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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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Caloha request terms to CL ontology #227

Closed paulacalipho closed 3 years ago

paulacalipho commented 11 years ago

Hello, we have a list of cell types for which neXtprot have annotations and/or expression data. Would it be possible to create the following terms in CL ontology? I added below the corresponding entries. Many thanks in advance Paula and Lydie from Calipho group

TS-2398 Nasopharyngeal epithelial cell TS-1252 Oral mucosa squamous cell TS-1256 Cerebral cortex glial cell TS-2377 Breast adipocyte TS-1269 Lymph node germinal center cell TS-1250 Esophageal squamous cell TS-1242 Pancreas exocrine glandular cell TS-1271 Appendix glandular cell TS-1272 Mammary gland glandular cell TS-1273 Uterine cervix glandular cell TS-1274 Colon glandular cell TS-1275 Duodenum glandular cell TS-1276 Epididymis glandular cell TS-1277 Oviduct glandular cell TS-1278 Gall bladder glandular cell TS-1279 Parathyroid glandular cell TS-1280 Prostate glandular cell TS-1281 Rectum glandular cell TS-1282 Salivary gland glandular cell TS-1283 Seminal vesicle glandular cell TS-1286 Small intestine glandular cell TS-2166 Thyroid gland glandular cell TS-2177 Adrenal gland glandular cell TS-1251 Uterine cervix squamous cell TS-1253 Tonsil squamous cell TS-1254 Vagina squamous cell TS-2397 Colon endothelial cell TS-2372 Cerebral cortex endothelial cell TS-0576 Lung macrophage TS-2170 Vulva/Anal skin epidermal cell TS-1257 Hippocampus glial cell TS-1258 Lateral ventricle glial cell TS-1261 Lateral ventricle neuron TS-2396 Cerebral cortex neuropil TS-2394 Neural progenitor TS-0385 Foreskin keratinocyte TS-0056 Articular chondrocyte TS-0384 Foreskin fibroblast TS-0643 Muscle fibroblast TS-2109 Bone marrow hematopoietic cell TS-2359 Cerebellar neuron TS-0618 Mesenchymal stem cell TS-0765 Peripheral blood granulocyte TS-0766 Peripheral blood leukocyte TS-0767 Peripheral blood lymphocyte TS-0768 Peripheral blood monocyte TS-0769 Peripheral blood neutrophil TS-0770 Peripheral blood T-cell TS-2370 Peripheral blood mononuclear cell

Here the corresponding entries: [Term] id: TS-2396 name: Cerebral cortex neuropil def: "Neuropil in the cerebral cortex." [NXP:PDR] relationship: part_of TS-0091 ! Cerebral cortex xref: UBERON:0013693 is_a: TS-2403 ! Neuropil

[Term] id: TS-2397 name: Colon endothelial cell def: "Vascular endothelium found in colon blood vessels." [NPX:PDR] synonym: "Colon endothelial cells" RELATED [] synonym: "Colonic endothelial cell" RELATED [] relationship: part_of TS-0162 ! Colon endothelium

[Term] id: TS-2398 name: Nasopharyngeal epithelial cell def: "Cell of the nasopharyngeal epithelium." [NPX:PDR] synonym: "Nasopharynx respiratory epithelial cells" RELATED [] is_a: TS-2026 ! Epithelial cell relationship: part_of TS-0662 ! Nasopharyngeal epithelium is_a: TS-2026 ! Epithelial cell

[Term] id: TS-1250 name: Esophageal squamous cell def: "A flat, scale-like epithelial cell that lines the upper and middle third of the esophageal lumen." [NCI_Thesaurus:Esophageal_Squamous_Cell] synonym: "Esophagus squamous cell" RELATED [] synonym: "Esophagus squamous epithelial cell" RELATED [] synonym: "Esophagus squamous epithelial cells" RELATED [] synonym: "Oesophageal squamous epithelial cell" RELATED [] synonym: "Oesophageal squamous epithelium" RELATED [] synonym: "Oesophagus squamous cell" RELATED [] synonym: "Oesophagus squamous epithelial cell" RELATED [] xref: BTO:0003635 xref: UBERON:0006920 is_a: TS-1249 ! Squamous cell relationship: part_of TS-0698 ! Esophageal epithelium

