Fixes #2784 - Improve stromal cell of endometrium

[Caroline-99]

• Fixes Improve stromal cell of endometrium  #2784

Note: I have added decidualized endometrial stromal cells as a narrow synonym for the term stromal cell of endometrium. Do you think it would be more accurate to add it as a narrow synonym for decidual cell instead?

[Caroline-99]

#gogoeditdiff

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-11-21/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-11-21/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

CD115-positive monocyte OR common dendritic progenitor http://purl.obolibrary.org/obo/CL_0001019

Removed

• CD115-positive monocyte OR common dendritic progenitor SubClassOf PR_000050567

CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0001030

Removed

• CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor SubClassOf PR_000050567

CD14-positive monocyte http://purl.obolibrary.org/obo/CL_0001054

Removed

• CD14-positive monocyte SubClassOf PR_000050567

CD16-negative, CD56-bright natural killer cell, human http://purl.obolibrary.org/obo/CL_0000938

Removed

• CD16-negative, CD56-bright natural killer cell, human SubClassOf PR_000050567

CD16-positive, CD56-dim natural killer cell, human http://purl.obolibrary.org/obo/CL_0000939

Removed

• CD16-positive, CD56-dim natural killer cell, human SubClassOf PR_000050567

CD25+ mast cell http://purl.obolibrary.org/obo/CL_0011023

Removed

• CD25+ mast cell SubClassOf PR_000050567

CD27-high, CD11b-high natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002347

Removed

• CD27-high, CD11b-high natural killer cell, mouse SubClassOf PR_000050567

CD27-high, CD11b-low natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002349

Removed

• CD27-high, CD11b-low natural killer cell, mouse SubClassOf PR_000050567

CD27-low, CD11b-high natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002348

Removed

• CD27-low, CD11b-high natural killer cell, mouse SubClassOf PR_000050567

CD27-low, CD11b-low immature natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002345

Removed

• CD27-low, CD11b-low immature natural killer cell, mouse SubClassOf PR_000050567

CD34-negative, CD117-positive innate lymphoid cell, human http://purl.obolibrary.org/obo/CL_0001072

Removed

• CD34-negative, CD117-positive innate lymphoid cell, human SubClassOf PR_000050567

CD34-negative, CD41-positive, CD42-positive megakaryocyte cell http://purl.obolibrary.org/obo/CL_0002026

Removed

• CD34-negative, CD41-positive, CD42-positive megakaryocyte cell SubClassOf PR_000050567

CD34-positive, CD38-negative hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0001024

Removed

• CD34-positive, CD38-negative hematopoietic stem cell SubClassOf PR_000050567

CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0000995

Removed

• CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor SubClassOf PR_000050567

CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0002005

Removed

• CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell SubClassOf PR_000050567

CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002025

Removed

• CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell SubClassOf PR_000050567

CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002023

Removed

• CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell SubClassOf PR_000050567

CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human http://purl.obolibrary.org/obo/CL_0001074

Removed

• CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human SubClassOf PR_000050567

CD56-negative, CD161-positive immature natural killer cell, human http://purl.obolibrary.org/obo/CL_0002344

Removed

• CD56-negative, CD161-positive immature natural killer cell, human SubClassOf PR_000050567

CD56-positive, CD161-positive immature natural killer cell, human http://purl.obolibrary.org/obo/CL_0002338

Removed

• CD56-positive, CD161-positive immature natural killer cell, human SubClassOf PR_000050567

CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor http://purl.obolibrary.org/obo/CL_0001012

Removed

• CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor SubClassOf PR_000050567

CD7-positive lymphoid progenitor cell http://purl.obolibrary.org/obo/CL_0001028

Removed

• CD7-positive lymphoid progenitor cell SubClassOf PR_000050567

CD71-negative, GlyA-positive orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0002018

Removed

• CD71-negative, GlyA-positive orthochromatic erythroblast SubClassOf PR_000050567

