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190106 release
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@dosumis
dosumis committed Jan 6, 2020
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1,020 changes: 569 additions & 451 deletions cl-base.json
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92 changes: 67 additions & 25 deletions cl-base.obo
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format-version: 1.2
data-version: cl/releases/2019-08-12/cl-base.owl
data-version: cl/releases/2020-01-06/cl-base.owl
subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens"
synonymtypedef: LATIN "latin term"
Expand Down Expand Up @@ -232,9 +232,6 @@ xref: FBbt:00004954
xref: FMA:67338
xref: WBbt:0006798
is_a: CL:0000408 {is_inferred="true"} ! male gamete
intersection_of: CL:0000408 ! male gamete
intersection_of: RO:0002215 GO:0030317
intersection_of: RO:0002215 GO:0048240
relationship: BFO:0000051 GO:0005929
relationship: RO:0002202 CL:0000018 ! spermatid

Expand Down Expand Up @@ -475,7 +472,7 @@ namespace: cell
def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544]
comment: Originally this term had some plant germ line cell children.
subset: ubprop:upper_level
is_a: CL:0000548 ! animal cell
is_a: CL:0000003 ! native cell
disjoint_from: CL:0002371 ! somatic cell
relationship: RO:0002215 GO:0022414

Expand Down Expand Up @@ -2015,7 +2012,7 @@ id: CL:0000171
name: pancreatic A cell
namespace: cell
def: "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." [GOC:tfm, ISBN:0721662544]
synonym: "alpha cell of iselt of Langerhans" EXACT []
synonym: "alpha cell of islet of Langerhans" EXACT []
synonym: "pancreatic alpha cell" EXACT []
xref: BTO:0000990
xref: FMA:70585
Expand Down Expand Up @@ -5825,6 +5822,7 @@ xref: BTO:0000802
xref: CALOHA:TS-0030
xref: FMA:83023
is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage
is_a: CL:1001603 ! lung macrophage
intersection_of: CL:0000864 ! tissue-resident macrophage
intersection_of: has_low_plasma_membrane_amount PR:000001012
intersection_of: lacks_plasma_membrane_part PR:000001206
Expand Down Expand Up @@ -6595,6 +6593,7 @@ synonym: "epithelial cell of visceral layer of glomerular capsule" BROAD [FMA:70
synonym: "glomerular podocyte" EXACT [FMA:70967]
synonym: "podocyte" EXACT []
xref: BTO:0002295
xref: FMA:70967
is_a: CL:0002518 ! kidney epithelial cell
is_a: CL:0002522 ! renal filtration cell
relationship: BFO:0000050 UBERON:0005751
Expand Down Expand Up @@ -6941,6 +6940,7 @@ id: CL:0000691
name: stellate interneuron
namespace: cell
is_a: CL:0000099 ! interneuron
is_a: CL:0000122 ! stellate neuron

[Term]
id: CL:0000692
Expand Down Expand Up @@ -7325,6 +7325,7 @@ is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell
intersection_of: CL:0000988 ! hematopoietic cell
intersection_of: RO:0002215 GO:0001667
relationship: BFO:0000050 UBERON:0002405
relationship: RO:0002160 NCBITaxon:7742
relationship: RO:0002202 CL:0000037 ! hematopoietic stem cell

[Term]
Expand Down Expand Up @@ -8405,6 +8406,7 @@ synonym: "suppressor T cell" BROAD []
synonym: "suppressor T lymphocyte" BROAD []
synonym: "suppressor T-cell" BROAD []
synonym: "suppressor T-lymphocyte" BROAD []
synonym: "Treg" EXACT []
xref: BTO:0004520
xref: FMA:84070
is_a: CL:0002419 {is_inferred="true"} ! mature T cell
Expand Down Expand Up @@ -12978,7 +12980,7 @@ creation_date: 2010-04-28T02:13:46Z
id: CL:0002051
name: CD38-high pre-BCR positive cell
namespace: cell
def: "A pre-BCR positive T cell that is CD38-high." [GOC:tfm, PMID:18432934]
def: "A pre-BCR positive B cell that is CD38-high." [GOC:tfm, PMID:18432934]
comment: Markers are associated with human cells.
synonym: "large pre-B cell type I" RELATED []
is_a: CL:0000952 {is_inferred="true"} ! preBCR-positive large pre-B-II cell
Expand Down Expand Up @@ -14247,7 +14249,7 @@ creation_date: 2010-08-24T02:15:16Z

