Changing labels and definitions for 'envenomation' terms

[pgaudet]

Hello,

The multiorganism group has proposed (some time ago already!) to change 'envenomation' terms, which specifically refer to organisms with fangs, to 'toxin-mediated', which is broader. Definitions of toxin and venoms from chatgpt:

Toxins: Passive, broad term for any naturally produced poison.
Venoms: Subtype of toxins with active delivery mechanisms and specific biological purposes like defense or predation.

• Parent class of this group of terms: current name: envenomation resulting in modulation of process in another organism
• Proposed new name: toxin-mediated perturbation of process in another organism
• Current definition: The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the manifestation of some change or damage to the bitten organism.
• Proposed: The biological effect of a poisonous substance produced by one organism to disrupt the normal functioning of another organism, at the molecular, cellular or organism level.
• • Comment: This term covers both toxins and venoms. Toxins are delivered passively through ingestion, absorption, or exposure, while venoms are a type of toxin actively delivered through specialized mechanisms such as stings or bites.

@FJungo
@mgiglio99
@dsiegele
@genegodbold

Please review and suggest any improvements you'd like.

[pgaudet]

Change labels of the 54 children as follows:

• envenomation resulting in blood agglutination in another organism >> rename >> toxin-mediated blood agglutination in another organism
• envenomation resulting in blood vessel extracellular matrix damage, causing hemorrhagic damage in another organism >> rename >> toxin-mediated blood vessel extracellular matrix damage, causing hemorrhagic damage in another organism
• envenomation resulting in damage of muscle extracellular matrix in another organism >> rename >> toxin-mediated damage of muscle extracellular matrix in another organism
• envenomation resulting in depletion of circulating fibrinogen in another organism >> rename >> toxin-mediated depletion of circulating fibrinogen in another organism
• envenomation resulting in fibrinogenolysis in another organism >> rename >> toxin-mediated fibrinogenolysis in another organism
• envenomation resulting in fibrinolysis in another organism >> rename >> toxin-mediated fibrinolysis in another organism
• envenomation resulting in hemorrhagic damage in another organism >> rename >> toxin-mediated hemorrhagic damage in another organism
• envenomation resulting in impairment of hemostasis in another organism >> rename >> toxin-mediated impairment of hemostasis in another organism
• envenomation resulting in induction of edema in another organism >> rename >> toxin-mediated induction of edema in another organism
• envenomation resulting in modulation of G protein-coupled receptor activity in another organism >> rename >> toxin-mediated perturbation of G protein-coupled receptor activity in another organism
• envenomation resulting in modulation of acid-sensing ion channel activity in another organism >> rename >> toxin-mediated perturbation of acid-sensing ion channel activity in another organism
• envenomation resulting in modulation of blood coagulation in another organism >> rename >> toxin-mediated perturbation of blood coagulation in another organism
• envenomation resulting in modulation of blood pressure in another organism >> rename >> toxin-mediated perturbation of blood pressure in another organism
• envenomation resulting in modulation of calcium channel activity in another organism >> rename >> toxin-mediated perturbation of calcium channel activity in another organism
• envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in another organism >> rename >> toxin-mediated perturbation of glucagon-like peptide receptor 1 activity in another organism
• envenomation resulting in modulation of ion channel activity in another organism >> rename >> toxin-mediated perturbation of ion channel activity in another organism
• envenomation resulting in modulation of mast cell degranulation in another organism >> rename >> toxin-mediated perturbation of mast cell degranulation in another organism
• envenomation resulting in modulation of platelet aggregation in another organism >> rename >> toxin-mediated perturbation of platelet aggregation in another organism
• envenomation resulting in modulation of receptor activity in another organism >> rename >> toxin-mediated perturbation of receptor activity in another organism
• envenomation resulting in modulation of sensory perception of pain in another organism >> rename >> toxin-mediated perturbation of sensory perception of pain in another organism
• envenomation resulting in modulation of signal transduction in another organism >> rename >> toxin-mediated perturbation of signal transduction in another organism
• envenomation resulting in modulation of transmission of nerve impulse in another organism >> rename >> toxin-mediated perturbation of transmission of nerve impulse in another organism
• envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in another organism >> rename >> toxin-mediated perturbation of vasoactive intestinal polypeptide receptor activity in another organism
• envenomation resulting in modulation of voltage-gated potassium channel activity in another organism >> rename >> toxin-mediated perturbation of voltage-gated potassium channel activity in another organism
• envenomation resulting in modulation of voltage-gated sodium channel activity in another organism >> rename >> toxin-mediated perturbation of voltage-gated sodium channel activity in another organism
• envenomation resulting in muscle damage in another organism >> rename >> toxin-mediated muscle damage in another organism
• envenomation resulting in myocyte killing in another organism >> rename >> toxin-mediated myocyte killing in another organism
