Eliminating "(whole)" from FoodOn product labels

[Damion Dooley]

We had started to take an approach in past of allowing ambiguity directly in classes defined within foodon such as "chicken (whole or parts)". We will keep such classes that we've already set up, but going into the future, if a biosample or other record wants to indicate ambiguity, then in addition to pointing to the animal or organ or plant or plant part that the biosample derived from, it will need to add a generic "animal (whole or parts)", "animal organ (whole or parts)" or "vegetable (whole or parts)" reference for example, to indicate ambiguity.  FoodOn will comprehensively name individual items like "apple" and "piece of apple" for convenience, and as the foundation for further processing.

In connection with that, we have existing entries such as "apple (whole)".  We will be removing the "(whole)" suffix, but ensure that the "whole" semantic is maintained both in term definition ("A pome fruit ...") and axiomatization.  This will lessen the visual disconnect between the fields talking about what the biosample derives from (was "apple (whole)", now just "apple") and statement of ambiguity ("fruit (whole or parts)").  We welcome feedback on this.

[Robert Warren]

Damion,

I think that this is good practice. We spend most of our time talking about ontological issues but, at the end of the day, the 90% use case is the string that is going to be displayed to the end user. 

Qualifiers are programmatically easy to add if they are needed by the application, but unwieldy to remove through parsing.

-rhw 

On Sun, 2 Apr 2023 at 19:32, Damion Dooley <damion...@gmail.com> wrote:

We had started to take an approach in past of allowing ambiguity directly in classes defined within foodon such as "chicken (whole or parts)". We will keep such classes that we've already set up, but going into the future, if a biosample or other record wants to indicate ambiguity, then in addition to pointing to the animal or organ or plant or plant part that the biosample derived from, it will need to add a generic "animal (whole or parts)", "animal organ (whole or parts)" or "vegetable (whole or parts)" reference for example, to indicate ambiguity.  FoodOn will comprehensively name individual items like "apple" and "piece of apple" for convenience, and as the foundation for further processing.

In connection with that, we have existing entries such as "apple (whole)".  We will be removing the "(whole)" suffix, but ensure that the "whole" semantic is maintained both in term definition ("A pome fruit ...") and axiomatization.  This will lessen the visual disconnect between the fields talking about what the biosample derives from (was "apple (whole)", now just "apple") and statement of ambiguity ("fruit (whole or parts)").  We welcome feedback on this.

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