search

MaastrichtU-IDS / semanticscience

The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.
https://sio.semanticscience.org
61 stars 12 forks source link

why is submolecule not a subclass of covalently connected entity? #94

Closed cmungall closed 3 years ago

cmungall commented 3 years ago

image

Submolecule:

A covalently connected molecular entity:

I'm trying to interpret the significance of the difference in textual definitions, which are almost identical. Isn't the "collection of" implicit in the first definition?

Minor aside: the text def of CCE says "CCME" but the label of the class is CCE. I recommend following OBO style and not including the term name in the def to avoid redundancy/sync issues

mbrush commented 3 years ago

Going to piggyback on this ticket to ask a couple other questions about the SIO chemical entity hierarchy.

  1. The phrase "molecular entity" is used in the textual definitions in several chemical entity subclasses: a. Chemical substance: A chemical substance is a chemical complex of weakly interacting molecular entities, and may include bulk solvent. b. Submolecular entity: A submolecular entity is a part of a molecular entity. c. Covalently connected entity : A covalently connected molecular entity is the mereological sum of a collection of covalently bonded atoms.

But ‘molecular entity’ is not a SIO class, and the phrase is not defined clearly in these definitions. This makes it hard to understand what these SIO classes mean and how they are meant to be related to other SIO classes. Does the notion of a ‘molecular entity’ as used in these text definitions map to a specific SIO class?

  1. I noticed SIO:chemical entity is asserted to be equivalent to CHEBI:23367 molecular entity. I think that SIO:chemical entity more closely maps to ChEBI:24431 ‘chemical entity’.
micheldumontier commented 3 years ago

Thanks for reporting these issues. I've taken both of your feedback and refactored the ontology and modified definitions.

sio-refactored

chemical substance: A chemical substance is a chemical entity composed of two or more weakly interacting chemical entities.

molecule: A molecule is single chemical entity composed of fully covalently bonded atoms.

submolecular entity: A submolecular entity is a part of a molecule or a particle smaller than a molecule.

submolecule: A submolecule is any part of a molecule.

cmungall commented 3 years ago

Thanks! I see the change on OLS, so I will close this now!