• envenomation resulting in negative regulation of acid-sensing ion channel activity in another organism >> rename >> toxin-mediated suppression of acid-sensing ion channel activity in another organism
• envenomation resulting in negative regulation of blood coagulation in another organism >> rename >> toxin-mediated suppression of blood coagulation in another organism
• envenomation resulting in negative regulation of blood pressure in another organism >> rename >> toxin-mediated suppression of blood pressure in another organism
• envenomation resulting in negative regulation of calcium channel activity in another organism >> rename >> toxin-mediated suppression of calcium channel activity in another organism
• envenomation resulting in negative regulation of heart rate in another organism >> rename >> toxin-mediated suppression of heart rate in another organism
• envenomation resulting in negative regulation of high voltage-gated calcium channel activity in another organism >> rename >> toxin-mediated suppression of high voltage-gated calcium channel activity in another organism
• envenomation resulting in negative regulation of low voltage-gated calcium channel activity in another organism >> rename >> toxin-mediated suppression of low voltage-gated calcium channel activity in another organism
• envenomation resulting in negative regulation of platelet aggregation in another organism >> rename >> toxin-mediated suppression of platelet aggregation in another organism
• envenomation resulting in negative regulation of sensory perception of pain in another organism >> rename >> toxin-mediated suppression of sensory perception of pain in another organism
• envenomation resulting in negative regulation of voltage-gated calcium channel activity in another organism >> rename >> toxin-mediated suppression of voltage-gated calcium channel activity in another organism
• envenomation resulting in negative regulation of voltage-gated potassium channel activity in another organism >> rename >> toxin-mediated suppression of voltage-gated potassium channel activity in another organism
• envenomation resulting in negative regulation of voltage-gated sodium channel activity in another organism >> rename >> toxin-mediated suppression of voltage-gated sodium channel activity in another organism
• envenomation resulting in occlusion of the pore of voltage-gated potassium channel in another organism >> rename >> toxin-mediated occlusion of the pore of voltage-gated potassium channel in another organism
• envenomation resulting in plasminogen activation in another organism >> rename >> toxin-mediated plasminogen activation in another organism
• envenomation resulting in pore formation in membrane of another organism >> rename >> toxin-mediated pore formation in membrane of another organism
• envenomation resulting in positive regulation of G protein-coupled receptor activity in another organism >> rename >> toxin-mediated activation of G protein-coupled receptor activity in another organism
• envenomation resulting in positive regulation of acid-sensing ion channel activity in another organism >> rename >> toxin-mediated activation of acid-sensing ion channel activity in another organism
• envenomation resulting in positive regulation of blood coagulation in another organism >> rename >> toxin-mediated activation of blood coagulation in another organism
• envenomation resulting in positive regulation of blood pressure in another organism >> rename >> toxin-mediated activation of blood pressure in another organism
• envenomation resulting in positive regulation of glucagon-like peptide receptor 1 activity in another organism >> rename >> toxin-mediated activation of glucagon-like peptide receptor 1 activity in another organism
• envenomation resulting in positive regulation of mast cell degranulation in another organism >> rename >> toxin-mediated activation of mast cell degranulation in another organism
• envenomation resulting in positive regulation of platelet aggregation in another organism >> rename >> toxin-mediated activation of platelet aggregation in another organism
• envenomation resulting in positive regulation of signal transduction in another organism >> rename >> toxin-mediated activation of signal transduction in another organism
• envenomation resulting in positive regulation of vasoactive intestinal polypeptide receptor activity in another organism >> rename >> toxin-mediated activation of vasoactive intestinal polypeptide receptor activity in another organism
• envenomation resulting in positive regulation of voltage-gated sodium channel activity in another organism >> rename >> toxin-mediated activation of voltage-gated sodium channel activity in another organism
• envenomation resulting in slowing of activation kinetics of voltage-gated potassium channel in another organism >> rename >> toxin-mediated slowing of activation kinetics of voltage-gated potassium channel in another organism
• envenomation resulting in vasodilation in another organism >> rename >> toxin-mediated vasodilation in another organism

[pgaudet]

• Also, we need to change the definitions for all the terms. Right now the pattern is:
  A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with xxx'
• • New definition - for example 'toxin-mediated perturbation of xxx in another organism'
    A process in which a poisonous substance produced by an organism alters xxx in another organism'
• We will also need to change all envenomation synonym scope to 'narrow'

[FJungo]

Hello
Thank you Pascale for continuing this project!
I propose the following definitions that differ slightly from that of ChatGPT, since a toxin is toxic independently of its delivery mode. Most of venom proteins (actively delivered by a specialized apparatus) are toxins. However, the idea can be maintained without explicitly definiting toxin and venom.

