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please add a new term, sinus of lymph node.

Open jmfostel opened this issue 5 months ago • 2 comments

**Preferred term label: sinus of lymph node Synonyms lymphatic sinus, lymph node sinus Definition (free text, please give PubMed ID) a lymph node sinus consisting of subcapsular, paracortical and medullary sinuses.

i work with pathologists at NIEHS. we have many findings in the lymphatic sinus, and i am looking for a term in UBERON to map these to. i have several pathology findings in the lmphatic sinus and i am looking for an antomy term.

reference 1: Non neoplastic Lesion Atlas, NIEHS: https://ntp.niehs.nih.gov/atlas/nnl A guide for standardizing terminology in toxicologic pathology for rodents

Lymphatic sinus Ectasia: https://ntp.niehs.nih.gov/atlas/nnl/immune-system/lymph-node/LymphaticSinusEctasia Lymphatic sinus ectasia can involve the subcapsular, paracortical, or medullary sinuses of lymph nodes

Sinus Erythrocytosis: https://ntp.niehs.nih.gov/atlas/nnl/immune-system/lymph-node/SinusErythrocytosis

Reference 2: goRENI goRENI is the standard reference for nomenclature and diagnostic criteria in toxicologic pathology and at the same time the Internet discussion platform for the global initiative "INHAND" - the International Harmonization of Nomenclature and Diagnostic criteria. https://www.goreni.org/gr3_index.php

Dilatation sinus: https://www.goreni.org/gr3_diag_text.php?mno=6950&tno=1069 Diffuse or focal dilatation of subcapsular, paracortical, or medullary sinuses.

Erythrocytes, intrasinusoidal: https://www.goreni.org/gr3_diag_text.php?mno=6206&tno=1069 Erythrocytes are transported to lymph node sinuses via lymphatic drainage from extranodal site of hemorrhage

PubMed: • PMID: 28955180 refers to the mouse lymphatic sinus in Figure 1.

Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon) lymph node UBERON:0000029

we would request that the current UBERON terms be related, possibly as children. the new term lymphatic sinus is composed of all three: trabecular sinus of lymph node UBERON:8410032 subcapsular sinus of lymph node UBERON:8410032 lymph node paracortical sinus UBERON:8410074

Your nano-attribution (ORCID) 0000-0001-5858-4393

thank you!

jmfostel avatar Jul 15 '25 20:07 jmfostel

@dragon-ai-agent please add the requested term as follows:

name: sinus of lymph node Synonyms: lymphatic sinus, lymph node sinus Definition: A sinus located in a lymph node. Lymph nodes have subcapsular, cortical/trabacular) and medullary sinuses. intersection_of: sinus intersection_of: part_of lymph node

wikipedia is sufficient for refernence: https://en.wikipedia.org/wiki/Lymph_node. make sure you use standard curie pattern to for it.

dosumis avatar Nov 03 '25 14:11 dosumis

I have successfully added the requested term for sinus of lymph node.

Term details:

  • ID: UBERON:9900001
  • Name: sinus of lymph node
  • Synonyms: lymphatic sinus, lymph node sinus
  • Definition: A sinus located in a lymph node. Lymph nodes have subcapsular, cortical (trabecular) and medullary sinuses.
  • Logical definition:
    • intersection_of: UBERON:0000464 (anatomical space)
    • intersection_of: part_of UBERON:0000029 (lymph node)
  • Reference: Wikipedia:Lymph_node
  • Attribution: Credited to John Fostel (ORCID: 0000-0001-5858-4393)

This term serves as a grouping class for the existing specific lymph node sinus terms:

  • UBERON:0005463 (subcapsular sinus of lymph node)
  • UBERON:8410032 (trabecular sinus of lymph node)
  • UBERON:8410074 (lymph node paracortical sinus)
  • UBERON:0009744 (lymph node medullary sinus)

I've created pull request #3621 for review. Please let me know if any adjustments are needed.

@dragon-ai-agent

dragon-ai-agent avatar Nov 03 '25 14:11 dragon-ai-agent