NM_001005 describes both particle size and zeta potential

[vedina]

Please check

 <owl:Class rdf:about="&resource;NM_001005">
        <rdfs:label>particle size descriptor</rdfs:label>
        <rdfs:subClassOf rdf:resource="&resource;NM_000005"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="&obo;IAO_0000136"/>
                <owl:someValuesFrom rdf:resource="&resource;NM_000001"/>
            </owl:Restriction>
        </rdfs:subClassOf>
    <description>Describes the particle size. The actual approach to describes it is
      undefined at this level.</description>
    </owl:Class>

    <owl:Class rdf:about="&resource;NM_001005">
        <rdfs:label>zetapotential descriptor</rdfs:label>
        <rdfs:subClassOf rdf:resource="&resource;NM_000006"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="&obo;IAO_0000136"/>
                <owl:someValuesFrom rdf:resource="&resource;NM_000001"/>
            </owl:Restriction>
        </rdfs:subClassOf>
    <description>Describes the zeta potential of the nanomaterial. The potential
      may be experimental, predicited, or originating from a read-across approach.</description>
    </owl:Class>

[jannahastings]

Hi, this is in the internal/descriptors/nm.owl file? This file was deprecated, we have migrated all the nanomaterial descriptors into the main enanomapper.owl and dependent files, for example, for particle size use NPO_1694 and for zeta potential use NPO_1302.

[egonw]

Janna, do you have a list of all mappings? I should update my source code too...

[jannahastings]

No — now that would have been a good thing to do when I did the migration, right? :-(… I’ll add it to my list of things to do…

Janna

On 15 Jun 2015, at 11:57, Egon Willighagen [email protected] wrote:

Janna, do you have a list of all mappings? I should update my source code too...

— Reply to this email directly or view it on GitHub https://github.com/enanomapper/ontologies/issues/23#issuecomment-112017686.

[vedina]

I probably used nm.owl indeed

[jannahastings]

Here is the mapping as requested:

NM_000001 (nanomaterial): NPO_199 NM_000101 (carbon nanotube): NPO_606 NM_000102 (graphene): not in ENM, should it be? Would be imported as CHEBI:36973. NM_000100 (metal oxide): NPO_1541 (metal oxide nanoparticle) NM_000103 (two element metal oxide): not in ENM, should it be? NM_000004 (nanomaterial quality): not needed; maps to BFO_0000019 (quality) NM_000005 (metal oxide descriptor): not needed; maps to CHEMINF_000123 (chemical descriptor) NM_001004 (heat of formation): maps to CHEMINF_000241 (enthalpy of formation, has heat of formation as a synonym) NM_001001 (ionization enthalpy): CHEMINF_000191(ionization energy descriptor) NM_001002 (metal atom count): CHEMINF_000448 NM_001003 (oxygen atom count): CHEMINF_000449 NM_001005 (particle size descriptor): NPO_1694 (particle size) NM_001005 (zetapotential descriptor): NPO_1302 (zeta potential) NM_001000 (composition mass descriptor): Not in ENM, but we have e.g. CHEMINF_000083 (mass descriptor) to build on. NM_000002 (nanomaterial information format specification): map to CHEMINF_000014 which I just now renamed to 'chemical entity information format specification'; in the future we might decide to create a special subclass of this class.
NM_001009 (band energies): is this CHEMINF_000487 (energy band gap)? NM_001008 (metal element mass): CHEMINF_000488 (metal element mass descriptor) NM_001006 (metal group descriptor): map to CHEMINF_000516 (group of an atom) NM_001007 (metal period descriptor): map to CHEMINF_001523 (period of an atom)

[vedina]

Thanks, the mapping looks good. I'll also ask for entries able to represent

• volumetric distribution
• counted distribution
• mass based distribution

The issue is that means for the parameters which are measured not as single values but as distribution (size , hydrodynamic diameter , etc.) can be calculated based on volume, number of particles or mass. Thus we find mass median diameter or mass median aerodynamic diameter , which are different from statistical mean or median based on number of particles. (and there are studies which works better as descriptors).

[fehrhart]

close?

[vedina]

Do we have these (types) of distributions in the ontology already?

[DeniseSl22]

All terms with the word "distribution" in them:

• volumetric distribution == volume of distribution

• counted distribution --> not found, we do have "size distribution" (2x, see red box above, @egonw how to handle this?), and "particle size distribution" :

• mass based distribution --> not found, see https://en.wikipedia.org/wiki/Mass_distribution ; term doesn't seem to exist in bioportal search query, so might make sense to mint one for ourselves.