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Add sparql check for annotations #1659

Merged
merged 3 commits into from
Jul 15, 2022
Merged

Add sparql check for annotations #1659

merged 3 commits into from
Jul 15, 2022

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anitacaron
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@anitacaron anitacaron requested a review from matentzn July 14, 2022 16:00
@anitacaron anitacaron self-assigned this Jul 14, 2022
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github-actions bot commented Jul 14, 2022

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-07-15/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-07-15/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

B cell zone reticular cell http://purl.obolibrary.org/obo/CL_0009104

Removed

Added

ILC1 http://purl.obolibrary.org/obo/CL_0001068

Removed

Added

Leydig stem cell http://purl.obolibrary.org/obo/CL_0009091

Removed

Added

T cell zone reticular cell http://purl.obolibrary.org/obo/CL_0009105

Removed

Added

T follicular regulatory cell http://purl.obolibrary.org/obo/CL_0009113

Removed

Added

abnormal cell http://purl.obolibrary.org/obo/CL_0001061

Removed

Added

blood vessel smooth muscle cell http://purl.obolibrary.org/obo/CL_0019018

Removed

Added

centrilobular region hepatocyte http://purl.obolibrary.org/obo/CL_0019029

Removed

Added

centroblast http://purl.obolibrary.org/obo/CL_0009112

Removed

Added

centrocyte http://purl.obolibrary.org/obo/CL_0009111

Removed

Added

circulating angiogenic cell http://purl.obolibrary.org/obo/CL_0009088

Removed

Added

colony forming unit – Hill cell http://purl.obolibrary.org/obo/CL_0009085

Removed

Added

committed double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009082

Removed

Added

effector memory CD4-positive, alpha-beta T cell, terminally differentiated http://purl.obolibrary.org/obo/CL_0001087

Removed

Added

embryonic skeletal muscle fiber http://purl.obolibrary.org/obo/CL_0009097

Removed

Added

endothelial cell of hepatic portal vein http://purl.obolibrary.org/obo/CL_0009094

Removed

Added

endothelial cell of pericentral hepatic sinusoid http://purl.obolibrary.org/obo/CL_0019022

Removed

Added

endothelial cell of periportal hepatic sinusoid http://purl.obolibrary.org/obo/CL_0019021

Removed

Added

endothelial cell of placenta http://purl.obolibrary.org/obo/CL_0009092

Removed

Added

endothelial cell of respiratory system lymphatic vessel http://purl.obolibrary.org/obo/CL_0009086

Removed

Added

endothelial cell of uterus http://purl.obolibrary.org/obo/CL_0009095

Removed

Added

endothelial colony forming cell http://purl.obolibrary.org/obo/CL_0009090

Removed

Added

epithelial cell of endometrial gland http://purl.obolibrary.org/obo/CL_0009084

Removed

Added

esophagus non-keratinized squamous epithelial cell http://purl.obolibrary.org/obo/CL_0009096

Removed

Added

extrahepatic cholangiocyte http://purl.obolibrary.org/obo/CL_0019020

Removed

Added

fallopian tube ciliated cell http://purl.obolibrary.org/obo/CL_4030007

Removed

Added

fallopian tube secretory epithelial cell http://purl.obolibrary.org/obo/CL_4030006

Removed

Added

fetal and neonatal skeletal muscle fiber http://purl.obolibrary.org/obo/CL_0009098

Removed

Added

fibro/adipogenic progenitor cell http://purl.obolibrary.org/obo/CL_0009099

Removed

Added

fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_0009101

Removed

Added

fused extravillous trophoblast http://purl.obolibrary.org/obo/CL_0009087

Removed

Added

group 1 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001067

Removed

Added

group 2 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001069

Removed

Added

group 3 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001071

Removed

Added

hepatic portal fibroblast http://purl.obolibrary.org/obo/CL_0009100

Removed

Added

innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001065

Removed

Added

intestinal tuft cell http://purl.obolibrary.org/obo/CL_0019032

Removed

Added

intestine goblet cell http://purl.obolibrary.org/obo/CL_0019031

Removed

Added

lung parenchyma resident eosinophil http://purl.obolibrary.org/obo/CL_0019015

Removed

Added

lung pericyte http://purl.obolibrary.org/obo/CL_0009089

Removed

Added

lymph node fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_0009102

Removed

Added

lymph node marginal reticular cell http://purl.obolibrary.org/obo/CL_0009103

Removed

Added

lymphatic endothelial cell of medulla ceiling http://purl.obolibrary.org/obo/CL_0009110