CD9-positive, CD41-positive megakaryocyte cell http://purl.obolibrary.org/obo/CL_0002027

Removed

• CD9-positive, CD41-positive megakaryocyte cell SubClassOf PR_000050567

DN1 thymic pro-T cell http://purl.obolibrary.org/obo/CL_0000894

Removed

• DN1 thymic pro-T cell SubClassOf PR_000050567

DN2 thymocyte http://purl.obolibrary.org/obo/CL_0000806

Removed

• DN2 thymocyte SubClassOf PR_000050567

DN3 thymocyte http://purl.obolibrary.org/obo/CL_0000807

Removed

• DN3 thymocyte SubClassOf PR_000050567

DN4 thymocyte http://purl.obolibrary.org/obo/CL_0000808

Removed

• DN4 thymocyte SubClassOf PR_000050567

Dx5-negative, NK1.1-positive immature natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002346

Removed

• Dx5-negative, NK1.1-positive immature natural killer cell, mouse SubClassOf PR_000050567

GO_0046697 http://purl.obolibrary.org/obo/GO_0046697

Added

• Class: GO_0046697

GlyA-positive erythrocyte http://purl.obolibrary.org/obo/CL_0002021

Removed

• GlyA-positive erythrocyte SubClassOf PR_000050567

ILC1, human http://purl.obolibrary.org/obo/CL_0001077

Removed

• ILC1, human SubClassOf PR_000050567

Kit and Sca1-positive hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0001008

Removed

• Kit and Sca1-positive hematopoietic stem cell SubClassOf PR_000050567

Kit-negative, Ly-76 high orthochromatophilic erythroblasts http://purl.obolibrary.org/obo/CL_0002017

Removed

• Kit-negative, Ly-76 high orthochromatophilic erythroblasts SubClassOf PR_000050567

Kit-positive macrophage dendritic cell progenitor http://purl.obolibrary.org/obo/CL_0002011

Removed

• Kit-positive macrophage dendritic cell progenitor SubClassOf PR_000050567

Kit-positive megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002024

Removed

• Kit-positive megakaryocyte progenitor cell SubClassOf PR_000050567

Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0002006

Removed

• Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell SubClassOf PR_000050567

Kupffer cell http://purl.obolibrary.org/obo/CL_0000091

Removed

• Kupffer cell SubClassOf PR_000050567

L cone cell http://purl.obolibrary.org/obo/CL_0003048

Removed

• L cone cell SubClassOf PR_000050567

Ly-76 high positive erythrocyte http://purl.obolibrary.org/obo/CL_0002022

Removed

• Ly-76 high positive erythrocyte SubClassOf PR_000050567

M cone cell http://purl.obolibrary.org/obo/CL_0003049

Removed

• M cone cell SubClassOf PR_000050567

NK1.1-positive natural killer cell, mouse http://purl.obolibrary.org/obo/CL_0002438

