@cmungall cmungall released this Jul 10, 2018

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Merge pull request #510 from obophenotype/pre-release

Pre release

@cmungall cmungall released this Dec 13, 2017 · 6 commits to master since this release

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commit f392949
Author: Chris Mungall cjm@berkeleybop.org
Date: Mon Dec 11 16:24:43 2017 -0800

repaired obsolete go refs

commit 5c65a88
Author: Chris Mungall cjm@berkeleybop.org
Date: Mon Dec 11 16:18:15 2017 -0800

Updated axioms that were pointing at obsolete class for release #493 .. using the new robot repair command https://github.com/ontodev/robot/

commit 4bfdc2a
Author: Chris Mungall cjm@berkeleybop.org
Date: Mon Oct 9 09:19:10 2017 -0700

obsoleting classes in dicty, fixes #279

commit de3765b
Author: Nicole Vasilevsky vasilevs@ohsu.edu
Date: Tue Sep 19 18:17:32 2017 -0700

added synonyms to
CL:0002265 ! type D cell of colon
CL:0002266 ! type D cell of small intestine
CL:0002267 ! type D cell of stomach

closes #484

@cmungall cmungall released this Jul 29, 2017 · 17 commits to master since this release

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Minor bugfix

commit f00bd8b
Merge: f74f3a0 37a2fb2
Author: Chris Mungall cjm@berkeleybop.org
Date: Fri Jul 21 17:47:06 2017 -0700

Merge pull request #480 from obophenotype/issue-467-fix-ns

namespace and def APs were inverted. Fixed.

@cmungall cmungall released this Apr 14, 2017 · 28 commits to master since this release

Assets 2

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

@cmungall cmungall released this Nov 23, 2016 · 49 commits to master since this release

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Bug fix releases

fixes #453 and #455

@cmungall cmungall released this Sep 2, 2016 · 58 commits to master since this release

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v2016-09-02

new release

@cmungall cmungall released this Feb 2, 2016 · 68 commits to master since this release

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v2016-02-01

new release draft

@cmungall cmungall released this Aug 8, 2015 · 96 commits to master since this release

Assets 2

Added logical def for meso-epithelial cell