'response to' vs 'cellular response to'

[gocentral]

I am confused by these two categories of terms. It seems strange that there are no 'cellular response to' terms describing responses to many of the metal ions,

For instance, we have 'response to copper ion', but no term to describe 'cellular response to copper ion'. In fact we have no 'cellular response to metal ions', terms apart from the 'cellular response to iron/zinc/potassium ion starvation' terms.

This seems odd, as I'd bet that most of the responses to metal ions being recorded by curators are at the level of cellular changes 'in secretion, enzyme production, gene expression, etc.'. This confusion extends to responses to other simuli such as pH, ATP, X-ray, purine ... why are there only 'response to' terms for these?

Reported by: edimmer

Original Ticket: geneontology/ontology-requests/6741

[gocentral]

assigning to Jen to take to the signaling task force

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: mah11

[gocentral]

Hi Emily,

It sounds to me as if the 'response to' terms were made before we thought of having 'cellulr response to' terms, and that the more generic 'response to' terms for individual substances were just made as that was the default option at the time. Perhaps the thing would be for curators to start requesting cellular terms as required. Or else if you see an entire set of terms that could have cellular children made then you could request them in a batch.

Does that seem reasonable?

Jen

Original comment by: jenclark

[gocentral]

Hi Jen,

You're probably right that the 'cellular response' terms were developed later. However I’m not sure that waiting for curators to request new terms would really work - the mess partially exists as curators are confused as to which 'response to' terms they can request and many make do with the existing ‘response to’ terms, even though they could be requesting new child terms. In addition, I wonder whether all responses to iron ions or ATP occur at a cellular level – therefore should some ‘cellular response to x’ and ‘response to x’ terms be merged ?

I suppose it depends on how much GO cares about the additional information content of ‘cellular response to x’ cf ‘response to x’. With the current state of this node, the ‘cellular response’ terms appear to provide little additional information :-(

If it does matter, then many of the descendants of terms such as: GO:0009725 response to hormone stimulus GO:0010038 response to metal GO:0009314 response to radiation GO:0009268 response to pH GO:0006970 response to osmotic stress GO:0009266 response to temperature stimulus GO:0010033 response to organic substance …should all have a ‘cellular response’ child terms.

Original comment by: edimmer

[gocentral]

Hi Emily,

Thanks for the list. In that case I think this project probably needs to go on the list of "big fixes" to be prioritized (Along with cross products and signaling and things like that). I will assign it back to Midori so that she and David can work out where it comes in the list.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• assigned_to: jenclark --> gomidori

Original comment by: jenclark

[gocentral]

David and I will have a chat about this, but in the meantime I'm unassigning it, because it's unlikely that I'll be the one to implement whatever we decide.

Original comment by: mah11

[gocentral]

• assigned_to: gomidori --> nobody

Original comment by: mah11

[gocentral]

OK, reclaiming this because David and I have decided to just go ahead and add 'cellular response to x' for everything. For annotations, whether to use the cellular term or the parent will depend on what evidence is presented in the paper.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

added so far ... (there will be lots more, so when it's done I'll attach a file with all new terms and IDs)

cellular response to 1-aminocyclopropane-1-carboxylic acid GO:0071213 cellular response to abiotic stimulus GO:0071214 cellular response to abscisic acid stimulus GO:0071215 cellular response to biotic stimulus GO:0071216 cellular response to external biotic stimulus GO:0071217 cellular response to misfolded protein GO:0071218 cellular response to molecule of bacterial origin GO:0071219 cellular response to bacterial lipoprotein GO:0071220 cellular response to bacterial lipopeptide GO:0071221 cellular response to lipopolysaccharide GO:0071222 cellular response to lipoteichoic acid GO:0071223 cellular response to peptidoglycan GO:0071224 cellular response to muramyl dipeptide GO:0071225 cellular response to molecule of fungal origin GO:0071226 cellular response to molecule of oomycetes origin GO:0071227 cellular response to tumor cell GO:0071228 cellular response to acid GO:0071229 cellular response to amino acid stimulus GO:0071230 cellular response to folic acid GO:0071231 cellular response to histidine GO:0071232 cellular response to leucine GO:0071232 cellular response to phenylalanine GO:0071234 cellular response to proline GO:0071235 cellular response to antibiotic GO:0071236 cellular response to bacteriocin GO:0071237 cellular response to brefeldin A GO:0071238 cellular response to streptomycin GO:0071239 cellular response to food GO:0071240 cellular response to inorganic substance GO:0071241 cellular response to ammonium ion GO:0071242 cellular response to arsenic GO:0071243 cellular response to carbon dioxide GO:0071244 cellular response to carbon monoxide GO:0071245 cellular response to chlorate GO:0071246 cellular response to chromate GO:0071247 cellular response to metal ion GO:0071248 cellular response to nitrate GO:0071249 cellular response to nitrite GO:0071250 cellular response to silicon dioxide GO:0071251 cellular response to sulfur dioxide GO:0071252

Original comment by: mah11

[gocentral]

just a few today ...

cellular response to electrical stimulus GO:0071257 cellular response to gravity GO:0071258 cellular response to magnetism GO:0071259 cellular response to mechanical stimulus GO:0071260

Original comment by: mah11

[gocentral]

added cellular response to aluminum ion GO:0071275 cellular response to cadmium ion GO:0071276 cellular response to calcium ion GO:0071277 cellular response to cesium ion GO:0071278 cellular response to cobalt ion GO:0071279 cellular response to copper ion GO:0071280 cellular response to iron ion GO:0071281 cellular response to iron(II) ion GO:0071282 cellular response to iron(III) ion GO:0071283 cellular response to lead ion GO:0071284 cellular response to lithium ion GO:0071285 cellular response to magnesium ion GO:0071286 cellular response to manganese ion GO:0071287 cellular response to mercury ion GO:0071288 cellular response to nickel ion GO:0071289 cellular response to platinum ion GO:0071290 cellular response to selenium ion GO:0071291 cellular response to silver ion GO:0071292 cellular response to tellurium ion GO:0071293 cellular response to zinc ion GO:0071294 cellular response to vitamin GO:0071295 cellular response to biotin GO:0071296 cellular response to cobalamin GO:0071297 cellular response to L-ascorbic acid GO:0071298 cellular response to vitamin A GO:0071299 cellular response to retinoic acid GO:0071300 cellular response to vitamin B1 GO:0071301 cellular response to vitamin B2 GO:0071302 cellular response to vitamin B3 GO:0071303 cellular response to vitamin B6 GO:0071304 cellular response to vitamin D GO:0071305 cellular response to vitamin E GO:0071306 cellular response to vitamin K GO:0071307 cellular response to menaquinone GO:0071308 cellular response to phylloquinone GO:0071309 cellular response to organic substance GO:0071310 cellular response to acetate GO:0071311 cellular response to alkaloid GO:0071312 cellular response to caffeine GO:0071313 cellular response to cocaine GO:0071314 cellular response to morphine GO:0071315 cellular response to nicotine GO:0071316 cellular response to isoquinoline alkaloid GO:0071317 cellular response to ATP GO:0071318 cellular response to benzoic acid GO:0071319 cellular response to cAMP GO:0071320 cellular response to cGMP GO:0071321 cellular response to carbohydrate stimulus GO:0071322 cellular response to chitin GO:0071323 cellular response to disaccharide stimulus GO:0071324 cellular response to mannitol stimulus GO:0071325 cellular response to monosaccharide stimulus GO:0071326 cellular response to trehalose stimulus GO:0071327 cellular response to maltose stimulus GO:0071328 cellular response to sucrose stimulus GO:0071329 cellular response to trehalose-6-phosphate stimulus GO:0071330 cellular response to hexose stimulus GO:0071331 cellular response to fructose stimulus GO:0071332 cellular response to glucose stimulus GO:0071333 cellular response to rhamnose stimulus GO:0071334

Original comment by: mah11

[gocentral]

added cellular response to cytokine stimulus GO:0071345 cellular response to interferon-gamma GO:0071346 cellular response to interleukin-1 GO:0071347 cellular response to interleukin-11 GO:0071348 cellular response to interleukin-12 GO:0071349 cellular response to interleukin-15 GO:0071350 cellular response to interleukin-18 GO:0071351 cellular response to interleukin-2 GO:0071352 cellular response to interleukin-4 GO:0071353 cellular response to interleukin-6 GO:0071354 cellular response to interleukin-9 GO:0071355 cellular response to tumor necrosis factor GO:0071356 cellular response to type I interferon GO:0071357 cellular response to type III interferon GO:0071358 cellular response to dsRNA GO:0071359 cellular response to exogenous dsRNA GO:0071360 cellular response to ethanol GO:0071361 cellular response to ether GO:0071362 cellular response to growth factor stimulus GO:0071363 cellular response to epidermal growth factor stimulus GO:0071364 cellular response to auxin stimulus GO:0071365 cellular response to indolebutyric acid stimulus GO:007166 cellular response to brassinosteroid stimulus GO:0071367 cellular response to cytokinin stimulus GO:0071368 cellular response to ethylene stimulus GO:0071369 cellular response to gibberellin stimulus GO:0071370 cellular response to gonadotropin stimulus GO:0071371 cellular response to follicle-stimulating hormone stimulus GO:0071372 cellular response to luteinizing hormone stimulus GO:0071373 cellular response to parathyroid hormone stimulus GO:071374 cellular response to peptide hormone stimulus GO:0071375 cellular response to corticotropin-releasing hormone stimulus GO:0071376 cellular response to glucagon stimulus GO:0071377 cellular response to growth hormone stimulus GO:0071378 cellular response to prostaglandin stimulus GO:0071379 cellular response to prostaglandin E stimulus GO:0071380 cellular response to prostaglandin F stimulus GO:0071381 cellular response to prostaglandin I stimulus GO:0071382 cellular response to steroid hormone stimulus GO:0071383 cellular response to corticosteroid stimulus GO:0071384 cellular response to glucocorticoid stimulus GO:0071385 cellular response to corticosterone stimulus GO:0071386 cellular response to cortisol stimulus GO:0071387 cellular response to cortisone stimulus GO:0071388 cellular response to mineralocorticoid stimulus GO:0071389 cellular response to ecdysone GO:0071390 cellular response to estrogen stimulus GO:0071391 cellular response to estradiol stimulus GO:0071392 cellular response to progesterone stimulus GO:0071393 cellular response to testosterone stimulus GO:0071394 cellular response to jasmonic acid stimulus GO:0071395 cellular response to lipid GO:0071396 cellular response to cholesterol GO:0071397 cellular response to fatty acid GO:0071398 cellular response to linoleic acid GO:0071399 cellular response to oleic acid GO:0071400 cellular response to triglyceride GO:0071401