Removed

• NK1.1-positive natural killer cell, mouse SubClassOf PR_000050567

PR_000050567 http://purl.obolibrary.org/obo/PR_000050567

Removed

• Class: PR_000050567

TAC3-positive medium spiny neuron http://purl.obolibrary.org/obo/CL_4042002

Removed

• TAC3-positive medium spiny neuron SubClassOf PR_000050567

TAC3-positive striatal interneuron http://purl.obolibrary.org/obo/CL_4042001

Removed

• TAC3-positive striatal interneuron SubClassOf PR_000050567

TCR-positive macrophage http://purl.obolibrary.org/obo/CL_4030058

Removed

• TCR-positive macrophage SubClassOf PR_000050567

UBERON_0001295 http://purl.obolibrary.org/obo/UBERON_0001295

Removed

• Class: UBERON_0001295

adipose macrophage http://purl.obolibrary.org/obo/CL_0002477

Removed

• adipose macrophage SubClassOf PR_000050567

alpha-beta T cell http://purl.obolibrary.org/obo/CL_0000789

Removed

• alpha-beta T cell SubClassOf PR_000050567

alveolar macrophage http://purl.obolibrary.org/obo/CL_0000583

Removed

• alveolar macrophage SubClassOf PR_000050567

angioblastic mesenchymal cell http://purl.obolibrary.org/obo/CL_0000566

Removed

• angioblastic mesenchymal cell SubClassOf PR_000050567

basophil mast progenitor cell http://purl.obolibrary.org/obo/CL_0002028

Removed

• basophil mast progenitor cell SubClassOf PR_000050567

basophil progenitor cell http://purl.obolibrary.org/obo/CL_0000613

Removed

• basophil progenitor cell SubClassOf PR_000050567

basophilic erythroblast http://purl.obolibrary.org/obo/CL_0000549

Removed

• basophilic erythroblast SubClassOf PR_000050567

bone marrow macrophage http://purl.obolibrary.org/obo/CL_0002476

Removed

• bone marrow macrophage SubClassOf PR_000050567

ciliated cell http://purl.obolibrary.org/obo/CL_0000064

Removed

• ciliated cell SubClassOf PR_000050567

classical monocyte http://purl.obolibrary.org/obo/CL_0000860

Removed

• classical monocyte SubClassOf PR_000050567

common myeloid progenitor, CD34-positive http://purl.obolibrary.org/obo/CL_0001059

Removed

• common myeloid progenitor, CD34-positive SubClassOf PR_000050567

decidual natural killer cell, human http://purl.obolibrary.org/obo/CL_0002343

Removed

• decidual natural killer cell, human SubClassOf PR_000050567

dendritic cell http://purl.obolibrary.org/obo/CL_0000451

Removed

• dendritic cell SubClassOf PR_000050567

early T lineage precursor http://purl.obolibrary.org/obo/CL_0002425

Removed

• early T lineage precursor SubClassOf PR_000050567

elicited macrophage http://purl.obolibrary.org/obo/CL_0000861

Removed

• elicited macrophage SubClassOf PR_000050567

eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0000611

Removed

• eosinophil progenitor cell SubClassOf PR_000050567

erythroid progenitor cell, mammalian http://purl.obolibrary.org/obo/CL_0001066

Removed

• erythroid progenitor cell, mammalian SubClassOf PR_000050567

fetal derived definitive erythrocyte http://purl.obolibrary.org/obo/CL_0002357

Removed

• fetal derived definitive erythrocyte SubClassOf PR_000050567

fetal liver hematopoietic progenitor cell http://purl.obolibrary.org/obo/CL_0002353

Removed

• fetal liver hematopoietic progenitor cell SubClassOf PR_000050567

gamma-delta T cell http://purl.obolibrary.org/obo/CL_0000798

Removed

• gamma-delta T cell SubClassOf PR_000050567

glomerular endothelial cell http://purl.obolibrary.org/obo/CL_0002188

Removed

• glomerular endothelial cell SubClassOf PR_000050567

granulocyte http://purl.obolibrary.org/obo/CL_0000094

Removed

• granulocyte SubClassOf PR_000050567

group 2 innate lymphoid cell, human http://purl.obolibrary.org/obo/CL_0001081

Removed

• group 2 innate lymphoid cell, human SubClassOf PR_000050567

group 2 innate lymphoid cell, mouse http://purl.obolibrary.org/obo/CL_0002089

Removed

• group 2 innate lymphoid cell, mouse SubClassOf PR_000050567

group 3 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001071

Removed

• group 3 innate lymphoid cell SubClassOf PR_000050567

hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0000837

Removed

• hematopoietic multipotent progenitor cell SubClassOf PR_000050567

hepatic stellate cell http://purl.obolibrary.org/obo/CL_0000632

Removed

• hepatic stellate cell SubClassOf PR_000050567

immature single positive thymocyte http://purl.obolibrary.org/obo/CL_0000805

Removed

• immature single positive thymocyte SubClassOf PR_000050567

luminal hormone-sensing cell of mammary gland http://purl.obolibrary.org/obo/CL_4033058

