workshops

Exercise 4: Adding a new nanoparticle to the ontology

Starting from the description in the previous section of the OWL Class definition of a nanomaterial, you will develop and OWL Class definition of a material that is not in the ontology yet.

Creating a new OWL Class definition for a nanomaterial

A recent paper [0] has a nice supplementary information section with toxicology data extracted from literature. The NanoSolveIT project is currently making this data available to modellers. As part of that process, the content needs to be annotated to with ontology terms, for example for the nanomaterials that are studied.

Because the NanoParticle Ontology has had a limited set of nanoparticles defined, we routinely have to add nanomaterials to the ontology. That is needed to have a unique ontology identifiers, allowing us to specifically specify what we are talking about.

But for this paper, the following nanomaterials are still missing:

Cr nanoparticle
Co nanoparticle
Bi nanoparticle
Mo nanoparticle
Co3O4 nanoparticle
CdO nanoparticle
MnO nanoparticle

Of course, first it must be checked if the NanoParticle Ontology and eNanoMapper Ontology indeed do not contain these materials, and if they do not, they need to be added.

Tasks

The goal of this part of the workshop is to develop an OWL Class definition for one of the missing items (or, if you prefer, for a nanomaterial you worked on yourself and that is missing).

Step 1: copy/paste the OWL Class definition:

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_9000245">
  <rdfs:subClassOf rdf:resource="http://purl.bioontology.org/ontology/npo#NPO_1384"/>
  <npo-ext:code rdf:datatype="http://www.w3.org/2001/XMLSchema#string">titanium nanoparticle</npo-ext:code>
  <rdfs:label xml:lang="en">titanium nanoparticle</rdfs:label>
  <owl:equivalentClass>
    <owl:Class>
      <owl:intersectionOf rdf:parseType="Collection">
        <rdf:Description rdf:about="http://purl.bioontology.org/ontology/npo#NPO_707"/>
        <owl:Restriction>
          <owl:onProperty rdf:resource="http://purl.bioontology.org/ontology/npo#has_component_part"/>
          <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33341"/>
        </owl:Restriction>
      </owl:intersectionOf>
    </owl:Class>
  </owl:equivalentClass>
  <synonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ti nanoparticle</synonym>
</owl:Class>

Step 2: update the IRI and replace ENM_9000245 with ENM_9000xxx (the ontology code will be assigned when your contribution gets incorporated into the released ontology)
Step 3: replace the npo-ext:code, rdfs:label, and synonym
Step 4: look up in the eNanoMapper ontology which more general ontology class is suitable for your materials, e.g. the IRI for metal nanoparticle or metal oxide nanoparticle and update the rdf:subClassOf line
Step 5: look up in the ChEBI ontology which term it has for the chemical that is part of this particle and update the owl:someValuesFrom line in the code

Contributing your work to the eNanoMapper ontology

When done, explain your solution with your neighbor (peer review) and consider submitting this term to the eNanoMapper ontology. For this, and this is optional but very much appreciated (and please do ask for help from the Workshop assistants), do:

Step 6: Visit https://github.com/ and log in
Step 7: Go to https://github.com/enanomapper/ontologies (and scan the README text)
Step 8: Got to https://github.com/enanomapper/ontologies/blob/master/internal/npo-ext.owl
Step 9: Look for the Edit this file link and click it
Step 10: An editor will open, and you can add your contribution somewhere to this file.
Step 11: When done, prepare the patch by scrolling to the bottom and adding a description of your work. The section to look for should look like:

Step 12: After you submitted the patch, make a Pull Request

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