[Term] id: TS-1251 name: Uterine cervix squamous cell def: "Squamous cell of uterine cervix epithelium." [NPX:PDR] synonym: "Cervix squamous cell" RELATED [] synonym: "Cervix squamous epithelial cell" RELATED [] synonym: "Cervix, uterine squamous epithelial cells" RELATED [] synonym: "Uterine cervix squamous epithelial cell" RELATED [] synonym: "Uterine cervix squamous epithelial cells" RELATED [] is_a: TS-1249 ! Squamous cell relationship: part_of TS-0137 ! Uterine cervix epithelium

[Term] id: TS-1252 name: Oral mucosa squamous cell def: "Squamous cell of oral epithelium." [NPX:PDR] synonym: "Oral cavity mucosa squamous cell" RELATED [] synonym: "Oral cavity mucosa squamous epithelial cell" RELATED [] synonym: "Oral mucosa squamous epithelial cell" RELATED [] synonym: "Oral mucosa squamous epithelial cells" RELATED [] is_a: TS-1249 ! Squamous cell relationship: part_of TS-0715 ! Oral epithelium

[Term] id: TS-1253 name: Tonsil squamous cell def: "Squamous cell of tonsil epithelium." [NPX:PDR] synonym: "Tonsil squamous epithelial cell" RELATED [] synonym: "Tonsil squamous epithelial cells" RELATED [] synonym: "Tonsillar squamous cell" RELATED [] synonym: "Tonsillar squamous epithelial cell" RELATED [] is_a: TS-1249 ! Squamous cell relationship: part_of TS-2070 ! Tonsil epithelium

[Term] id: TS-1254 name: Vagina squamous cell def: "Squamous cell of vaginal epithelium." [NPX:PDR] synonym: "Vagina squamous epithelial cell" RELATED [] synonym: "Vagina squamous epithelial cells" RELATED [] synonym: "Vaginal squamous cell" RELATED [] synonym: "Vaginal squamous epithelial cell" RELATED [] is_a: TS-1249 ! Squamous cell relationship: part_of TS-1325 ! Vaginal epithelium

[Term] id: TS-1256 name: Cerebral cortex glial cell def: "Glial cell of cerebral cortex." [NPX:PDR] synonym: "Brain cortex glial cell" RELATED [] synonym: "Cerebral cortex glial cells" RELATED [] synonym: "Cerebrum cortex glial cell" RELATED [] is_a: TS-0415 ! Glial cell relationship: part_of TS-0091 ! Cerebral cortex

[Term] id: TS-1257 name: Hippocampus glial cell def: "Glial cell of hippocampus." [NPX:PDR] synonym: "Hippocampal glial cell" RELATED [] synonym: "Hippocampus glial cells" RELATED [] synonym: "Hippocampus neuroglial cell" RELATED [] is_a: TS-0415 ! Glial cell relationship: part_of TS-0460 ! Hippocampus

[Term] id: TS-1258 name: Lateral ventricle glial cell def: "Glial cell of lateral ventricle." [NPX:PDR] synonym: "Lateral ventricle glial cells" RELATED [] is_a: TS-0415 ! Glial cell relationship: part_of TS-1230 ! Lateral ventricle

[Term] id: TS-1261 name: Lateral ventricle neuron def: "Neuron of lateral ventricle." [NPX:PDR] synonym: "Lateral ventricle neural cell" RELATED [] synonym: "Lateral ventricle neuronal cell" RELATED [] synonym: "Lateral ventricle neuronal cells" RELATED [] is_a: TS-0683 ! Neuron relationship: part_of TS-1230 ! Lateral ventricle

[Term] id: TS-2377 name: Breast adipocyte def: "Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma." [HPA:Breast] synonym: "Breast adipocytes" RELATED [] is_a: TS-0012 ! Adipocyte relationship: part_of TS-2083 ! Breast