[Term]
id: CL:0002143
name: dark chief cell of parathyroid cell
name: dark chief cell of parathyroid gland
namespace: cell
def: "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." [GOC:tfm, ISBN:0721662544]
xref: FMA:69080
Expand Down Expand Up @@ -14295,9 +14297,10 @@ creation_date: 2010-08-24T10:33:02Z

[Term]
id: CL:0002147
name: clear chief cell of parathyroid cell
name: clear chief cell of parathyroid gland
namespace: cell
def: "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells." [GOC:tfm, ISBN:0618947256]
synonym: "clear chief cell of parathyroid cell" EXACT []
xref: FMA:69081
is_a: CL:0000446 ! chief cell of parathyroid gland
created_by: tmeehan
Expand Down Expand Up @@ -14914,7 +14917,7 @@ creation_date: 2010-09-02T02:09:14Z

[Term]
id: CL:0002203
name: Brush cell of epithelium proper of large intestine
name: brush cell of epithelium proper of large intestine
namespace: cell
alt_id: CL:1000387
def: "Brush cell found in the epithelial layer of the colon." [GOC:tfm]
Expand Down Expand Up @@ -15694,7 +15697,7 @@ name: type D cell of colon
namespace: cell
def: "A D cell located in the colon." [GOC:tfm]
synonym: "colon D-cell" EXACT []
synonym: "colonc delta cell" EXACT []
synonym: "colonic delta cell" EXACT []
synonym: "delta cell of colon" EXACT []
xref: FMA:268744
is_a: CL:0000502 ! type D enteroendocrine cell
Expand Down Expand Up @@ -18449,7 +18452,9 @@ id: CL:0002489
name: double negative thymocyte
namespace: cell
def: "A thymocyte that lacks expression of CD4 and CD8." [GOC:tfm, MP:0002407]
synonym: "double negative T cell" BROAD []
comment: These are precursors to mature T cells; normally, they do not circulate, but are found in the thymus and they have not undergone rearrangement of the alpha and beta T cell receptor genes.
synonym: "CD4-CD8- T cell" EXACT [MP:0002407]
synonym: "double negative T cell" EXACT []
is_a: CL:0000893 {is_inferred="true"} ! thymocyte
intersection_of: CL:0000893 ! thymocyte
intersection_of: lacks_plasma_membrane_part PR:000001004
Expand Down Expand Up @@ -20777,7 +20782,7 @@ intersection_of: RO:0002215 GO:0036321
id: CL:0005019
name: pancreatic epsilon cell
namespace: cell
def: "Ghrelin secreting cells found in the found in the exocrine pancreas." [PMID:14970313]
def: "Ghrelin secreting cells found in the exocrine pancreas." [PMID:14970313]
comment: In mammals the endocrine pancreas is called the Islets of Langerhans.
synonym: "pancreatic E cell" EXACT []
is_a: CL:0005018 ! ghrelin secreting cell
Expand Down Expand Up @@ -21074,7 +21079,8 @@ created_by: haendel
id: CL:0007021
name: alarm substance cell
def: "Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992]" [ISBN-10:0412429403]
synonym: "club cell" EXACT [ISBN-10:0412429403]
synonym: "club cell" RELATED [https://github.com/obophenotype/cell-ontology/issues/583, ISBN-10:0412429403]
synonym: "club cell (zebrafish)" EXACT [https://github.com/obophenotype/cell-ontology/issues/583]
is_a: CL:0000473 ! defensive cell
relationship: BFO:0000050 UBERON:0001003
relationship: RO:0002215 GO:0032940
Expand Down Expand Up @@ -21402,6 +21408,7 @@ def: "Any cell in a salivary gland." []
xref: GOC:pr
xref: http://en.wikipedia.org/wiki/Salivary_gland
is_a: CL:0002371 ! somatic cell
relationship: BFO:0000050 UBERON:0001044

