oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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Labels 'produces' and 'produced by' are too broad / ambiguous #316

Open DanFaria opened 5 years ago

DanFaria commented 5 years ago

As defined, the relations labeled 'produces' and 'produced by' are intended to relate the material entity where a process occurs to an output of the process that is also a material entity and vice-versa. This is indeed one common usage of the labels in question, as in "tree produces resin". However, the labels are also commonly used to relate a process with its output, as in "petroleum is produced by pyrolysis", and even if the output is not a material entity, as in "DNA sequencing produces FASTQ files". I am concerned with the potential for these relations to be misused or misinterpreted due to their ambiguous label, though I am not sure if there is a less ambiguous but still simple alternative.

nlharris commented 3 years ago

Is there still need for an answer?

DanFaria commented 3 years ago

This was never a question in the first place ;-) I was merely expressing my concern about the intended scope of the relations with these labels (as defined) being much narrower than the natural language usage of their labels, and the potential for misuse/confusion this might generate. "produces" is commonly used to connect a process to its output (as per the examples I gave above), and indeed I see it is now listed an alternative term for "has output" (RO_0002234) in the latest version of the RO. My feeling is that using simply "produces" as the label for RO_0003000, which connects a material entity wherein a process occurs to the output of that process, is confusing, and a less ambiguous label (akin to "has output" for RO_0002234) would be preferable (though I am not sure a clean solution exists). If you don't think this in an issue or cannot find a clean solution for it, you can go ahead and close this.

nlharris commented 2 years ago

Can this be closed?