[Term] id: TS-1269 name: Lymph node germinal center cell def: "The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a lymph node." [MeSH:germinal_center;NPX:PDR] synonym: "Lymph node germinal center" RELATED [] synonym: "Lymph node germinal center cells" RELATED [] synonym: "Lymph node reaction center" RELATED [] synonym: "Lymph node reaction center cells" RELATED [] xref: FMA:55224 xref: UBERON:0009039 is_a: TS-1289 ! Lymph node lymphoid cell

[Term] id: TS-1271 name: Appendix glandular cell def: "Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] synonym: "Appendix glandular cells" RELATED [] synonym: "Caecal appendix glandular cell" RELATED [] synonym: "Cecal appendix glandular cell" RELATED [] synonym: "Vermiform appendix glandular cell" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2062 ! Appendix epithelium

[Term] id: TS-1272 name: Mammary gland glandular cell def: "Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts." [NPX:PDR;HPA:HPA] synonym: "Breast glandular cell" RELATED [] synonym: "Breast glandular cells" RELATED [] synonym: "Mammary glandular cell" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-0593 ! Mammary epithelium

[Term] id: TS-1273 name: Uterine cervix glandular cell def: "Glandular cell of uterine cervix epithelium." [NPX:PDR] synonym: "Cervix glandular cell" RELATED [] synonym: "Cervix, uterine glandular cell" RELATED [] synonym: "Cervix, uterine glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-0137 ! Uterine cervix epithelium

[Term] id: TS-1274 name: Colon glandular cell def: "Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] synonym: "Colon glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-0163 ! Colon epithelium

[Term] id: TS-1275 name: Duodenum glandular cell def: "Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell." [NPX:PDR] synonym: "Duodenum glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2087 ! Duodenal epithelium

[Term] id: TS-1276 name: Epididymis glandular cell def: "Glandular cell of epididymal epithelium." [NPX:PDR] synonym: "Epididymal glandular cell" RELATED [] synonym: "Epididymis glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2063 ! Epididymal epithelium

[Term] id: TS-1277 name: Oviduct glandular cell def: "Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells." [NPX:PDR;HPA:HPA] synonym: "Fallopian tube glandular cell" RELATED [] synonym: "Fallopian tube glandular cells" RELATED [] synonym: "Uterine tube glandular cell" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-1316 ! Oviduct epithelium

[Term] id: TS-1278 name: Gall bladder glandular cell def: "Glandular cell of gall bladder epithelium." [NPX:PDR] synonym: "Gall bladder glandular cells" RELATED [] synonym: "Gallbladder glandular cell" RELATED [] synonym: "Gallbladder glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-1304 ! Gall bladder epithelium

[Term] id: TS-1279 name: Parathyroid glandular cell def: "Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells." [NPX:PDR;HPA:HPA] synonym: "Parathyroid gland glandular cell" RELATED [] synonym: "Parathyroid gland glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2141 ! Parathyroid epithelium

[Term] id: TS-1280 name: Prostate glandular cell def: "Glandular cell of prostate epithelium. A secretory cell that produces and secretes prostatic fluid. Prostatic fluid contains citric acid, the enzyme fibrinolysin that liquefies the semen, acid phosphatase, a number of other enzymes and lipids. The secretion of the prostate is the first fraction of the ejaculate." [NCI_Thesaurus:Prostatic_Glandular_Cell] synonym: "Prostate glandular cells" RELATED [] xref: FMA:86774 is_a: TS-2085 ! Glandular cell relationship: part_of TS-2065 ! Prostate epithelium

[Term] id: TS-1281 name: Rectum glandular cell def: "Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] synonym: "Rectal glandular cell" RELATED [] synonym: "Rectum glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2066 ! Rectal epithelium

[Term] id: TS-1282 name: Salivary gland glandular cell def: "Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts." [NPX:PDR;HPA:HPA] synonym: "Salivary gland glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2067 ! Salivary gland epithelium

[Term] id: TS-1283 name: Seminal vesicle glandular cell def: "Glandular cell of seminal vesicle epithelium." [NPX:PDR] synonym: "Seminal vesicle glandular cells" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-2069 ! Seminal vesicle epithelium

