Following discussion with other SciBite curators, we'd like to suggest some changes for your consideration please in the 'poison' role branch.
CHEBI:64909 'poison' is defined as "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.".
It has synonyms such as "toxic agent" and "toxic substance".
It has subclass CHEBI:27026 'toxin', defined as "Poisonous substance produced by a biological organism such as a microbe, animal or plant."
However, in common speak and in biomedical literature, 'toxin' is often used to describe synthetic as well as biological harmful substances. 'poison' is used less frequently. (PubMed hits: 152k for toxin, 81k for poison.)
The Wikipedia section on toxin terminology admits that "Toxin, toxicant, and poison are often used interchangeably despite these subtle differences in definition."
Hence, would you consider renaming CHEBI:27026 'toxin' as 'biological toxin' please,
and CHEBI:64909 'poison' as 'toxin'?
(CHEBI:27026 should not have "toxin" or "toxins" as synonyms;
CHEBI:64909 could keep "poison" as a synonym.)
This would also place 'nephrotoxin' and 'neurotoxin' as subclasses of 'toxin', which most users would expect, from a lexical point of view.
I've also noticed a potential duplication:
CHEBI:61015 'nephrotoxin' "A poison that interferes with the function of the kidneys."
CHEBI:50909 'nephrotoxic agent' "A role played by a chemical compound exihibiting itself through the ability to induce damage to the kidney in animals."
Should the two terms be merged? With 'nephrotoxin' as primary label and 'nephrotoxic agent' as synonym?
From a semantic standpoint, I'd expect any role class whose label contains "toxic agent" or "toxin" to be a child of CHEBI:64909 (which has a synonym "toxic agent"), especially if that's renamed as 'toxin'.
So I'd suggest that CHEBI:50912 'cardiotoxic agent', CHEBI:50908 'hepatotoxic agent' and CHEBI:50902 'genotoxin' are given the additional superclass CHEBI:64909.
Lastly, looking at CHEBI:52209 'aetiopathogenetic role' ("A role played by the molecular entity or part thereof which causes the development of a pathological process.") and its children: should all current children of CHEBI:27026 have 'aetiopathogenetic role' as an additional superclass?
Dear CHEBI team,
Following discussion with other SciBite curators, we'd like to suggest some changes for your consideration please in the 'poison' role branch.
CHEBI:64909 'poison' is defined as "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.". It has synonyms such as "toxic agent" and "toxic substance". It has subclass CHEBI:27026 'toxin', defined as "Poisonous substance produced by a biological organism such as a microbe, animal or plant." However, in common speak and in biomedical literature, 'toxin' is often used to describe synthetic as well as biological harmful substances. 'poison' is used less frequently. (PubMed hits: 152k for toxin, 81k for poison.) The Wikipedia section on toxin terminology admits that "Toxin, toxicant, and poison are often used interchangeably despite these subtle differences in definition." Hence, would you consider renaming CHEBI:27026 'toxin' as 'biological toxin' please, and CHEBI:64909 'poison' as 'toxin'? (CHEBI:27026 should not have "toxin" or "toxins" as synonyms; CHEBI:64909 could keep "poison" as a synonym.) This would also place 'nephrotoxin' and 'neurotoxin' as subclasses of 'toxin', which most users would expect, from a lexical point of view.
I've also noticed a potential duplication: CHEBI:61015 'nephrotoxin' "A poison that interferes with the function of the kidneys." CHEBI:50909 'nephrotoxic agent' "A role played by a chemical compound exihibiting itself through the ability to induce damage to the kidney in animals." Should the two terms be merged? With 'nephrotoxin' as primary label and 'nephrotoxic agent' as synonym?
From a semantic standpoint, I'd expect any role class whose label contains "toxic agent" or "toxin" to be a child of CHEBI:64909 (which has a synonym "toxic agent"), especially if that's renamed as 'toxin'. So I'd suggest that CHEBI:50912 'cardiotoxic agent', CHEBI:50908 'hepatotoxic agent' and CHEBI:50902 'genotoxin' are given the additional superclass CHEBI:64909.
Lastly, looking at CHEBI:52209 'aetiopathogenetic role' ("A role played by the molecular entity or part thereof which causes the development of a pathological process.") and its children: should all current children of CHEBI:27026 have 'aetiopathogenetic role' as an additional superclass?
Thank you,
Paola