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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Review taxon rule for UBERON:0000029 lymph node #650

Closed paolaroncaglia closed 2 years ago

paolaroncaglia commented 9 years ago

Hi,

UBERON:0000029 lymph node is currently broadly restricted to only in taxon some Gnathostomata but has a comment homology_notes: Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] Should UBERON narrow its current constraint?

Stemmed from a request from Michael Rice (AgBase) to restrict GO:0048535 lymph node development to Mammalia (https://sourceforge.net/p/geneontology/ontology-requests/11527/).

Thanks,

Paola

RDruzinsky commented 9 years ago

This is actually a VERY interesting subject. Here are two recent, cool articles on lymphatic systems:

Hedrick et al. Journal of Applied Physiology Published 1 August 2013 Vol. 115 no. 3, 297-308 DOI: 10.1152/japplphysiol.00201.2013 Boehm Hess Swann 2012 Trends in Immunology, June 2012, Vol. 33, No. 6 doi:10.1016/j.it.2012.02.005 Basically, I think that true lymph nodes are mammalian (not sure if this includes marsupials, etc.), but birds and reptiles have lymph node-like Peyer's patches. Hedrick et al argue that in mammals the lymphatic system plays a much greater role in immune system surveillance than in other vertebrates.

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 druzinsk@uic.edu

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Wed, Feb 25, 2015 at 9:39 AM, paolaroncaglia notifications@github.com wrote:

Hi,

UBERON:0000029 lymph node is currently broadly restricted to only in taxon some Gnathostomata but has a comment homology_notes: Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] Should UBERON narrow its current constraint?

Stemmed from a request from Michael Rice (AgBase) to restrict GO:0048535 lymph node development to Mammalia (https://sourceforge.net/p/geneontology/ontology-requests/11527/).

Thanks,

Paola

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/650.

addiehl commented 9 years ago

Based on PMID:916458 (Thymus- and bursa-dependent areas in duck lymph nodes. Jpn J Vet Res. 1977 Apr;25(1-2):7-16, full text pdf available via Google), the duck lymph nodes are not described as gut-associated lymphoid tissue and are therefore not Peyer's patches. Although the internal structure shown differs from mammalian lymph nodes, the authors describe the duck lymph nodes as having germinal centers and T and BF (B cell)- dependent areas. We can arbitrarily declare these not be true lymph nodes, but they are lymphoid tissue distinct in morphology and location from Peyer's patches and similar in morphology to mammalian lymph nodes.

PMID:16889640 (Characterization of chicken epidermal dendritic cells. Immunology. 2006 Oct;119(2):278-88.) describes the migration of chicken dendritic cells into dermal "lymphoid nodules" and say furthermore "We suggest that these dermal nodules are responsible for some regional immunological functions similar to the mammalian lymph nodes."

While chickens and ducks appear to differ in regards to their lymphoid tissue types based on multiple references, we might consider creating a "lymphoid nodule" term for the birds with subtypes "dermal lymphoid nodule" and "avian lymph node" to better represent the range of lymphoid tissue in birds. I suspect there may be additional information in the literature about this topic, but haven't had sufficient time to investigate.

Then we can restrict "lymph node" to mammals. -- Alex

paolaroncaglia commented 3 years ago

@addiehl Could you please check if this ticket is now out of date? Thanks.

addiehl commented 3 years ago

My conclusion stands that "lymph node" should be restricted to 'Mammalia'. Per the papers previously cited, as well as a Google review, proper lymph nodes are only found in mammals, and not in birds, reptiles, amphibians, or fish.

Someone should make this change.

paolaroncaglia commented 3 years ago

Thanks @addiehl . 'lymph node' is currently never_in_taxon Teleostei and Serpentes. Looks like a couple more restrictions could still be added. I'll assign this ticket to myself as I've worked on lymph node terms for the SCA anatomograms - how do I make sure it's not auto-closed?

addiehl commented 3 years ago

I think only items with no activity in the last three years will be autoclosed. So this ticket is safe now (and even closed tickets can be reopened at will).

cmungall commented 3 years ago

Do we have evidence that lymph nodes are only in mammals

Older literature talks of lymph nodes in water fowl (swans, geese), e.g https://journals.sagepub.com/doi/pdf/10.1177/014107687907200914

https://www.aavac.com.au/files/1989-20.pdf

of course it is always possible to state "True Xs are only in T", where the definition of "True X" has T as a differentia. But ideally we would have a definition of true Xs that properly differentiates. What is the defining characteristic of a lymph node that

paolaroncaglia commented 2 years ago

@addiehl @cmungall @RDruzinsky Following up on the thorny subject of restricting ‘lymph node’ to mammals. Summing up this thread, the only argument preventing us to do that is that lymph nodes "similar to mammals'" have been described in some bird species. What the differentia is between these and true mammals’ lymph nodes is still not clear to me. :-) If Alex (or anyone else) could please suggest a definition pointing to such differentia, I’d be happy to create a new term ‘lymphoid nodule’ (with exact synonym “avian lymphoid nodule” and related synonym “avian lymph node”) as a subclass of ‘lymphoid nodule’ and restrict it to Aves. Then I can restrict ‘lymph node’ to mammals (and remove the current restrictions to never in Serpentes and Teleostei).

If we do the above, I would also

Looking forward to a suggestion for the missing differentia. Thank you all in advance!

Paola

uberon commented 2 years ago

I agree with your proposed course of action

is there a typo here:

I’d be happy to create a new term ‘lymphoid nodule’ (with exact synonym “avian lymphoid nodule” and related synonym “avian lymph node”) as a subclass of ‘lymphoid nodule’ and restrict it to Aves

I'm not clear on what the superclass of the proposed avian-specific class is

note we have an FMA-derived exact syn that may need relaxed:

id: UBERON:0000444 name: lymphoid follicle def: "." [https://github.com/obophenotype/uberon/issues/6, https://github.com/obophenotype/uberon/issues/7] synonym: "folliculus lymphaticus" RELATED [BTO:0002684] synonym: "lymphatic follicle" RELATED [BTO:0002684] synonym: "lymphatic nodule" RELATED [BTO:0002684] synonym: "lymphoid nodule" EXACT [FMA:55222] synonym: "nodular lymphoid tissue" EXACT [FMA:55222] synonym: "nodulus lymphaticus" RELATED [BTO:0002684] synonym: "nodulus lymphoideus" RELATED [BTO:0002684] xref: BTO:0002684 xref: FMA:55222 xref: NCIT:C33040 xref: SCTID:64626006 xref: UMLS:C0229654 {source="ncithesaurus:Lymphoid_Follicle"} is_a: UBERON:0001744 {source="FMA"} ! lymphoid tissue property_value: editor_note "introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'" xsd:string

Anyway, I think your plan is good, go ahead!

On Tue, Oct 26, 2021 at 2:36 AM paolaroncaglia @.***> wrote:

@addiehl https://github.com/addiehl @cmungall https://github.com/cmungall @RDruzinsky https://github.com/RDruzinsky Following up on the thorny subject of restricting ‘lymph node’ to mammals. Summing up this thread, the only argument preventing us to do that is that lymph nodes "similar to mammals'" have been described in some bird species. What the differentia is between these and true mammals’ lymph nodes is still not clear to me. :-) If Alex (or anyone else) could please suggest a definition pointing to such differentia, I’d be happy to create a new term ‘lymphoid nodule’ (with exact synonym “avian lymphoid nodule” and related synonym “avian lymph node”) as a subclass of ‘lymphoid nodule’ and restrict it to Aves. Then I can restrict ‘lymph node’ to mammals (and remove the current restrictions to never in Serpentes and Teleostei).

If we do the above, I would also

Looking forward to a suggestion for the missing differentia. Thank you all in advance!

Paola

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/650#issuecomment-951760977, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCASG7DJDSSDBLPSYJLUI2ADXANCNFSM4A4WWBQA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

paolaroncaglia commented 2 years ago

I agree with your proposed course of action

Thanks (@cmungall ?)

is there a typo here:

Yes, I meant ‘lymphoid nodule’ subclass of ‘lymphoid tissue’, sorry.

note we have an FMA-derived exact syn that may need relaxed

Thanks for catching that, I'll make it related.

Anyway, I think your plan is good, go ahead!

Will do! I'll give it a little time in case someone has suggestions for the definition/differentia. If not, I'll think of something. Thanks.

cmungall commented 2 years ago

Thanks @.*** https://github.com/cmungall ?)

lol yes it's me sometimes when i do github by mail it confuses me with the github account we use for the website!

paolaroncaglia commented 2 years ago

All done. The new term is UBERON:8410069 lymphoid nodule.