NeXO Database Policy


The goal of the NeXO Web database is to provide the research community with access to the Network-eXtracted Ontology (NeXO) and the Gene Ontology (GO) to which NeXO is aligned to. It aims to facilitate an intuitive framework for investigating biological machinery captured by both data-driven and manually-curated ontologies.

What is stored in the NeXO database?

NeXO Web database currently stores the NeXO ontology as well as the GO ontology version to which NeXO has been aligned to. For each ontology (NeXO or GO), the database stores the terms (identified by a numeric term id), term names and descriptions, terms alignments (for NeXO terms), as well as term-term relationships. The terms and term-term relationships together comprise the ontolgy directed acyclic graph. We also compute and store a tree version of each ontology to allow for easy and intuitive layout of the entire ontology structure. For the NeXO ontology we also store and make available the raw gene-gene/protein-protein interaction data that was used to compute the ontology.

NeXO Data Availability and Formats

The NeXO Database provides access to the current and archive versions of the NeXO ontology, NeXO gene annotations and associated network data used to construct NeXO. In each case we provide the ontology terms and term-term relationships in the OBO format and gene-to-term annotations in tab separated text format. We supply the tree version of the onotology and the raw interaction data in a tab separated format. Both the tree and the complete DAG version of NeXO is also available as a Cytoscape session file. These files as well as the GO ontologies to which NeXO has been aligned to are available from the Download page.

NeXO Update Policy and Versioning

NeXO Web Database follows a versioning system with major and minot releases. The initial NeXO ontology is assigned a release version 1.0. Subsequent major NeXO ontology releases are expected at a frequency of once per annum and assigned the subsequent major version number. The major releases will update the NeXO structure based on the complement of gene/protein interaction data accumulated throughout each year. The minor number in this versioning system is used to indicate NeXO versions with incremental updates and revisions made throughout the year between major releases. Minor updates are expected evey 3-4 months and will include alignments of NeXO to the current release of the Gene Ontology.

The NeXO term naming system will preserve term names between NeXO releases as long as the term itself is preserved in the new version of the ontology. Preserved terms are the ones that are determined as sufficiently aligned to the term in the previous ontology version according to the NeXO ontology alignment system. In particular, terms that have the same gene assignments in subsequent ontology releases are preserved.