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Releases: obophenotype/cell-ontology

v2023-10-19

19 Oct 13:57
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v2023-10-19

Detailed differences for this release can be viewed at https://github.com/obophenotype/cell-ontology/blob/64876e247f17994f617c734b0eeb976a1a1afcb2/src/ontology/diffs/cl-diff.md

Note that http://purl.obolibrary.org/obo/cl#abbreviation abbreviation has been replaced by http://purl.obolibrary.org/obo/OMO_0003000 abbreviation.

What's Changed

  • Standardised annotation property: abbreviation by @bvarner-ebi in #2159
  • Deleted reports folder from root by @bvarner-ebi in #2161
  • Edited subclasses of 'kidney cell' by @bvarner-ebi in #2163
  • Added new term 'TCR-positive macrophage' by @bvarner-ebi in #2162
  • Fixed unsat for syncytiotrophoblast cell by @aleixpuigb in #2165
  • Added new term onychocyte by @aleixpuigb in #2168
  • Edited Hofbauer cell by @aleixpuigb in #2170
  • Added RO:0002100 ‘has soma location’ to get_scope_query method by @ubyndr in #2174
  • Added new terms for region-agnostic L2/3-6 intratelencephalic projecting glutamatergic cortical neurons (by layer) by @bvarner-ebi in #2181
  • Updated reference term for general upper level slim by @aleixpuigb in #2186
  • Edited PURL for abbreviation in editing_guidelines.md by @bvarner-ebi in #2188
  • Added new term 'ureteric bud cell' by @bvarner-ebi in #2185
  • Changed foaf:depicted_by to foaf:depiction by @anitacaron in #2184
  • Added new terms for lactocyte subtypes by @aleixpuigb in #2189
  • Edited 'chandelier cell' by @bvarner-ebi in #2190
  • Added new terms for mammary luminal epithelial cells by @aleixpuigb in #2187
  • Refreshed imports 10-2023 by @bvarner-ebi in #2192
  • Edited and relabelled 'mammary alveolar cell' to lactocyte by @aleixpuigb in #2196
  • Removed CARO import by @anitacaron in #2199
  • Edited lactocyte textual definition by @aleixpuigb in #2201
  • Removed oort step from the release pipeline by @anitacaron in #2204
  • CL release 2023-10-19 by @bvarner-ebi in #2205

Full Changelog: v2023-09-21...v2023-10-19

v2023-09-21

21 Sep 10:18
d5f4029
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Detailed differences for this release can be viewed at https://github.com/obophenotype/cell-ontology/blob/559d87b58bcb355a4364f8dc9f17a9a296581657/src/ontology/diffs/cl-diff.md

Note that three classes have been obsoleted:
'animal cell'
'native cell'
'somatic cell'

What's Changed

  • Classified amacrine cells GABA vs glycine and dendrite field by @aleixpuigb in #2096
  • Edited 'polyploid cell' by @bvarner-ebi in #2129
  • Edited editing_guidelines.md regarding cross-references by @bvarner-ebi in #2130
  • Updated synonym type on "subcapsular thymic epithelial cell" by @bvarner-ebi in #2131
  • Removed synonyms that were the same as labels by @aleixpuigb in #2132
  • Added label synonym polysemy check by @anitacaron in #2112
  • Removed import folder in the root level by @anitacaron in #2135
  • Added OMO as import by @anitacaron in #2134
  • Refreshed imports 09-2023 by @bvarner-ebi in #2142
  • Made plural synonym annotations consistent by @bvarner-ebi in #2143
  • Added new term 'airway submucosal gland duct ciliated cell' by @aleixpuigb in #2145
  • Edited text definition of 'L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex' by @bvarner-ebi in #2149
  • Added synonym to 'luteal cell' by @aleixpuigb in #2146
  • Obsoleted 'native cell' and 'animal cell' by @bvarner-ebi in #2147
  • Obsoleted 'somatic cell' by @bvarner-ebi in #2151
  • Shortened labels for BDS terms by @shawntanzk in #1806
  • Added new term 'mesenchymal stem cell of orbital adipose tissue' by @paulacalipho in #2153
  • Refreshed imports 09-2023 by @bvarner-ebi in #2156
  • CL release 2023-09-21 by @bvarner-ebi in #2157

