Are new classes/definitions required for chemical composition?

[RichardLMR]

The scenario I am thinking about would be assigning an entry for the ISA-TAB-Nano Material file "Material Chemical Name" field, but this could be a more generally applicable concern.

There appears a need for suitable, generic chemical names (based upona quick search of both eNM and CHEBI via BioPortal) e.g. "titanium dioxide nanoparticle" appears but not a generic "titanium dioxide". My understanding is that, according to some definitions at least, "nanoparticle" means all three dimensions are in the nanoscale range so this might not be most appropriate for a "titanium dioxide" nanomaterial of some other form. The ChEBI definition of "titanium dioxide" is perhaps problematic due to the suggestion that it is a molecular entity associated with the synonym "O=[Ti]=O", whereas nanomaterial TiO2 is more likely a crystal structure (Ti---O---Ti etc.) which is not based on such discrete molecular entities. Are there any possible ways to address this? Other ontology imports? De novo creation?

[jannahastings]

Nina, I have assigned you as I would be interested to hear your thoughts on this challenge. Feel free to assign back to me after commenting. Thanks!

[vedina]

Some initial observations:

Particle (and subclass nanoparticle) is a

• eNM : subclass of molecular entity
• NPO : subclass of chemical entity , while molecular entity a separate class.
  The NPO approach seems more appropriate to me.

Nanomaterial

• eNM & NPO : subclass of chemical substance , which is a subclass of material entity
• NPO : subclass of chemical substance , which is a subclass of material entity

If I understand right the logic, the nanoparticle itself is not declared as nanomaterial, but as an individual particle. However, what experiments are characterizing is the material in its entirety, not the individual particles. In this sense, the nanoparticle formulation entity should probably be used in the context of experimental data, and we shall provide means to specify what the formulation consists of.

@RichardLMR is correct, the current ontologies (both eNM and NPO) do not distinguish between the crystal phases of materials.

• eNM and NPO have have entry for titanium dioxide nanoparticle, which in NPO does not assume it is a molecular entity (see above).
• CHEBI has two separate entities, titanium dioxide representing the molecular entity and titanium dioxide nanoparticle which also is a (non direct) descendant of molecular entity . The statement that
  titanium dioxide nanoparticle (CHEBI:51050) is a titanium dioxide (CHEBI:32234) is not correct IMHO.
• molecular entity is defined as Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. .
• Rutile, anatase, brukite, tittanium oxide nanotubes are all TiO2, hence referring to the chemical formula is not wrong. It should not be specified as same as relationship however.
• In the database we represent nanomaterials as substances, and each component can link to a chemical entity, including e.g. crystal structure loaded from PDB file.

Crystal

• NPO: subclass of chemical substance , parallel branch to nanomaterial
• eNM (missing?)
• SNOMEDCT: crystal is a subclass of substance (solid substance to be exact), but not a subclass of chemical or material SNOMEDCT/264297004
• BIOMO Biological Observation Matrix Ontology: crystal structure is a subclass of molecular structure SIO_001100

A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid.

• OPB Ontology of Physics for Biology : Crystal OPB_01475

A chemical substance consisting of atoms, ions, and/or molecules 
that are arranged in an ordered pattern extending in all three spatial dimensions.

Future challenges - mixture of nanomaterials

@vedrin Looking at the ontologies discrepancies may give much food for an epistemology essay :)

I think the key point is can molecular entity represent crystal structures?

OPB may worth looking at, they do distinguish between Discrete chemical structure and Molecule (with crystal subclass of the first, but not of the second).

CODATA UDS is also instructive (roughly summarizing, crystallinity and chemical composition are characterisations of the nanoobject). Company catalogs are useful as well.

and finally (or should we start with)

IUPAC

Chemical substance

Matter of constant composition best characterized by the entities 
(molecules, formula units, atoms) it is composed of. 
Physical properties such as density, refractive index, electric conductivity, 
melting point etc. characterize the chemical substance.

Constituent

Chemical species present in a system; often called a component, 
although the term component has a more restricted meaning in 
physical chemistry.

Component

Constituent of a mixture the amount or concentration of which can be 
varied independently. The number of components in a given system 
is the minimum number of independent species necessary to define
the composition in all the phases of a system.

Molecule

An electrically neutral entity consisting of more than one atom (n > 1). 
Rigorously, a molecule, in which  n > 1 must correspond to a 
depression on the potential energy surface that is deep enough 
to confine at least one vibrational state.

Crystallinity

The presence of three-dimensional order on the level of atomic dimensions. 
Crystallinity may be detected by diffraction techniques, heat-of-fusion measurements, etc. 
The amount of disorder within the crystalline region is not incompatible with this concept.

mixture, phase domain (micro-,nano-) , nanodomain morphology, nanocomposite