[no change]
• Parent class of this group of terms: current name: envenomation resulting in modulation of process in another organism
• Proposed new name: toxin-mediated perturbation of process in another organism
• Current definition: The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the manifestation of some change or damage to the bitten organism.
• Proposed: The biological effect of a poisonous substance produced by one organism to disrupt the normal functioning of another organism, at the molecular, cellular or organism level.
o [Pascale proposition] Comment: This term covers both toxins and venoms. Toxins are delivered passively through ingestion, absorption, or exposure, while venoms are a type of toxin actively delivered through specialized mechanisms such as stings or bites.
o [My proposition] Comment: This term covers all proteins that show toxicity, regardless of the mode of penetration into the host. Penetration can occur passively through ingestion, absorption, or exposure, or actively through specialized mechanisms such as stings or bites by venomous animals, for example.
...
Every terms sound good, except those with “suppression”.
I suggest to use: inhibition (most terms) and reduction (with blood pressure, and heart rate):
toxin-mediated reduction of blood pressure in another organism
toxin-mediated reduction of heart rate in another organism
...
The new definition you propose are ok for me.
New definition - for example 'toxin-mediated perturbation of xxx in another organism'
A process in which a poisonous substance produced by an organism alters xxx in another organism'

Many thanks !

[genegodbold]

My thoughts:

• I want to make sure Cnidaria aren't neglected as they do a lot of stinging with their polyps (anemones and jelllyfish)
• I like the "toxin-mediated perturbation...in another organism" syntax but if this is adopted we might have overlap with "symbiont-mediated perturbation" for bacteria that produce toxins. The former makes more sense for the Clostridial neurotoxins. The Clostridia genus isn't really symbiotic (I don't think) or pathogenic EXCEPT for the toxins they produce. However, other bacteria, like Bacillus anthracis, make several toxins that are part of a coordinated symbiotic (pathogenic) response so those toxic proteins (lethal factor, edema factor) could be annotated with either or both of the terms. Not that this is a big deal, I'm just thinking...
• Bacterial toxins often have an effect INSIDE the target (host) cell and require one or more subunits to mediate attachment and invasion of the toxic subunit. To the best of my knowledge, venoms always affect things on the OUTSIDE of the cell or in tissues that they can reach through the circulation. So they don't have required chaperone subunits.
• I think we should avoid terms for toxins that is the same as normal (homeostatic) regulation. These things are generating unusual, often life-threatening changes that aren't evolved to produce a balanced response or meant to guarantee a return to normality. So I'd avoid "inhibition"

[FJungo]

My answer:

• I want to make sure Cnidaria aren't neglected as they do a lot of stinging with their polyps (anemones and jelllyfish)
  

--> Sea anemones and jellyfishes are considered as venomous animals. This precision can be added in the comment:
Comment: This term covers all proteins that show toxicity, regardless of the mode of penetration into the host. Penetration can occur passively through ingestion, absorption, or exposure, or actively through specialized mechanisms such as stings or bites by venomous animals (snakes, scorpions, sea anemones, etc.), for example.
[..]

• Bacterial toxins often have an effect INSIDE the target (host) cell and require one or more subunits to mediate attachment and invasion of the toxic subunit. To the best of my knowledge, venoms always affect things on the OUTSIDE of the cell or in tissues that they can reach through the circulation. So they don't have required chaperone subunits.
  

--> Like you, to my knowledge, venom toxins do not require chaperone subunits.

• I think we should avoid terms for toxins that is the same as normal (homeostatic) regulation. These things are generating unusual, often life-threatening changes that aren't evolved to produce a balanced response or meant to guarantee a return to normality. So I'd avoid "inhibition"
  

--> What about also using "perturbation" instead of suppression or inhibition ?
--> With the criteria of normal regulation (homeostasis), should we also avoid "activation" ?

All the best, F.

[genegodbold]

--> What about also using "perturbation" instead of suppression or inhibition ?
Perturbation lacks a direction but it could be a parent term for a "suppression"/"activation" pair

The homeostatic terms I was thinking about were "positive/negative reguation" but there could be others.

--> With the criteria of normal regulation (homeostasis), should we also avoid "activation" ?
Yes, you're right. But what? :-)
Inciting?

[genegodbold]

@FJungo, how do you do those nice little text boxes from a previous comment that you then respond to?