Full Changelog: v2023-08-24...v2023-09-21

v2023-08-24

24 Aug 09:37
b57cb4e
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What's Changed

  • Released diff poster by @shawntanzk in #1732
  • Edited editor guidelines regarding CL labels with anatomical references by @bvarner-ebi in #2078
  • Changed telocyte and lymphoblast subclass to seperate subclass by @shawntanzk in #2087
  • Replaced invalid DOI IRIs in xrefs with doi: CURIE strings by @balhoff in #2089
  • Edited 'olfactory granule cell' by @bvarner-ebi in #2085
  • Edited abbreviation related synonyms by @aleixpuigb in #2091
  • Added new terms for retinal ganglion cells by @aleixpuigb in #2090
  • Obsoleted 'acid secreting cell' and Edited 'parietal cell' by @bvarner-ebi in #2098
  • Merged 'choroid plexus cell' into 'choroid plexus epithelial cell' by @bvarner-ebi in #2088
  • Edited 'pain receptor cell' by @bvarner-ebi in #2104
  • Added 'depicted by' statements to SwissBioPics by @lubianat in #2092
  • Removed IAO from imports by @anitacaron in #2093
  • Made additional edits to 'pain receptor cell' by @bvarner-ebi in #2105
  • Edited editor guidelines regarding annotation property 'see also' by @bvarner-ebi in #2109
  • Added "cell" to synonyms of 'syncytiotrophoblast cell' by @shawntanzk in #2108
  • Removed horizontal cell parent term from amacrine cells by @aleixpuigb in #2107
  • Edited editor guidelines regarding MeSH cross-references by @bvarner-ebi in #2115
  • Edited editor guidelines regarding URL cross-references by @bvarner-ebi in #2116
  • Edited MeSH Tree Number cross-references by @bvarner-ebi in #2114
  • Added new term 'perivascular cell' by @aleixpuigb in #2120
  • Edited 'lung neuroendocrine cell' by @bvarner-ebi in #2118
  • Refreshed imports 08-2023 by @bvarner-ebi in #2123
  • CL release 2023-08-24 by @bvarner-ebi in #2125

Full Changelog: v2023-07-20...v2023-08-24

v2023-07-20

20 Jul 08:43
3f96269
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What's Changed

  • Added new design pattern GitHub issue template by @bvarner-ebi in #2038
  • Updated CL issue templates by @bvarner-ebi in #2040
  • Added new term 'eccentric medium spiny neuron' by @bvarner-ebi in #2041
  • Added retina cell type synonyms by @bvarner-ebi in #2046
  • Added has soma location 'retinal bipolar neuron' by @aleixpuigb in #2050
  • Removed GSE dbxrefs by @bvarner-ebi in #2052
  • Edited 'folliculostellate cell' by @aleixpuigb in #2047
  • Replaced synapsed_by with 'synapsed by' in 'cartwheel cell' by @bvarner-ebi in #2055
  • Deleted synapsed_by from CL by @bvarner-ebi in #2057
  • Edited hierarchy 'bronchiolar smooth muscle cell' by @aleixpuigb in #2062
  • Added logical definition and synonym to lung megakaryocyte by @aleixpuigb in #2060
  • Updated editor guidelines re: standardising database_cross_reference and contributor annotations by @bvarner-ebi in #2058
  • Added symbols for BDS terms by @shawntanzk in #1808
  • Edited 'cerebellar granule cell' and 'granule cell precursor' by @bvarner-ebi in #2067
  • Added SOP to create slims by @aleixpuigb in #2068
  • Edited 'endothelial cell of respiratory system lymphatic vessel' by @aleixpuigb in #2072
  • Edited 'dentate gyrus of hippocampal formation granule cell' by @bvarner-ebi in #2070
  • Refreshed imports 07-2023 by @bvarner-ebi in #2073
  • Edited 'pulmonary capillary endothelial cell' location by @aleixpuigb in #2075
  • Refreshed imports 07-2023 (update) by @bvarner-ebi in #2076
  • CL release 2023-07-20 by @bvarner-ebi in #2077