[Term] id: TS-1286 name: Small intestine glandular cell def: "A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) ." [NCI_Thesaurus:Small_Intestinal_Glandular_Cell;NPX:PDR] synonym: "Small bowel glandular cell" RELATED [] synonym: "Small intestinal glandular cell" RELATED [] synonym: "Small intestine glandular cells" RELATED [] xref: FMA:86928 is_a: TS-2085 ! Glandular cell relationship: part_of TS-2104 ! Small intestine epithelium

[Term] id: TS-1242 name: Pancreas exocrine glandular cell def: "Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts." [NPX:PDR;HPA:HPA] synonym: "Exocrine pancreas glandular cell" RELATED [] synonym: "Pancreas exocrine glandular cells" RELATED [] xref: BTO:0000028 is_a: TS-2085 ! Glandular cell relationship: part_of TS-2108 ! Exocrine pancreas epithelium

[Term] id: TS-2166 name: Thyroid gland glandular cell def: "Glandular cell of thyroid. Example: thyroid follicular cell, parafollicular cells (also called C cells)." [NPX:PDR;HPA:HPA] synonym: "Thyroid gland glandular cells" RELATED [] synonym: "Thyroid glandular cell" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-1047 ! Thyroid

[Term] id: TS-2177 name: Adrenal gland glandular cell def: "Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens." [NPX:PDR] synonym: "Adrenal gland glandular cells" RELATED [] synonym: "Adrenal glandular cell" RELATED [] synonym: "Suprarenal gland glandular cell" RELATED [] is_a: TS-2085 ! Glandular cell relationship: part_of TS-0015 ! Adrenal cortex

[Term] id: TS-2372 name: Cerebral cortex endothelial cell def: "Endothelial cells forming the walls of the capillaries within the cerebral cortex." [NPX:PDR] synonym: "Cerebral cortex endothelial cells" RELATED [] synonym: "Endothelial cells of cerebral cortex" RELATED [] relationship: part_of TS-0091 ! Cerebral cortex relationship: part_of TS-0092 ! Brain endothelium

[Term] id: TS-0576 name: Lung macrophage def: "Circulating macrophages and tissue macrophages (alveolar macrophages) of lung." [NPX:PDR;HPA:HPA] synonym: "Lung macrophages" RELATED [] is_a: TS-0587 ! Macrophage relationship: part_of TS-0568 ! Lung

[Term] id: TS-2170 name: Vulva/Anal skin epidermal cell def: "Any of the epidermal cells found in the vulva/anal skin epidermis." [NPX:PDR] synonym: "vulva/anal skin epidermal cells" RELATED [] is_a: TS-0283 ! Epidermis relationship: part_of TS-1231 ! Vulva/Anal skin

[Term] id: TS-2394 name: Neural progenitor cell def: "Neural progenitor cells are proliferative cells with a limited capacity for self-renewal and are often unipotent. Within the hippocampal subgranular cell layer, two different neural proliferative cells types exist: one that generates exclusively neuronal progeny and another that generates exclusively glial progeny. During development of the mammalian cerebral cortex, neurons are generated from two principal classes of neural progenitor cells: the apical progenitors and the basal progenitors or intermediate progenitor cells." [PMID:12591214/PMID:21224845] synonym: "Neural progenitor cells" RELATED [] is_a: TS-2040 ! Nervous system cell

[Term] id: TS-0385 name: Foreskin keratinocyte def: "Keratinocyte from foreskin." [NPX:PDR] is_a: TS-0500 ! Keratinocyte relationship: part_of TS-0383 ! Foreskin

[Term] id: TS-0056 name: Articular chondrocyte def: "Chondrocyte forming the hyaline cartilage found in joints." [NPX:PDR] is_a: TS-0138 ! Chondrocyte relationship: part_of TS-0055 ! Articular cartilage

[Term] id: TS-0384 name: Foreskin fibroblast def: "Fibroblast from foreskin." [NPX:PDR] is_a: TS-0935 ! Skin fibroblast relationship: part_of TS-0383 ! Foreskin

