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.
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
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).
Opening the ontology in Protégé
The stable version can be opened in Protégé with the following step:
- File → Open from URL...
- enter the URL http://purl.enanomapper.net/onto/enanomapper.owl
The development version is opened in the same way, but with a different URL:
- File → Open from URL...
- 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.
Please also check out these tutorials, developed by eNanoMapper, NanoCommons, and OpenRiskNet:
- Update external ontologies
- Download slimed results from Jenkins workspace for each of the external ontologies
- Replace the old *-slim.owl in ontologies/external/
- Update internal ontologies in ontologies/internal/
- Update the owl.versionInfo of enanomapper.owl
- Update the owl.versionInfo of enanomapper-dev.owl
- Release the whole repository in Github https://github.com/enanomapper/ontologies/releases
- Update the DOI number for new release: https://zenodo.org/record/260098#.WSLlGcbMyrM