Published April 14, 2017
| Version v2017-04-14
Software
Open
obophenotype/cell-ontology: 2017-04-14 release
Authors/Creators
- 1. Lawrence Berkeley National Laboratory
- 2. Oregon Health and Science University
- 3. University at Buffalo
- 4. @scibite
- 5. www.virtualflybrain.org
Description
New releases, fixes #462
- Fixed axiom annotation APs. Fixes #465
- Fixed xref for FMA supressor T lymphocyte, fixes #463
- Fixed malformed orcid IDs for neural crest cell definition references
- Added group 3 innate lymphoid cell and additional minor fixes to these cell types, Partial work on innate lymphoid cell request, including group 1 and group 2 ILCs #456 #449 #404
- added synonym to cell of skeletal muscle. closes #436
- made 'external supporting cell of Claudius' a related sun for 'claudius cell' addresses #458
- made 'sebocyte' a broad sun of 'acing cell of sebaceous gland' addresses #458
- made 'non-striated muscle cell' a narrow synonym of 'smooth muscle cell' addresses #458
- relabeled GAG secreting cell, made hyaluronic acid secreting cell a narrow synonym. Made hyaluronic acid secreting cell a narrow synonym for 'synovial cell' Addresses #458
- relabeled zygote to animal zygote. closes #454
- removed all animal cells have microvilli. Fixes #455
New classes:
[Term]
id: CL:0001061
name: abnormal cell
namespace: cell
def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd]
comment: https://github.com/obophenotype/cell-ontology/issues/448
xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913
is_a: CL:0000000 ! cell
is_a: GO:0005623 ! cell
intersection_of: GO:0005623 ! cell
intersection_of: bearer_of PATO:0000460 ! abnormal
relationship: bearer_of PATO:0000460 ! abnormal
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T18:53:32Z xsd:dateTime
[Term]
id: CL:0001062
name: effector memory CD8-positive, alpha-beta T cell, terminally differentiated
namespace: cell
@@ -13860,6 +13880,55 @@ relationship: lacks_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-p
relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7
[Term]
id: CL:0001063
name: neoplastic cell
namespace: cell
def: "An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism." [GOC:add, GOC:cg, GOC:wdd]
comment: https://github.com/obophenotype/cell-ontology/issues/448
synonym: "tumor cell" RELATED []
synonym: "tumour cell" RELATED []
xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922
is_a: CL:0001061 ! abnormal cell
intersection_of: CL:0001061 ! abnormal cell
intersection_of: bearer_of PATO:0002011 ! neoplastic
relationship: bearer_of PATO:0002011 ! neoplastic
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T19:16:26Z xsd:dateTime
[Term]
id: CL:0001064
name: malignant cell
namespace: cell
def: "A neoplastic cell that is capable of entering a surrounding tissue" [GOC:add, GOC:cg, GOC:wdd]
comment: https://github.com/obophenotype/cell-ontology/issues/448
synonym: "cancer cell" RELATED []
xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917
is_a: CL:0001063 ! neoplastic cell
intersection_of: CL:0001063 ! neoplastic cell
intersection_of: bearer_of PATO:0002097 ! neoplastic, malignant
relationship: bearer_of PATO:0002097 ! neoplastic, malignant
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T19:39:12Z xsd:dateTime
[Term]
id: CL:0001065
name: innate lymphoid cell
namespace: cell
def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
is_a: CL:0000542 ! lymphocyte
intersection_of: CL:0000542 ! lymphocyte
intersection_of: capable_of GO:0001816 ! cytokine production
intersection_of: capable_of GO:0045087 ! innate immune response
intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule
intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon
relationship: capable_of GO:0001816 ! cytokine production
relationship: capable_of GO:0045087 ! innate immune response
relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule
relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:20:48Z xsd:dateTime
[Term]
id: CL:0001066
name: erythroid progenitor cell, mammalian
namespace: cell
@@ -13901,10 +13970,45 @@ relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule
relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G
[Term]
id: CL:0001067
name: group 1 innate lymphoid cell
namespace: cell
def: "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." [GOC:add, GOC:dsd, PMID:23348417]
is_a: CL:0001065 ! innate lymphoid cell
intersection_of: CL:0001065 ! innate lymphoid cell
intersection_of: capable_of GO:0032609 ! interferon-gamma production
relationship: capable_of GO:0032609 ! interferon-gamma production
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:42:44Z xsd:dateTime
[Term]
id: CL:0001068
name: ILC1
namespace: cell
def: "A group 1 innate lymphoid cell that is non-cytotoxic." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
is_a: CL:0001067 ! group 1 innate lymphoid cell
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T20:54:12Z xsd:dateTime
[Term]
id: CL:0001069
name: group 2 innate lymphoid cell
namespace: cell
def: "An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation." [GOC:add, GOC:dsd, PMID:23292121, PMID:23562755]
synonym: "ILC2" EXACT []
synonym: "nuocyte" EXACT []
is_a: CL:0001065 ! innate lymphoid cell
intersection_of: CL:0001065 ! innate lymphoid cell
intersection_of: capable_of GO:0032634 ! interleukin-5 production
relationship: capable_of GO:0032634 ! interleukin-5 production
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T21:20:08Z xsd:dateTime
[Term]
id: CL:0001070
name: beige adipocyte
namespace: cell
-def: "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." [] {comment="PMID:22796012", comment="GOC:ymb", comment="GOC:add", comment="GOC:cvs", comment="PMID:25851693"}
def: "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." [GOC:add, GOC:cvs, GOC:ymb, PMID:22796012, PMID:25851693]
synonym: "beige brown adipocyte" EXACT []
synonym: "beige fat cell" EXACT []
synonym: "beige/brite adipocyte" EXACT []
@@ -13915,6 +14019,19 @@ is_a: CL:0000136 ! fat cell
relationship: part_of UBERON:0001347 ! white adipose tissue
[Term]
id: CL:0001071
name: group 3 innate lymphoid cell
namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
namespace: cell
synonym: "ILC3" EXACT []
is_a: CL:0001065 ! innate lymphoid cell
intersection_of: CL:0001065 ! innate lymphoid cell
intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2
relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
property_value: http://purl.org/dc/elements/1.1/date 2017-01-31T20:21:26Z xsd:dateTime
Files
obophenotype/cell-ontology-v2017-04-14.zip
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Additional details
Related works
- Is supplement to
- https://github.com/obophenotype/cell-ontology/tree/v2017-04-14 (URL)