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190106 release

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dosumis committed Jan 6, 2020
1 parent 9050042 commit bf2f51954a45c580e86ce98d85cecc4850492588
Showing with 89,646 additions and 39,496 deletions.
  1. +569 −451 cl-base.json
  2. +67 −25 cl-base.obo
  3. +184 −81 cl-base.owl
  4. +2,557 −582 cl-basic.json
  5. +68 −24 cl-basic.obo
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  7. +5,042 −4,747 cl-full.json
  8. +536 −373 cl-full.obo
  9. +1,228 −1,041 cl-full.owl
  10. +4,146 −3,951 cl-non-classified.json
  11. +529 −369 cl-non-classified.obo
  12. +1,179 −1,029 cl-non-classified.owl
  13. +2,765 −648 cl-simple.json
  14. +68 −51 cl-simple.obo
  15. +911 −54 cl-simple.owl
  16. +4,849 −4,554 cl.json
  17. +79 −24 cl.obo
  18. +1,225 −1,038 cl.owl
  19. +31 −23 imports/chebi_import.json
  20. +11 −9 imports/chebi_import.obo
  21. +40 −22 imports/chebi_import.owl
  22. +198 −198 imports/clo_import.json
  23. +23 −23 imports/clo_import.obo
  24. +39 −39 imports/clo_import.owl
  25. +1,438 −1,612 imports/go_import.json
  26. +346 −321 imports/go_import.obo
  27. +904 −1,222 imports/go_import.owl
  28. +36 −36 imports/ncbitaxon_import.json
  29. +10,376 −1,058 imports/pato_import.json
  30. +3,242 −4 imports/pato_import.obo
  31. +9,100 −75 imports/pato_import.owl
  32. +74 −71 imports/ro_import.json
  33. +10 −9 imports/ro_import.obo
  34. +36 −25 imports/ro_import.owl
  35. +1,351 −1,351 imports/uberon_import.json
  36. +3 −7 imports/uberon_import.obo
  37. +1 −5 imports/uberon_import.owl
  38. +1 −1 patterns/definitions.owl
  39. +31 −23 src/ontology/imports/chebi_import.json
  40. +11 −9 src/ontology/imports/chebi_import.obo
  41. +40 −22 src/ontology/imports/chebi_import.owl
  42. +198 −198 src/ontology/imports/clo_import.json
  43. +23 −23 src/ontology/imports/clo_import.obo
  44. +39 −39 src/ontology/imports/clo_import.owl
  45. +1,438 −1,612 src/ontology/imports/go_import.json
  46. +346 −321 src/ontology/imports/go_import.obo
  47. +904 −1,222 src/ontology/imports/go_import.owl
  48. +36 −36 src/ontology/imports/ncbitaxon_import.json
  49. +10,376 −1,058 src/ontology/imports/pato_import.json
  50. +3,242 −4 src/ontology/imports/pato_import.obo
  51. +9,100 −75 src/ontology/imports/pato_import.owl
  52. +74 −71 src/ontology/imports/ro_import.json
  53. +10 −9 src/ontology/imports/ro_import.obo
  54. +36 −25 src/ontology/imports/ro_import.owl
  55. +1,351 −1,351 src/ontology/imports/uberon_import.json
  56. +3 −7 src/ontology/imports/uberon_import.obo
  57. +1 −5 src/ontology/imports/uberon_import.owl
  58. +1,921 −1,916 src/ontology/ontologyterms.txt
  59. 0 src/ontology/prepare_release.sh
  60. +184 −175 src/ontology/reports/basic-report.tsv
  61. +1 −2 src/ontology/reports/class-count-by-prefix.tsv
  62. +1,957 −1,953 src/ontology/reports/edges.tsv
  63. +3 −0 src/ontology/reports/obsoletes.tsv
  64. +3,163 −3,145 src/ontology/reports/synonyms.tsv
  65. +996 −996 src/ontology/reports/xrefs.tsv
  66. +1 −1 src/patterns/definitions.owl
  67. +6 −6 src/patterns/pattern_owl_seed.txt
1,020 cl-base.json

Large diffs are not rendered by default.

@@ -1,5 +1,5 @@
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"
@@ -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

@@ -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

@@ -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
@@ -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
@@ -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
@@ -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
@@ -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]
@@ -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
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

[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

[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

[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]
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
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
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
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
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
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

[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 []

[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
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

2 comments on commit bf2f519

@nathancfox

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nathancfox replied Jan 9, 2020

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

@matentzn

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matentzn replied Jan 9, 2020

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

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