2.0 – Cytoscape plugin for Ontology-based Similarity Assessment of Biological Networks

SimTrek 2.0

:: DESCRIPTION

SimTrek is a Cytoscape plugin for ontology-based similarity assessment of biological networks.

::DEVELOPER

SimTrek team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SimTrek

:: MORE INFORMATION

Citation

Wang H, Zheng H, Azuaje F (2010)
Ontology- and graph-based similarity assessment in biological networks,
Bioinformatics (2010)doi: 10.1093/bioinformatics/btq477

MONA – Multilevel ONtology Analysis

MONA

:: DESCRIPTION

MONA is a model-based Bayesian method for inferring interpretable GO term probabilities in a modular framework, such that any combination of omics-levels can be analysed.

::DEVELOPER

Computational Cell Maps, Institute of Computational Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows 7
  • Microsoft .NET Framework 4.0
:: DOWNLOAD

 MONA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Nov;41(21):9622-33. doi: 10.1093/nar/gkt752. Epub 2013 Aug 23.
A modular framework for gene set analysis integrating multilevel omics data.
Sass S, Buettner F, Mueller NS, Theis FJ.

OVA – Ontology Variant Analysis Tool

OVA

:: DESCRIPTION

OVA  (ontology variant analysis) is an online variant filtering and prioritisation application. Ontology Variant Analysis Tool can filter your VCF files on a wide array of criteria. Remaining genes are prioritisated based on their functional and phenotypic profile similarity to a user supplied phenotype.

::DEVELOPER

OVA Team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.
Antanaviciute A, Watson CM, Harrison SM, Lascelles C, Crinnion L, Markham AF, Bonthron DT, Carr IM.
Bioinformatics. 2015 Aug 12. pii: btv473.

dcGOR 1.0.6 – Analysing Ontologies and Protein Domain Annotations

dcGOR 1.0.6

:: DESCRIPTION

dcGOR is an open-source R package for analysing domain-centric ontologies and annotations  (dcGO and others)

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dcGOR

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2014 Oct 30;10(10):e1003929. doi: 10.1371/journal.pcbi.1003929. eCollection 2014.
dcGOR: an R package for analysing ontologies and protein domain annotations.
Fang H

dnet 1.1.5 – Integrative Analysis of Omics data in terms of Network, Evolution and Ontology

dnet 1.1.5

:: DESCRIPTION

dnet is an open-source R package for omics data integrative analysis in terms of network, evolution and ontology

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dnet

:: MORE INFORMATION

Citation:

Genome Med. 2014 Aug 26;6(8):64. doi: 10.1186/s13073-014-0064-8.
The ‘dnet’ approach promotes emerging research on cancer patient survival.
Fang H, Gough J

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