rg: positive regulation of interleukin-2 production

[gocentral]

Hi,

Could I please have as a child of :

GO:0001819 positive regulation of cytokine production >GO:New positive regulation of interleukin production >>GO:NEW positive regulation of interleukin-2 production >>>GO:NEW positive regulation of interleukin-2 production in T cells

It would be nice to have regulation terms for all the interleukin production terms...

cheers,

Evelyn

NOTE TO SELF FOR ANNOTATION UPDATE:

---

Paper:15125833, RNAi experiment MALT1 (Q9UDY8is Clone Master)...remember to also update IC annotation in Q9Y4K3, O43318, and TRAF2(Q12933)

Reported by: camon

Original Ticket: "geneontology/ontology-requests/3695":https://sourceforge.net/p/geneontology/ontology-requests/3695

[gocentral]

Logged In: YES user_id=436423 Originator: NO

erm, there aren't any interleukin production terms. Also, I wonder whether there should be 'interleukin biosynthesis' and 'interleukin production' grouping terms ... I'll see if Alex has time to advise ... m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Midori and Evelyn,

Interleukins are cytokines, and do not represent a gene family per se, but rather several gene families, most of which have other non-'interleukin' members. The only commonality is a lexical similarity in the name and a vague connection to being secreted by lymphocytes or affecting the function of the immune system. The naming of a protein as an 'interleukin' appears to be rather arbitrary and a point of pride among some immunologists, whereas other proteins could validly be called interleukins if the discoverers had cared to do so. PMID: 12103349 and PMID: 12464567 offer some useful comment on this point. The so-called "IL-14" is an example of an interleukin named in haste without proper molecular validation.

Thus I find that any delineation of cytokines into interleukins and non-interleukins is without merit, and therefore we should not make separate 'interleukin biosynthesis' and 'interleukin production' terms, as the processes involved have no more true commonalities that the general processes of 'cytokine synthesis' and 'cytokine production.' Indeed, it has been my long term desire (and half-written SF item) to reorganize cytokine binding/receptor activity and cytokine receptor bindiing terms in MF according to the structural characteristics of the cytokines being bound, some of which happen to be named as interleukins and most not.

Thus, any regulation terms related to production or biosynthesis of specific cytokines ought best be direct children of "regulaiton of cytokine production" or "regulation of cytokine biosynthesis" with appropriate relationships.

-- Alex

Original comment by: addiehl

[gocentral]

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Hi,

Although alot of cytokines use similar pathways I think it is a real loss of information not to indicate exactly what cytokine/ interleukin was produced. MGI may have a notes field but we do not . We do not yet have this slot facility so although I can indeed annotate to cytokine production, the specific information is lost and thats a great shame. Don't you think that some one would want to ever query 'what proteins upregulate interleukin-2 production/biosynthesis', IL-2 being a key T-cell growth factor. A decision not to include this term ensures that they can never ask that question of our databases.

Evelyn

Original comment by: ecamon

[gocentral]

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Ev -- I think Alex isn't saying we can't add a specific term such as 'interleukin-2 production' (though MGI wouldn't need it because they'd use their notes field); what he's saying is that we should not have grouping terms like 'interleukin production'. Instead, 'interleukin-2 production' would go directly under 'cytokine production'.

If Alex confirms my interpretation, I can add the interleukin-2 terms.

m

Original comment by: mah11

[gocentral]

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Evelyn and Midori,

Indeed I am all for the terms refering to specific cytokines, including interleukins, I just don't think it's appropriate to segregrate terms relating to interleukins under a general 'production of interleukin' category as I think it is a misleading and false division. I would love to have specific 'production of interleukin 2,' 'production of osteopontin,' 'production of GM-CSF/CSF2' etc. terms, because I do think terms relating to specific cytokines would be useful, and I've often wondered how long it would take before they were asked for. The main concern for me is including all the relevant synonyms for the various cytokines, as the gene nomenclature varies from the common usage.

-- Alex

Original comment by: addiehl

[gocentral]

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Well, I can make a start by adding specific "production of your favorite cytokine" terms. I am more daunted by the prospect of trying to get complete sets of synonyms, but I don't see any reason why term addition should wait. We can add synonyms to the terms any time once they're in the ontology.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

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Midori,

Most synonyms should be found at HUGO and MGI (non-overlapping sets, I'm afraid).

-- Alex

Original comment by: addiehl

[gocentral]

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Thanks Guys,

I did not mean to sound abrupt. Having a carzy day and I did misinterpret as I thought you did not want the specific annotations.

approved HGNC gene name is IL2 synonyms as from UniProt are: IL-2 T-cell growth factor TCGF Aldesleukin

cheers Evelyn

Original comment by: ecamon

[gocentral]

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Making some progress ... my, but there are a lot of cytokines! A couple of questions:

Alex: Should 'regulation of cytokine biosynthesis' terms be is_a 'regulation of cytokine production' terms?

Ev: Are all of those IL2 synonyms exact? If not, what scope for each?

thanks, m

Original comment by: mah11

[gocentral]

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Midori,

I wasn't expecting you to create all the specific terms immediately, but if you want to.

Because cytokine biosynthesis has a part_of relationship to cytokine production, I would recommend at best that regulation of cytokine biosynthesis have also a part_of relationship to cytokine production. Arguably, it should have no relationship at all, or even an is_a of relationship. I don't mean to be flippant here; this situation came up when I was doing the immune ontology, and I decided to not have any relationship between the regulation terms of a child part_of parent pair. I think I would like Chris Mungall to weigh in on this question since I would appreciate his guidance.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Original comment by: mah11

[gocentral]

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Hi Alex,

Thanks for your reply. I've just added lots of terms (listed in the attached file); it wasn't too onerous because I figured out a way to semi-automate the additions. Filling in synonyms will be much more time-consuming, so I'll do it incrementally (and you're most welcome to contribute if you have a spare moment).

I'll ask Chris what he recommends for the regulation of production/regulation of biosynthesis relationships, and leave them unrelated in the meantime.

m

Original comment by: mah11

[gocentral]

• summary: EASY:REFGEN:positive regulation of interleukin-2 production --> rg: positive regulation of interleukin-2 production

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Midori,

By the way, did you change the title of this SF item, so it no longer includes the word "EASY?" Of course, anything I touch never stays easy, does it?

-- Alex

Original comment by: addiehl

[gocentral]

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I've added 'IL-n' synonyms for the interleukin production terms. m

Original comment by: mah11

[gocentral]

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closing; please reopen or create a new SF item for synonym requests

Original comment by: mah11

[gocentral]

• status: open --> closed-accepted

Original comment by: mah11