Original comment by: mah11

[gocentral]

monday: cellular response to lipoprotein stimulus GO:0071402 cellular response to high density lipoprotein stimulus GO:0071403 cellular response to low-density lipoprotein stimulus GO:0071404 cellular response to methanol GO:0071405 cellular response to methylmercury GO:0071406 cellular response to organic cyclic substance GO:0071407 cellular response to cycloalkane GO:0071408 cellular response to cycloheximide GO:0071409 cellular response to cyclopentenone GO:0071410 cellular response to fluoxetine GO:0071411 cellular response to genistein GO:0071412 cellular response to hydroxyisoflavone GO:0071413 cellular response to methotrexate GO:0071414 cellular response to purine GO:0071415 cellular response to tropane GO:0071416 cellular response to organic nitrogen GO:0071417 cellular response to amine stimulus GO:0071418 cellular response to amphetamine GO:0071419 cellular response to histamine GO:0071420

today: cellular response to pheromone GO:0071444 cellular response to protein stimulus GO:0071445 cellular response to salicylic acid stimulus GO:0071446 cellular response to hydroperoxide GO:0071447 cellular response to alkyl hydroperoxide GO:0071448 cellular response to lipid hydroperoxide GO:0071449 cellular response to oxygen radical GO:0071450 cellular response to superoxide GO:0071451 cellular response to singlet oxygen GO:0071452 cellular response to oxygen levels GO:0071453 cellular response to anoxia GO:0071454 cellular response to hyperoxia GO:0071455 cellular response to hypoxia GO:0071456 cellular response to ozone GO:0071457

Original comment by: mah11

[gocentral]

last ones I'll add for this item:

cellular response to redox state GO:0071461 cellular response to water GO:0071462 cellular response to humidity GO:0071463 cellular response to hydrostatic pressure GO:0071464 cellular response to desiccation GO:0071465 cellular response to xenobiotic stimulus GO:0071466 cellular response to pH GO:0071467 cellular response to acidity GO:0071468 cellular response to alkalinity GO:0071469 cellular response to osmotic stress GO:0071470 cellular response to non-ionic osmotic stress GO:0071471 cellular response to salt stress GO:0071472 cellular response to cation stress GO:0071473 cellular hyperosmotic response GO:0071474 cellular hyperosmotic salinity response GO:0071475 cellular hypotonic response GO:0071476 cellular hypotonic salinity response GO:0071477 cellular response to radiation GO:0071478 cellular response to ionizing radiation GO:0071479 cellular response to gamma radiation GO:0071480 cellular response to X-ray GO:0071481 cellular response to light stimulus GO:0071482 cellular response to blue light GO:0071483 cellular response to light intensity GO:0071484 cellular response to absence of light GO:0071485 cellular response to high light intensity GO:0071486 cellular response to low light intensity stimulus GO:0071487 cellular response to very low light intensity stimulus GO:0071488 cellular response to red or far red light GO:0071489 cellular response to far red light GO:0071490 cellular response to red light GO:0071491 cellular response to UV-A GO:0071492 cellular response to UV-B GO:0071493 cellular response to UV-C GO:0071494 cellular response to endogenous stimulus GO:0071495 cellular response to external stimulus GO:0071496 cellular response to freezing GO:0071497 cellular response to fluid shear stress GO:0071498 cellular response to laminar fluid shear stress GO:0071499 cellular response to nitrosative stress GO:0071500 cellular response to sterol depletion GO:0071501 cellular response to temperature stimulus GO:0071502

I'll also attach the file with all terms in one lot.

Original comment by: mah11

[gocentral]

Original comment by: mah11

[gocentral]

and now I can close!

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• labels: 397373 --> New term request
• status: open --> closed-accepted

Original comment by: mah11