The eNanoMapper ontology
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README.md

Ontologies

The eNanoMapper ontologies aim to provide a comprehensive suite of ontologies for the nanomaterial safety assessment domain (see http://www.enanomapper.net for project information). The full suite of ontologies can be found assembled by imports in the primary enanomapper.owl file.

Internal

ontology-metadata-slim.owl - excerpt of the IAO (http://information-artifact-ontology.googlecode.com/) including metadata (annotation properties) only. nm.owl - nanomaterial descriptors ontology using the CHEMINF ontology

External

We import the NanoParticle Ontology (see http://nano-ontology.org); CHEMINF (https://github.com/semanticchemistry/semanticchemistry/); parts of ChEBI (http://www.ebi.ac.uk/chebi); and others (TBD).

DOI

Version 3: DOI

Version 4: DOI

Opening the ontology in Protégé

The stable version can be opened in Protégé with the following step:

  1. File → Open from URL...
  2. enter the URL http://purl.enanomapper.net/onto/enanomapper.owl

The development version is opened in the same way, but with a different URL:

  1. File → Open from URL...
  2. enter the URL http://purl.enanomapper.net/onto/enanomapper-dev.owl

Building and validating the ontology

During (and after) the eNanoMapper project the ontology was autobuilt using scripts on a Jenkins server. The main OWL file (enanomapper.owl) refers to slimmed versions of external ontologies, complemented with internal files adding additional terms. The slimming of the external ontologies is done with the Slimmer tool, with these commands (for the BioAssay Ontology):

rm -f *.owl
rm -f *.owl.*
wget -O bao_complete.owl http://www.bioassayontology.org/bao/bao_complete.owl
rm -f bao.props*
rm -f bao.iris*
wget https://raw.githubusercontent.com/enanomapper/ontologies/master/config/bao.props
wget https://raw.githubusercontent.com/enanomapper/ontologies/master/config/bao.iris
java -cp ../Slimmer/target/slimmer-0.0.1-SNAPSHOT-jar-with-dependencies.jar com.github.enanomapper.Slimmer .

The bao.props and bao.iris files contain all the information needed to describe which parts of the BAO ontology is retained in the slimmed version.

Tutorials

Please also check out these tutorials, developed by eNanoMapper, NanoCommons, and OpenRiskNet:

Making Releases

  1. Update external ontologies
    • Download slimed results from Jenkins workspace for each of the external ontologies
    • Replace the old *-slim.owl in ontologies/external/
  2. Update internal ontologies in ontologies/internal/
  3. Update the owl.versionInfo of enanomapper.owl
  4. Update the owl.versionInfo of enanomapper-dev.owl
  5. Release the whole repository in Github https://github.com/enanomapper/ontologies/releases
  6. Update the DOI number for new release: https://zenodo.org/record/260098#.WSLlGcbMyrM