Full Changelog: v2023-06-22...v2023-07-20

v2023-06-22

22 Jun 12:45
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What's Changed

  • Defined 'follicle stem cell' and restricted it to arthropods. by @gouttegd in #1985
  • Fixed myofibroblast part of connective tissue by @aleixpuigb in #1992
  • Fixed platelet EA by @aleixpuigb in #1993
  • Added new term 'von Economo neuron' by @bvarner-ebi in #1998
  • Added new term 'CD8+ CD103+ lung TRM' by @aleixpuigb in #1995
  • Added text definition to 'granule cell' by @bvarner-ebi in #2009
  • Fixed dbxref URLs by @bvarner-ebi in #2011
  • Updated definitions for bladder urothelial cell types by @bvarner-ebi in #2016
  • Updated 'medium spiny neuron' by @bvarner-ebi in #2014
  • Added NCIt mappings by @bvarner-ebi in #2017
  • Added new dorsal striatum medium spiny neuron subtypes by @bvarner-ebi in #2005
  • Added new term 'pre-type II pneumocyte' by @paulacalipho in #2003
  • Added new urothelial cell types by @bvarner-ebi in #2024
  • Updated relations_guide.md by @dosumis in #1824
  • Added new ventral striatum medium spiny neuron subtypes by @bvarner-ebi in #2019
  • Added some guidelines for term editors. by @gouttegd in #2010
  • Updated 'urothelial cell' by @bvarner-ebi in #2025
  • Added new alveolar macrophages by @aleixpuigb in #2023
  • Updated 'basal cell of urothelium' by @bvarner-ebi in #2029
  • Refreshed imports 06-2023 by @bvarner-ebi in #2035
  • Added new lung terms by @aleixpuigb in #2033
  • Added a general cell type upper slim by @aleixpuigb in #1979
  • CL release 2023-06-22 by @bvarner-ebi in #2036

Full Changelog: v2023-05-22...2023-06-22

v2023-05-22

22 May 11:16
574b186
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What's Changed

Full Changelog: v2023-04-20...v2023-05-22

v2023-04-20

20 Apr 11:04
c40778d
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What's Changed

  • Added Metazoan cell classes as subclasses to 'animal cell' by @bvarner-ebi in #1906
  • Added expresses vimentin to cell type by @bvarner-ebi in #1907
  • Added full stop to text definition by @bvarner-ebi in #1924
  • Fixed typo amgydala excitatory neuron by @aleixpuigb in #1928
  • Obsoleted 'primary pigment cell'. by @gouttegd in #1932
  • Obsoleted clade-specific germ line stem cell terms by @gouttegd in #1937
  • Fixed logical definition of 'Schwann cell' by @bvarner-ebi in #1936
  • Updated definitions for 'rosehip neuron' by @bvarner-ebi in #1938
  • Added blood_and_immune_upper_slim by @bvarner-ebi in #1917
  • Added bipolar cell types by @aleixpuigb in #1922
  • Added upper slim validation and coverage report by @ubyndr in #1939
  • Added 3 new cell types by @paulacalipho in #1920
  • CL release 2023-04-20 by @bvarner-ebi in #1952

