precomposed terms: response to X ion involved in chemotaxis

[gocentral]

Hello,

I'd like to request a couple of precomposed process terms: cellular response to potassium ion/calcium ion involved in chemotaxis to cAMP.

These seem to be common. References: PMID 21239624, 19363786, 8937985.

NEW: cellular response to potassium ion involved in chemotaxis to cAMP part_of: GO:0043327: chemotaxis to cAMP is_a: GO:0035865: cellular response to potassium ion

NEW: cellular response to calcium ion involved in chemotaxis to cAMP part_of: GO:0043327: chemotaxis to cAMP is_a: GO:0071277: cellular response to calcium ion

Here is a suggested Def (replace potassium with calcium and vice versa): The directed movement of a motile cell in response to of 3',5'-cAMP that results in a change in state or activity (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus.

Thanks and Happy Holidays! Petra

Reported by: pfey

Original Ticket: geneontology/ontology-requests/9071

[gocentral]

Hi Petra,

Happy holidays to you, too - I'll look at this request in the New Year if it's ok for you.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Paola, Sure, absolutely ok! Also, FYI, I discussed these precomposed terms with Val and Midori when discussing column 16 usage, and they recommended using precomposed terms when it's a combination of processes that occurs generally.

I'm off next week, have a nice time and a happy new year! Petra

Original comment by: pfey

[gocentral]

You can use TG for this

Original comment by: cmungall

[gocentral]

Hi Petra,

I'd like to test the new TermGenie to create these 2 new terms. The developers are still doing some final fixes to it, so I'm setting this request to pending while I wait to be sure that everything works correctly. It should be a matter of a few days at most, but if you need the terms urgently, please let me know. Otherwise I'll be in touch shortly.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> pending

Original comment by: paolaroncaglia

[gocentral]

Hi Petra, I've added the two new terms below using the new TermGenie:

ID: GO:1900013 Label: cellular response to potassium ion involved in chemotaxis to cAMP ID: GO:1900014 Label: cellular response to calcium ion involved in chemotaxis to cAMP

These terms are not live in the ontology yet, but should be within a couple of days. If they aren't, please let me know. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: pending --> closed-accepted

Original comment by: paolaroncaglia

[gocentral]

Hi Petra,

On second thought, there has been further discussion about these terms among us editors. I'm copying below the relevant comments. Could you please look into this, and provide us with more feedback so we can figure out what terms would be the best for your annotations?

Many thanks, Paola

Comments:

The cellular response terms are broad. They start with: detection of a stimulus. They end with: a change in state or activity of a cell. They include both the signaling pathway AND the downstream cellular response (e.g. transcription).

Therefore it's unusual to have a 'response to' term as part of a wider process (e.g. involved in another process).

I think we can still make pre-composed terms [as Val and Midori suggested], but I think the existing terms [i.e. not-yet-committed 1900013 and GO:1900014 below] are the wrong way round. Skimming the papers, I think the main points are:

-Cells migrate towards the chemoattractant, cAMP

-Extracellular Ca++ or K+ influence the migration of Dicty cells towards cAMP.

-Nhe1 is a participant in regulating the migration of the Dicty cells towards cAMP in the presence of (extracellular) K+. Nhe1 may act as a sensor for K+ or as a transporter.

So I think a better term would be along the lines:

positive chemotaxis to cAMP in response to potassium ion ; GO:NEW is_a: cellular response to K+ is_a: positive chemotaxis to cAMP synonym: K+ facilitation of chemoattraction to cAMP [PMID:21239624] synonym: potassium ion facilitation of chemoattraction to cAMP [PMID:21239624] synonym: chemoattraction to cAMP in response to potassium ion

Its hard to say whether Nhe1 is regulating the chemotaxis or is a participant in the process: there are terms for 'positive regulation of positive chemotaxis to cAMP' (E.g. GO:0061124) if we want to expand the above term.

Original comment by: paolaroncaglia

[gocentral]

• status: closed-accepted --> open

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

Thanks to you and everyone to thinks so much about that. Well, I did some thinking and discussed this with the researcher now. As a consequence, I want to change the term, and then agree with the swapping of order, so let me know what you think. The researcher said the K+ or Ca2+ facilitation is just more general for cell motility and he didn't like the close link to cAMP chemotaxis, at least for the nhe1 gene. So now I propose:

NEW: cell motility in response to potassium ion is_a: cellular response to potassium ion is_a: cell motility SYNONYMS: potassium ion facilitation of cell motility K+ facilitation of cell motility

And the same for calcium.

Thanks for the discussion and prompting me to go back with a more neutral eye and then involving the researcher! Petra

Original comment by: pfey

[gocentral]

Hi Petra, these are done:

GO:0097230 cell motility in response to potassium ion GO:0097231 cell motility in response to calcium ion

Thanks! Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia