Closed paolaroncaglia closed 2 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.
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
@addiehl Could you please check if this ticket is now out of date? Thanks.
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.
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?
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).
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
@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
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
- Add AP to ‘lymph node’: ’see also’ (this ticket)
- Add as def dbxrefs to the new term the papers cited in this thread and ORCIDs of contributors, so PMID:23640588 PMID:22483556 PMID:916458 PMID:16889640 PMID:552577 http://orcid.org/0000-0002-1572-1316 http://orcid.org/0000-0001-9990-8331 http://orcid.org/0000-0002-6601-2165
Looking forward to a suggestion for the missing differentia. Thank you all in advance!
Paola
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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.
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!
All done. The new term is UBERON:8410069 lymphoid nodule.
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