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NeXO specifications


Unique identifier OMICS_15306
Name NeXO
Alternative name Network-extracted Ontology
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 1.0
Maintained No



This tool is not available anymore.

Publications for Network-extracted Ontology

NeXO citations


FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

BMC Genomics
PMCID: 5836822
PMID: 29504895
DOI: 10.1186/s12864-018-4474-7

[…] ficance of the functional connectivity of the set of genes involved in histone deubiquitination [GO:0016578] as being equal to 6.48e-21, calculated by the ANDSystem, which can be a functional module (NeXO:8805) according to the NeXO ontology []. […]


Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems

Cell Syst
PMCID: 4772745
PMID: 26949740
DOI: 10.1016/j.cels.2016.02.003

[…] ndom forest library from the Python scikit-learn package (); the modified code is available at While trees grown at approximately 29% (GO) or 37% (NeXO) of the maximal depth did improve performance slightly (<0.02 gain in correlation, ), we chose to grow trees to maximal depth because it is unclear how significant this gain is and whether it wou […]


Open source libraries and frameworks for biological data visualisation: A guide for developers

PMCID: 4409855
PMID: 25475079
DOI: 10.1002/pmic.201400377

[…] ctions. Different bioinformatics tools have already used this library. One example is NetworkAnalyst [], a tool for protein–protein interaction network analysis and visual exploration. Another one is NeXO Web [], the NeXO ontology database and related visualisation platform. […]


TermGenie – a web application for pattern based ontology class generation

J Biomed Semantics
PMCID: 4417543
PMID: 25937883
DOI: 10.1186/2041-1480-5-48

[…] n ontology. The best use is in early stages of ontology projects as it generates mostly list of candidate classes. For a more mature and formalized ontology, a more axiomatized result is required.The Network-Extracted Ontology (NeXO) [] is an example of an orthogonal, data-driven approach to ontology generation. This approach takes as input a sufficiently large and dense network (i.e. gene and pro […]


Sequence Analysis of the Genome of Piscine Orthoreovirus (PRV) Associated with Heart and Skeletal Muscle Inflammation (HSMI) in Atlantic Salmon (Salmo salar)

PLoS One
PMCID: 3726481
PMID: 23922911
DOI: 10.1371/journal.pone.0070075

[…] or myristoylation . No myristoylation- or S-palmitoylation sites were predicted for the hypothetical p8 protein. In contrast, S-palmitoylation sites were predicted for p11, at C13 and C14. Assuming a Nexo/Ccyt surface membrane topology for p11, the location of these sites differ from the S-palmitoylation sites in ARV- and NBV p10, which are located between their transmembrane and polybasic regions […]


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NeXO institution(s)
Department of Medicine, University of California San Diego, La Jolla, CA, USA
NeXO funding source(s)
This work was supported by the National Resource for Network Biology under a grant from the National Institute of General Medical Sciences (GM103504).

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