Removed

Added

lymphatic endothelial cell of subcapsular sinus ceiling http://purl.obolibrary.org/obo/CL_0009107

Removed

Added

lymphatic endothelial cell of subcapsular sinus floor http://purl.obolibrary.org/obo/CL_0009108

Removed

Added

lymphatic endothelial cell of trabecula http://purl.obolibrary.org/obo/CL_0009109

Removed

Added

lymphatic vessel smooth muscle cell http://purl.obolibrary.org/obo/CL_0019017

Removed

Added

malignant cell http://purl.obolibrary.org/obo/CL_0001064

Removed

Added

medullary reticular cell http://purl.obolibrary.org/obo/CL_0009106

Removed

Added

midzonal region hepatocyte http://purl.obolibrary.org/obo/CL_0019028

Removed

Added

monocytoid B cell http://purl.obolibrary.org/obo/CL_0009114

Removed

Added

neoplastic cell http://purl.obolibrary.org/obo/CL_0001063

Removed

Added

periportal region hepatocyte http://purl.obolibrary.org/obo/CL_0019026

Removed

Added

pronephric podocyte http://purl.obolibrary.org/obo/CL_4030008

Removed

Added

rearranging double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009083

Removed

Added

smooth muscle cell of placenta http://purl.obolibrary.org/obo/CL_0009093

Removed

Added

specified double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009081

Removed

Added

thymic nurse cell http://purl.obolibrary.org/obo/CL_4030004

Removed

Added

tracheobronchial chondrocyte http://purl.obolibrary.org/obo/CL_0019002

Removed

Added

tracheobronchial goblet cell http://purl.obolibrary.org/obo/CL_0019003

Removed

Added

tracheobronchial serous cell http://purl.obolibrary.org/obo/CL_0019001

Removed

Added

tracheobronchial smooth muscle cell http://purl.obolibrary.org/obo/CL_0019019

Removed

Added

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github-actions bot commented Jul 14, 2022

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

B cell zone reticular cell http://purl.obolibrary.org/obo/CL_0009104

Removed

Added

ILC1 http://purl.obolibrary.org/obo/CL_0001068

Removed

Added

Leydig stem cell http://purl.obolibrary.org/obo/CL_0009091

Removed

Added

T cell zone reticular cell http://purl.obolibrary.org/obo/CL_0009105

Removed

Added

T follicular regulatory cell http://purl.obolibrary.org/obo/CL_0009113

Removed

Added

abnormal cell http://purl.obolibrary.org/obo/CL_0001061

Removed

Added

blood vessel smooth muscle cell http://purl.obolibrary.org/obo/CL_0019018

Removed

Added

centrilobular region hepatocyte http://purl.obolibrary.org/obo/CL_0019029

Removed

Added

centroblast http://purl.obolibrary.org/obo/CL_0009112

Removed

Added

centrocyte http://purl.obolibrary.org/obo/CL_0009111

Removed

Added

circulating angiogenic cell http://purl.obolibrary.org/obo/CL_0009088

Removed

Added

colony forming unit – Hill cell http://purl.obolibrary.org/obo/CL_0009085

Removed

Added

committed double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009082

Removed

Added

date http://purl.org/dc/terms/date

Added

  • AnnotationProperty: date

date http://purl.org/dc/elements/1.1/date

Removed

  • AnnotationProperty: date

effector memory CD4-positive, alpha-beta T cell, terminally differentiated http://purl.obolibrary.org/obo/CL_0001087

Removed

Added

embryonic skeletal muscle fiber http://purl.obolibrary.org/obo/CL_0009097

Removed

Added

endothelial cell of hepatic portal vein http://purl.obolibrary.org/obo/CL_0009094

Removed

Added

endothelial cell of pericentral hepatic sinusoid http://purl.obolibrary.org/obo/CL_0019022

Removed

Added

endothelial cell of periportal hepatic sinusoid http://purl.obolibrary.org/obo/CL_0019021

Removed

Added

endothelial cell of placenta http://purl.obolibrary.org/obo/CL_0009092

Removed

Added

endothelial cell of respiratory system lymphatic vessel http://purl.obolibrary.org/obo/CL_0009086

Removed

Added

endothelial cell of uterus http://purl.obolibrary.org/obo/CL_0009095

Removed

Added

endothelial colony forming cell http://purl.obolibrary.org/obo/CL_0009090

Removed

Added

epithelial cell of endometrial gland http://purl.obolibrary.org/obo/CL_0009084

Removed

Added

esophagus non-keratinized squamous epithelial cell http://purl.obolibrary.org/obo/CL_0009096

