Toxic terms for obsoletion

[gocentral]

The following are terms under 'lysin' and 'toxin' that I would like to obsolete because they represent gene products or classes of gene products and not true molecular functions.

GO:0019844 endotoxin Any microbial toxin that cannot be easily separated from the structure of the cell. GO:0019845 exotoxin A toxin formed by a microorganism and secreted into the surrounding medium. GO:0019849 cytotoxin Acts as to cause injury to other living cells. GO:0019846 enterotoxin Acts as to cause injury to the intestinal mucosa of other living organisms. GO:0019847 neurotoxin Acts to inhibit neural function in another living organism.

- These are toxins differentiated solely by the cellular/anatomical region in which they act - this isn't a valid functional classification endotoxin --> toxin ; GO:0015070, intracellular ; GO:000 exotoxin --> toxin ; GO:0015070, extracellular ; GO:0005576 cytotoxin --> toxin ; GO:0019849 enterotoxin --> toxin ; GO:0015070 neurotoxin --> toxin ; GO:0015070 The extra information in 'enterotoxin' and 'neurotoxin' should be captured in an anatomical ontology - it is beyond the scope of GO.

GO:0019848 conotoxin Acts to inhibit neural function in another organism by inhibiting voltage-gated calcium ion channels and neurotransmitter release. (GO) Conotoxins inhibit voltage-gated calcium channels, thereby blocking synaptic transmission. (online def)

• Gene product, not a function. -->calcium channel inhibitor activity ; GO:0019855 negative regulation of neurotransmitter secretion ; GO:0046NEW

GO:0008229 opsonin Binds to microorganisms or other particulate material (for example, foreign erythrocytes) to increase the susceptibility of the latter to phagocytosis. -->antigen binding activity ; GO:0003823

GO:0015465 lysin activity (1 annotation) An agent that can lyse cells.

• This is a gene product and not an activity. The activity of the lysin is a process. -->cytolysis ; GO:0019835

GO:0015466 autolysin activity (0 annotations) An agent that can lyse the cell in which it is synthesized. -->cytolysis ; GO:0019835

GO:0015484 hemolysin activity (14 annotations, 11 of which have 'hemolysin' in the gene product name) Any substance that causes the lysis of red blood cells; any bacterial exotoxin that ruptures blood-cell membranes. hemolysin is a gene product; the activity is actually a process --> hemolysis ; GO:0019836

GO:0015642 bacteriolytic toxin (0 annotations) Acts as to cause lysis of bacterial cells. -->a specific class of toxins. cytolysis ; GO:0019835

GO:0015470 bacteriocin (0 annotations) Polypeptide antibiotic secreted by bacteria and able to kill bacteria of susceptible strains after absorption by specific cell surface receptor. -->gene product cytolysis ; GO:0019835 receptor binding ; GO:0005102

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/791":https://sourceforge.net/p/geneontology/ontology-requests/791

[gocentral]

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If there are no objections, I will obsolete these terms on May 7th.

Original comment by: girlwithglasses

[gocentral]

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A couple of toxins that slipped through the net:

pore-forming toxin activity ; GO:0015289 def: Catalysis of the transport of electrolytes and other small molecules across a cell membrane. They are synthesized by one cell and secreted for insertion into the membrane of another cell where they form transmembrane pores. They may exert their toxic effects by allowing the free flow of electrolytes and other small molecules across the membrane, or they may allow entry into the target cell cytoplasm of a toxin protein that ultimately kills the cell. -->toxin ; GO:0015070 pore formation ; GO:0046new, child of membrane organization and biogenesis ; GO:0016044 pore complex ; GO:0046new, child of membrane ; GO:0016020 structural molecule activity ; GO:0005198

channel-forming toxin activity ; GO:0015469 No def. -->toxin ; GO:000 This is more difficult because of the difference between channels and pores. Is there one? On the TC-DB site (where I presume this term originated), the two are used interchangeably. Pores are usually defined as 'a small opening in a membrane'; a channel has connotations of being a passageway through which substances pass. If they are synonymous, this can be annotated to 'pore complex' and 'pore formation', and these terms can be given the synonyms 'channel complex' and 'channel formation' respectively.

Original comment by: girlwithglasses

[gocentral]

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All obsoleted. Suggested the same alternative component and process terms for 'channel-forming toxin activity' as those for 'pore-forming toxin activity'.

Original comment by: girlwithglasses

[gocentral]

• status: open --> closed-fixed

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

New terms added: GO:0046928 regulation of neurotransmitter secretion GO:0046929 negative regulation of neurotransmitter secretion GO:0046930 pore complex GO:0046931 pore complex biogenesis

Original comment by: girlwithglasses