[Term] id: TS-0643 name: Muscle fibroblast def: "Fibroblast from muscle organ." [NPX:PDR] is_a: TS-0362 ! Fibroblast

[Term] id: TS-2109 name: Bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] synonym: "Bone marrow hematopoietic cells" RELATED [] synonym: "Bone marrow poietic cells" RELATED [] is_a: TS-2017 ! Hematopoietic cell relationship: part_of TS-2142 ! Hematopoietic tissue

[Term] id: TS-2359 name: Cerebellar neuron def: "Neuron of the cerebellum." [NPX:PDR] synonym: "Cerebellum neuron" RELATED [] xref: FMA:84665 is_a: TS-0683 ! Neuron relationship: part_of TS-0125 ! Cerebellum

[Term] id: TS-0618 name: Mesenchymal stem cell def: "Cells that can develop into distinct mesenchymal tissue such as bone; tendons; muscles; adipose tissue; cartilage; nerve tissue; and blood and blood vessels." [MeSH:Mesenchymal_Stem_Cells] synonym: "MSC stem cell" RELATED [] synonym: "Multipotent mesenchymal stromal cell" RELATED [] synonym: "Multipotent MSC stem cell" RELATED [] xref: BTO:0003298 xref: MESH:D044982 is_a: TS-2086 ! Stem cell

[Term] id: TS-0765 name: Peripheral blood granulocyte def: "Granulocytes found in peripheral blood." [NPX:PDR] is_a: TS-0422 ! Granulocyte is_a: TS-0766 ! Peripheral blood leukocyte

[Term] id: TS-0766 name: Peripheral blood leukocyte def: "Leukocytes found in peripheral blood." [NPX:PDR] synonym: "Peripheral blood leucocyte" RELATED [] is_a: TS-0549 ! Leukocyte relationship: part_of TS-0771 ! Peripheral blood

[Term] id: TS-0767 name: Peripheral blood lymphocyte def: "Lymphocytes found in peripheral blood." [NPX:PDR] is_a: TS-0583 ! Lymphocyte is_a: TS-0766 ! Peripheral blood leukocyte

[Term] id: TS-0768 name: Peripheral blood monocyte def: "Monocytes found in peripheral blood." [NPX:PDR] xref: FMA:86713 is_a: TS-0638 ! Monocyte is_a: TS-0766 ! Peripheral blood leukocyte

[Term] id: TS-0769 name: Peripheral blood neutrophil def: "Neutrophils found in peripheral blood." [NPX:PDR] is_a: TS-0688 ! Neutrophil is_a: TS-0765 ! Peripheral blood granulocyte

[Term] id: TS-0770 name: Peripheral blood T-cell def: "T-cells found in peripheral blood." [NPX:PDR] synonym: "Peripheral blood T cell" RELATED [] synonym: "Peripheral blood T lymphocyte" RELATED [] synonym: "Peripheral blood T-lymphocyte" RELATED [] is_a: TS-0767 ! Peripheral blood lymphocyte is_a: TS-1001 ! T-cell

[Term] id: TS-2370 name: Peripheral blood mononuclear cell def: "A monocyte found in the general circulation." [NCI_Thesaurus:Peripheral_Blood_Mononuclear_Cell] xref: BTO:0001025 is_a: TS-0766 ! Peripheral blood leukocyte

cmungall commented 11 years ago

Transferred to https://code.google.com/p/cell-ontology/issues/detail?id=30

cmungall commented 11 years ago

New terms

Will be in CL release today:

Pending

paulacalipho commented 11 years ago

Hello Thank you for this Paula

paulacalipho commented 11 years ago

TS-0768 Peripheral blood monocyte was mapped to xref: CL:0000842 = mononuclear cell Should be mapped to Monocyte CL:0000576 (according to CL ontology definition monocytes are considered in peripheral blood: Monocyte= Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells)

TS-2370 Peripheral blood mononuclear cell mapping to CL is pending. We just want to inform we corrected the definition. Now is: "A peripheral blood cell with a single nucleus. This category includes lymphocytes and monocytes"

Thanks Paula

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.