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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



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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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