New Contributors

Full Changelog: v2023-03-21...v2023-04-20

v2023-03-21

21 Mar 15:03
ad357be
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What's Changed

  • Documented policy on delegating import refresh to the tech support group. by @gouttegd in #1852
  • Assigned numeric IDs to native CL object properties by @bvarner-ebi in #1854
  • Normalised CL to Protege 5.6.1 by @bvarner-ebi in #1858
  • Fixed all the alt-id violations and activating QC by @matentzn in #1862
  • Addressed typo parasol GCR by @aleixpuigb in #1869
  • Added 'retinal astrocyte' by @aleixpuigb in #1871
  • Edited 'enteroendocrine cell' by @aleixpuigb in #1864
  • Edited 'GnRH neuron' by @aleixpuigb in #1872
  • Added 'CD24+, CD-133+, vimentin+ proximal tubular cell' by @bvarner-ebi in #1873
  • Added photoreceptor synonyms by @bvarner-ebi in #1877
  • Edited 'corneal endothelial cell' by @aleixpuigb in #1878
  • Added 'anatomical structure' superclass to cell by @bvarner-ebi in #1882
  • Refreshed imports by @bvarner-ebi in #1890
  • Edited megakaryocyte by @aleixpuigb in #1891
  • Refreshed imports by @bvarner-ebi in #1895
  • Edited logical definition 'visceral muscle cell' by @aleixpuigb in #1893
  • Edited 'paneth cell' part_of by @aleixpuigb in #1900
  • Replaced lacks_part with CL:4030045 lacks_part by @bvarner-ebi in #1898
  • Added new respiratory terms by @aleixpuigb in #1896
  • Edited logical definition of 'endocrine cell' by @aleixpuigb in #1897
  • Removed CHEBI import from ODK config by @anitacaron in #1903
  • Release-2023-03-21b by @bvarner-ebi in #1904

Full Changelog: v2023-02-19...v2023-03-21

February 2023 release (no changes)

19 Feb 12:10
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This is a technical normalisation release with the new ODK set up.

v2023-02-15

15 Feb 12:20
f223d1c
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What's Changed (excerpt)

  • Fixed text definition typo for iridophore by @aleixpuigb in #1792
  • Edited 'stromal cell of endometrium' @bvarner-ebi in #1794
  • Fixed typo and changed parent term for 'apocrine cell' by @aleixpuigb in #1801
  • Fixed text definition typo in 'anterior lateral line neuromast mantle cell' by @aleixpuigb in #1797
  • Added new term 'Axl dendritic cell' by @lubianat in #1687
  • Changed has_completed to obo:RO_0002353 by @shawntanzk in #1770
  • Changed 'memory T cell' has_completed by @shawntanzk in #1709
  • Added 'dental pulp stem cell' and edited 'dental pulp cell' by @bvarner-ebi in #1790
  • Changed definition of 'anterior horn motor neuron' by @shawntanzk in #1812
  • Added synonym "metazoan cell" to 'animal cell' by @aleixpuigb in #1818
  • Merged 'neuroendocrine cell' and 'neurosecretory neuron' by @aleixpuigb in #1804
  • Updated mappings: Allow the use of semapv:crossSpeciesExactMatch by @gouttegd in #1821
  • Added new terms early and late spermatid by @bvarner-ebi in #1825
  • Added new term 'respiratory ciliated cell' by @bvarner-ebi in #1819
  • Edited 'perineurial cell' by @bvarner-ebi in #1832
  • Added branch status warning to diff report by @ubyndr in #1787
  • Addressed trigger with comment added to branch-status by @ubyndr in #1839
  • Added missing conditional statement to branch-status action by @ubyndr in #1840
  • Added new term 'suprabasal keratinocyte' by @aleixpuigb in #1826
  • Imported 'blood nerve barrier' from UBERON by @aleixpuigb in #1842
  • Added new term 'peg cell' by @aleixpuigb in #1828
  • Added new endometrial ciliated cell terms by @bvarner-ebi in #1843
  • Added Compound terms for HubMap by @anitacaron in #1722
  • Fixed typo "KDNy" by @bvarner-ebi in #1845
  • Updated cl-idranges.owl by @aleixpuigb in #1847
  • Removed CHEBI term and CHEBI import from CL by @bvarner-ebi in #1846
  • Fixed logical definition of child terms of 'brush cell of tracheobronchial tree' by @aleixpuigb in #1836
  • Release 2023-02-15 by @bvarner-ebi in #1848

Full Changelog: v2023-01-09...v2023-02-15