obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
Other
5 stars 3 forks source link

spleen proliferative zone vs marginal sinus #117

Open cmungall opened 6 years ago

cmungall commented 6 years ago

in uberon we have two distinct classes, one excludes rodents:

[Term]
id: UBERON:0005353
name: spleen perifollicular zone
def: "The compartment located between the marginal zone and the red pulp harboring scattered B and T lymphocytes[MP]." [MP:0010245]
property_value: taxon_notes "The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents." xsd:string {source="MP:0002363"}
property_value: editor_note "TODO - check spleen marginal sinus" xsd:string
is_a: UBERON:0010000 ! multicellular anatomical structure
relationship: part_of UBERON:0002106 ! spleen
relationship: contributes_to_morphology_of UBERON:0002106 ! spleen
relationship: never_in_taxon NCBITaxon:9989 ! Rodentia
relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens
subset: pheno_slim
xref: EMAPA:37964 {source="MA:th"} ! spleen perifollicular zone

[Term]
id: UBERON:0010398
name: spleen marginal sinus
def: "The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood" [MP:MP]
property_value: editor_note "Note that there is no consensus in the literature about which compartments constitute the white pulp or the ramifications of the microvasculature. In addition, notable differences exist between humans and rodents. In this ontology, the marginal sinus (which may not exist in human) has been included as part of the white pulp. The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents." xsd:string {source="MP:0002363"}
synonym: "splenic marginal sinus" EXACT [MP:0002363]
is_a: UBERON:0001959 ! white pulp of spleen
relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens
xref: MA:0000754 ! spleen marginal sinus
xref: NCIT:C49776 ! splenic marginal sinus
xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"}
subset: pheno_slim

This was influenced by the MP class:

[Term]
id: MP:0010245
name: abnormal spleen perifollicular zone morphology
namespace: MPheno.ontology
def: "any structural anomaly of the compartment located between the marginal zone and the red pulp harboring scattered B and T lymphocytes" [PMID:11485909, PMID:9415041]
comment: Note that there is no consensus in the literature about whether the perifollicular zone (which does not exist in rodents) is part of the splenic red or white pulp. Notable differences in the structure of the spleen exist between humans and rodents. In this ontology, the marginal sinus (which doen not exist in human) has been included as part of the white pulp and may be the rodent functional equivalent of the human perifollicular zone.
is_a: MP:0000689  ! abnormal spleen morphology

The MP class says it does not exist in rodents and indeed there are no MGI annotations to it: http://www.informatics.jax.org/vocab/mp_ontology/MP:0010245

FWIW there are no annotations to the EMAPA class http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:37964

cmungall commented 6 years ago

For now I am moving the EMAPA xref in Uberon to spleen marginal sinus, where it will sit alongside MA:0000754 but am open to other configurations...