Removed

Added

extrahepatic cholangiocyte http://purl.obolibrary.org/obo/CL_0019020

Removed

Added

fallopian tube ciliated cell http://purl.obolibrary.org/obo/CL_4030007

Removed

Added

fallopian tube secretory epithelial cell http://purl.obolibrary.org/obo/CL_4030006

Removed

Added

fetal and neonatal skeletal muscle fiber http://purl.obolibrary.org/obo/CL_0009098

Removed

Added

fibro/adipogenic progenitor cell http://purl.obolibrary.org/obo/CL_0009099

Removed

Added

fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_0009101

Removed

Added

fused extravillous trophoblast http://purl.obolibrary.org/obo/CL_0009087

Removed

Added

group 1 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001067

Removed

Added

group 2 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001069

Removed

Added

group 3 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001071

Removed

Added

hepatic portal fibroblast http://purl.obolibrary.org/obo/CL_0009100

Removed

Added

innate lymphoid cell http://purl.obolibrary.org/obo/CL_0001065

Removed

Added

intestinal tuft cell http://purl.obolibrary.org/obo/CL_0019032

Removed

Added

intestine goblet cell http://purl.obolibrary.org/obo/CL_0019031

Removed

Added

lung parenchyma resident eosinophil http://purl.obolibrary.org/obo/CL_0019015

Removed

Added

lung pericyte http://purl.obolibrary.org/obo/CL_0009089

Removed

Added

lymph node fibroblastic reticular cell http://purl.obolibrary.org/obo/CL_0009102

Removed

Added

lymph node marginal reticular cell http://purl.obolibrary.org/obo/CL_0009103

Removed

Added

lymphatic endothelial cell of medulla ceiling http://purl.obolibrary.org/obo/CL_0009110

Removed

Added

lymphatic endothelial cell of subcapsular sinus ceiling http://purl.obolibrary.org/obo/CL_0009107

Removed

Added

lymphatic endothelial cell of subcapsular sinus floor http://purl.obolibrary.org/obo/CL_0009108

Removed

Added

lymphatic endothelial cell of trabecula http://purl.obolibrary.org/obo/CL_0009109

Removed

Added

lymphatic vessel smooth muscle cell http://purl.obolibrary.org/obo/CL_0019017

Removed

Added

malignant cell http://purl.obolibrary.org/obo/CL_0001064

Removed

Added

medullary reticular cell http://purl.obolibrary.org/obo/CL_0009106

Removed

Added

midzonal region hepatocyte http://purl.obolibrary.org/obo/CL_0019028

Removed

Added

monocytoid B cell http://purl.obolibrary.org/obo/CL_0009114

Removed

Added

neoplastic cell http://purl.obolibrary.org/obo/CL_0001063

Removed

Added

periportal region hepatocyte http://purl.obolibrary.org/obo/CL_0019026

Removed

Added

pronephric podocyte http://purl.obolibrary.org/obo/CL_4030008

Removed

Added

rearranging double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009083

Removed

Added

smooth muscle cell of placenta http://purl.obolibrary.org/obo/CL_0009093

Removed

Added

specified double negative thymocyte (Homo sapiens) http://purl.obolibrary.org/obo/CL_0009081

Removed

Added

thymic nurse cell http://purl.obolibrary.org/obo/CL_4030004

Removed

Added

tracheobronchial chondrocyte http://purl.obolibrary.org/obo/CL_0019002

Removed

Added

tracheobronchial goblet cell http://purl.obolibrary.org/obo/CL_0019003

Removed

Added

tracheobronchial serous cell http://purl.obolibrary.org/obo/CL_0019001

Removed

Added

tracheobronchial smooth muscle cell http://purl.obolibrary.org/obo/CL_0019019

Removed

Added

<http://purl.obolibrary.org/obo/RO_0040042>,
<http://purl.obolibrary.org/obo/term_editor>,
<http://purl.org/dc/terms/date>,
<http://purl.org/dc/elements/1.1/description>,
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dce should not be needed.

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wherever its used, change to dct

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Even in the ontology? It's not included here.

@matentzn
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Excellent, thank you!

@anitacaron anitacaron merged commit 7cd63ff into master Jul 15, 2022
@anitacaron anitacaron deleted the sparql-check branch February 6, 2023 11:20
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2 participants