Ontology curation error fixes

[mshadbolt]

List of ontology curation errors that I discovered when preparing zooma data source as well as those identified by other components

Corrections based on HumanCellAtlas/dcp2#13 https://docs.google.com/spreadsheets/d/1Wk7SGxEz00AkNokYv3YlFHJVF9U6THKcrvgHARsnau8/edit#gid=0

• All projects with library_preparation.method.ontology set as EFO:0009310 and
  • library_preparation.end_bias 3 prime tag OR 3 prime bias should have the ontology updated to EFO:0009899 and ontology_label updated to label for that term
  • library_preparation.end_bias 5 prime tag or 5 prime bias should have ontology updated to EFO:0009900
• All projects with library_preparation.method set as a 10x method should have 3 prime tag (not 3 prime end bias) set in the library_preparation.end_bias field

Project specific corrections:

Requires bulk update

Single cell RNAseq characterisation of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation - 2043c65a-1cf8-4828-a656-9e247d4e64f1

• All cell_suspension.timecourse.unit.ontology fields should be changed to UO:0000033, the correct ontology for 'day' where cell_suspension.timecourse.unit.text is 'day'
• The model organ for the cell line 557606a0-96dd-40cc-bb72-94d5711bb8ec should be changed to UBERON:0000922 (I couldn't find this term in the ui, not sure why

BM_PC - a29952d9-925e-40f4-8a1c-274f118f1f51:

• All donor_organism.development_stage.ontology should be changed to the correct term for human adult - HsapDv:0000087
• All specimen_from_organism.organ ontologies should be changed to the correct term for bone UBERON:0002481 and ontology label bone tissue

Single cell transcriptome analysis of human pancreas - cddab57b-6868-4be4-806f-395ed9dd635a

• all donor_organism.development_stage.ontology should be changed to the correct term for human adult - HsapDv:0000087

GSE67833_neural_stem_cells - e8808cc8-4ca0-4096-80f2-bba73600cba6

• current curations for organ in specimen_from_organism entities should be in 'organ_part'
• organ should be set to 'brain' - UBERON:0000955

Non-specific 'cortex' term (UBERON:0001851) in specimen_from_organism.organ_parts should be changed to organ specific cortex term, either kidney or brain, for the following projects:

• scRNAseqSystemicComparison - cerebral cortex UBERON:0000956
• Diabetic Nephropathy snRNA-seq - cortex of kidney UBERON:0001225
• AllelicExpressionPatterns - cerebral cortex UBERON:0000956
• 1M Neurons - cerebral cortex UBERON:0000956
• HumanBrainSubstantiaNigra - cerebral cortex UBERON:0000956

Easy to do manual fixes:

Pitx2DevelopingHeart - 7027adc6-c9c9-46f3-84ee-9badc3a4f53b

• 45b47d43-ab70-48d9-a205-4b0509bf7114 - donor_organism.organism_age_unit.ontology should be UO:0000033
• There is onedonor_organism.genus_species set as Mus musculus castaneus , which I think should just be Mus musculus
• donor_organism.organism_age_unit text says 'day' but ontology is 'week'

HumanIsletType2Diabetes - 7adede6a-0ab7-45e6-9b67-ffe7466bec1f

• donor_organism.ethnicity where text is Hispanic should be changed to HANCESTRO:0014

Things to investigate further

• Was it intentional to use 'liver primordium' rather than 'liver' for 'AllelicExpressionPatterns' liver specimens? - curated by Rachel Schwartz

EpithelialDiversityHealthInflammation - c893cb57-5c9f-4f26-9312-21b85be84313

• There is a mismatch between the 'text' field and 'ontology' field for some specimens where a non-inflamed sample was taken from a patient with uclerative colitis, i.e. the text says 'ulcerative colitis' but the ontology says 'normal' which I think is confusing but not sure which part needs to be corrected

HumanFirstTrimesterPlacentaDecidua - 1cd1f41f-f81a-486b-a05b-66ec60f81dcf

• specimens with text 'decidua' and 'chorion membrane' have been curated as placenta

HeartSingleCellsAndNucleiSeq - ad98d3cd-26fb-4ee3-99c9-8a2ab085e737

• donor_organism.disease text given as diabetes but ontology curated as hypertension (MONDO:0005015), probably a mistake in ordering on an array field

DevelopingMouseKidneyHumanKidneyOrganoids - 7b947aa2-43a7-4082-afff-222a3e3a4635

• donor_organism.gestational_age_unit.text given as '12', should be 'week' or similar

General thoughts

• We have two terms that we currently use to indicate 'skin' as an organ, 'zone of skin' and 'skin of body' we should probably pick one and try to be consistent

[ofanobilbao]

Just a thought, that maybe this ticket needs splitting in separate tickets.