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enanomapper / ontologies

The eNanoMapper ontology
https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0005-5
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some CHEBI classes do not have any parent class #229

Closed lwinckers closed 4 years ago

lwinckers commented 4 years ago

I noted that the following CHEBI classes do not have any parent class and do not show up on bioportal unless you specifically search for them.

It is about the following CHEBI classes: CHEBI 27569: selenium atom CHEBI 27638: cobalt atom CHEBI 28685: molybdenum atom CHEBI 31794: magnesium oxide CHEBI 33341: titanium atom CHEBI 51110: copper(II) sulfide CHEBI 60533: γ-poly(L-glutamic acid) polymer CHEBI 85541: elemental molecular entity

structure as seen in Protegé: image

Example of specific search for one of these classes: image

I do not know if we should manually attend parent classes to these, or how to tackle this problem!?

lwinckers commented 4 years ago

Need to check if adding atom will fix this --> did the edit in config/bfo.iris (https://github.com/enanomapper/ontologies/pull/236/files)

egonw commented 4 years ago

I have pushed a patch that replaces the 'atom' parts with their respective 'molecular entity' parts. Let's see how that goes,

egonw commented 4 years ago

So, nanoparticles have a chemical content, they consist of material. So, first they consisted of atoms, not bad, but those atoms were always neutral (well, 0 valency) and in retrospect maybe that may not be the best representation. So, I first updated the affected classes to have an axiom mentioning the corresponding materials. In the second step I added these materials to our ontology, under the right super class.