Removed

• luminal hormone-sensing cell of mammary gland SubClassOf PR_000050567

lymph node macrophage http://purl.obolibrary.org/obo/CL_0000868

Removed

• lymph node macrophage SubClassOf PR_000050567

lymphocyte of B lineage, CD19-positive http://purl.obolibrary.org/obo/CL_0001200

Removed

• lymphocyte of B lineage, CD19-positive SubClassOf PR_000050567

mast cell http://purl.obolibrary.org/obo/CL_0000097

Removed

• mast cell SubClassOf PR_000050567

mast cell progenitor http://purl.obolibrary.org/obo/CL_0000831

Removed

• mast cell progenitor SubClassOf PR_000050567

mature T cell http://purl.obolibrary.org/obo/CL_0002419

Removed

• mature T cell SubClassOf PR_000050567

microglial cell http://purl.obolibrary.org/obo/CL_0000129

Removed

• microglial cell SubClassOf PR_000050567

monoblast http://purl.obolibrary.org/obo/CL_0000040

Removed

• monoblast SubClassOf PR_000050567

myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0000889

Removed

• myeloid suppressor cell SubClassOf PR_000050567

natural helper lymphocyte http://purl.obolibrary.org/obo/CL_0002679

Removed

• natural helper lymphocyte SubClassOf PR_000050567

neutrophilic myeloblast http://purl.obolibrary.org/obo/CL_0000042

Removed

• neutrophilic myeloblast SubClassOf PR_000050567

non-classical monocyte http://purl.obolibrary.org/obo/CL_0000875

Removed

• non-classical monocyte SubClassOf PR_000050567

osteoclast http://purl.obolibrary.org/obo/CL_0000092

Removed

• osteoclast SubClassOf PR_000050567

parafollicular cell http://purl.obolibrary.org/obo/CL_0000570

Removed

• parafollicular cell SubClassOf PR_000050567

peritoneal macrophage http://purl.obolibrary.org/obo/CL_0000581

Removed

• peritoneal macrophage SubClassOf PR_000050567

perivascular macrophage http://purl.obolibrary.org/obo/CL_0000881

Removed

• perivascular macrophage SubClassOf PR_000050567

plasma cell http://purl.obolibrary.org/obo/CL_0000786

Removed

• plasma cell SubClassOf PR_000050567

polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0000550

Removed

• polychromatophilic erythroblast SubClassOf PR_000050567

pre-conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002010

Removed

• pre-conventional dendritic cell SubClassOf PR_000050567

pre-natural killer cell http://purl.obolibrary.org/obo/CL_0000937

Removed

• pre-natural killer cell SubClassOf PR_000050567

primitive erythroid progenitor http://purl.obolibrary.org/obo/CL_0002361

Removed

• primitive erythroid progenitor SubClassOf PR_000050567

primitive red blood cell http://purl.obolibrary.org/obo/CL_0002355

Removed

• primitive red blood cell SubClassOf PR_000050567

pro-B cell http://purl.obolibrary.org/obo/CL_0000826

Removed

• pro-B cell SubClassOf PR_000050567

pro-NK cell http://purl.obolibrary.org/obo/CL_0000825

Removed

• pro-NK cell SubClassOf PR_000050567

proerythroblast http://purl.obolibrary.org/obo/CL_0000547

Removed

• proerythroblast SubClassOf PR_000050567

promonocyte http://purl.obolibrary.org/obo/CL_0000559

Removed

• promonocyte SubClassOf PR_000050567

promyelocyte http://purl.obolibrary.org/obo/CL_0000836

Removed

• promyelocyte SubClassOf PR_000050567

reticulocyte http://purl.obolibrary.org/obo/CL_0000558

Removed

• reticulocyte SubClassOf PR_000050567

splenic marginal zone macrophage http://purl.obolibrary.org/obo/CL_0000872

Removed

• splenic marginal zone macrophage SubClassOf PR_000050567

splenic metallophillic macrophage http://purl.obolibrary.org/obo/CL_0000873