[Term]
id: CL:0010000
Expand Down Expand Up @@ -21647,6 +21654,47 @@ def: "A cell of the neural crest. Neural crest cells are multipotent. Premigrato
is_a: CL:0000048 ! multi fate stem cell
is_a: CL:0002321 ! embryonic cell

[Term]
id: CL:0011013
name: motile sperm cell
def: "A sperm cell that is cabaple of motion (motility)." [PMID:30612620]
is_a: CL:0000019 ! sperm
intersection_of: CL:0000019 ! sperm
intersection_of: RO:0002215 GO:0097722
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: CL:0011014
name: non-motile sperm cell
def: "A sperm cell that is not cabaple of motion (motility)." [PMID:30612620]
is_a: CL:0000019 ! sperm
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: CL:0011015
name: amoeboid sperm cell
def: "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." [PMID:17708982]
is_a: CL:0011013 ! motile sperm cell
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: CL:0011016
name: flagellated sperm cell
def: "A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion." [https://www.lexico.com/en/definition/flagellum, PMID:30612620]
is_a: CL:0011013 ! motile sperm cell
intersection_of: CL:0011013 ! motile sperm cell
intersection_of: RO:0002215 GO:0030317
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: CL:0011018
name: lymphoid tissue–inducer cell
def: "A hematopoietic cell that express ROR gamma t and IL-7R alpha in the absence of lineage markers (e.g. CD3, CD19, B220, CD11c, Gr-1), with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Lymphoid tissue-inducer cells are key to the development of lymph nodes and Peyer’s patches." [PMID:19029905, PMID:21601793, PMID:9354470]
synonym: "LTi" EXACT []
synonym: "lymphoid tissue inducer cell" EXACT []
is_a: CL:0000988 ! hematopoietic cell
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: CL:0011100
name: galanergic neuron
Expand Down Expand Up @@ -22407,7 +22455,7 @@ relationship: BFO:0000050 UBERON:0009970

[Term]
id: CL:1000323
name: pylroric gastric gland goblet cell
name: pyloric gastric gland goblet cell
namespace: cell
def: "A goblet cell that is part of the epithelium of pyloric gland." [GOC:tfm]
synonym: "goblet cell of epithelium of pyloric gland" EXACT []
Expand Down Expand Up @@ -23426,16 +23474,9 @@ intersection_of: BFO:0000050 UBERON:0001230

[Term]
id: CL:1000451
name: epithelial cell of visceral layer of glomerular capsule
namespace: cell
def: "An epithelial cell that is part of the visceral layer of glomerular capsule." [GOC:tfm]
comment: consider merging into CL:0000653
synonym: "glomerular podocyte" NARROW [FMA:70967]
xref: FMA:70967
is_a: CL:0000066 {is_inferred="true"} ! epithelial cell
is_a: CL:0002371 {is_inferred="true"} ! somatic cell
intersection_of: CL:0000066 ! epithelial cell
intersection_of: BFO:0000050 UBERON:0005751
name: obsolete epithelial cell of visceral layer of glomerular capsule
is_obsolete: true
replaced_by: CL:0000653

[Term]
id: CL:1000452
Expand Down Expand Up @@ -24955,6 +24996,7 @@ synonym: "glomerular layer cell" EXACT [NIFSTD:nifext_122]
synonym: "olfactory bulb (accessory) glomerular layer cell" EXACT [NIFSTD:nifext_122]
synonym: "olfactory bulb glomerular layer cell" EXACT [NIFSTD:nifext_122]
synonym: "olfactory bulb glomerularal cell" EXACT [MP:0009943]
synonym: "olfactory bulb periglomerular cell" EXACT []
synonym: "periglomerular cell" EXACT [NIFSTD:nifext_122]
xref: BTO:0003796
xref: NIFSTD:nifext_122
Expand Down
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2 comments on commit bf2f519

@nathancfox
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Why is this commit named 190106 release? Should it be 200106?

@matentzn
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Probably just a typo. The release is named correctly: https://github.com/obophenotype/cell-ontology/releases/tag/v2020-01-06

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