Removed

• splenic metallophillic macrophage SubClassOf PR_000050567

splenic red pulp macrophage http://purl.obolibrary.org/obo/CL_0000874

Removed

• splenic red pulp macrophage SubClassOf PR_000050567

splenic white pulp macrophage http://purl.obolibrary.org/obo/CL_0000876

Removed

• splenic white pulp macrophage SubClassOf PR_000050567

stromal cell of endometrium http://purl.obolibrary.org/obo/CL_0002255

Removed

• stromal cell of endometrium IAO_0000115 "A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell."

  • hasDbXref "Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs)"

  • hasDbXref "PMID:11331626"

  • hasDbXref "https://doi.org/10.1038/s41591-020-1040-z"

  • hasDbXref "PMID:30309298"

  • hasDbXref "PMID:30013421"

• stromal cell of endometrium EquivalentTo stromal cell and (BFO_0000050 some UBERON_0001295)

• stromal cell of endometrium SubClassOf stromal cell

  • is_inferred "true"

Added

• stromal cell of endometrium IAO_0000115 "A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone."

  • hasDbXref "Wikipedia:Decidualization"

  • hasDbXref "PMID:11331626"

  • hasDbXref "PMID:31907034"

  • hasDbXref "https://doi.org/10.1038/s41591-020-1040-z"

  • hasDbXref "PMID:30309298"

  • hasDbXref "PMID:30013421"

• stromal cell of endometrium hasNarrowSynonym "decidualized endometrial stromal cell"

  • hasDbXref "PMID:31907034"

• stromal cell of endometrium hasBroadSynonym "stromal cell of uterus"

• stromal cell of endometrium EquivalentTo stromal cell and (BFO_0000050 some UBERON_0002337)

• stromal cell of endometrium SubClassOf RO_0002215 some GO_0046697

• stromal cell of endometrium SubClassOf stromal cell

yolk sac hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0002354

Removed

• yolk sac hematopoietic stem cell SubClassOf PR_000050567

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

decidualization http://purl.obolibrary.org/obo/GO_0046697

Added

• Class: decidualization

stromal cell of endometrium http://purl.obolibrary.org/obo/CL_0002255

Removed

• stromal cell of endometrium definition "A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell."

  • database_cross_reference "PMID:11331626"

  • database_cross_reference "PMID:30013421"

  • database_cross_reference "PMID:30309298"

  • database_cross_reference "Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs)"

  • database_cross_reference "https://doi.org/10.1038/s41591-020-1040-z"

• stromal cell of endometrium EquivalentTo stromal cell and (part of some endometrium)

• stromal cell of endometrium SubClassOf stromal cell

  • is_inferred "true"

• stromal cell of endometrium SubClassOf part of some endometrial stroma

Added

• stromal cell of endometrium definition "A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone."

  • database_cross_reference "Wikipedia:Decidualization"

  • database_cross_reference "PMID:11331626"

  • database_cross_reference "PMID:30013421"

  • database_cross_reference "PMID:31907034"

  • database_cross_reference "PMID:30309298"

  • database_cross_reference "https://doi.org/10.1038/s41591-020-1040-z"

• stromal cell of endometrium has narrow synonym "decidualized endometrial stromal cell"

  • database_cross_reference "PMID:31907034"

• stromal cell of endometrium has_broad_synonym "stromal cell of uterus"

• stromal cell of endometrium EquivalentTo stromal cell and (part of some endometrial stroma)

• stromal cell of endometrium SubClassOf capable of some decidualization