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Update ontology label for metadata validation tests (SCP-5953) #385

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Mar 13, 2025
Merged

Update ontology label for metadata validation tests (SCP-5953) #385

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3486c28
update ontology label for test inputs and refs
jlchang Mar 12, 2025
aedbcf1
Update minified ontologies via GitHub Actions
invalid-email-address Mar 12, 2025
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Binary file modified ingest/validation/ontologies/cl.min.tsv.gz
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Binary file modified ingest/validation/ontologies/mondo.min.tsv.gz
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3 changes: 1 addition & 2 deletions ingest/validation/ontologies/version.txt
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1738072997 # validation cache key

1741807191 # validation cache key
8 changes: 4 additions & 4 deletions tests/data/annotation/metadata/convention/valid_array_v2.1.2.txt
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NAME disease__time_since_onset disease__time_since_onset__unit organ_region organ_region__ontology_label donor disease__treated species species__ontology_label geographical_region geographical_region__ontology_label library_preparation_protocol library_preparation_protocol__ontology_label organ organ__ontology_label sex is_living organism_age__unit organism_age__unit_label ethnicity__ontology_label ethnicity organism_age disease disease__ontology_label cell_type cell_type__ontology_label donor_id biosample_id biosample_type preservation_method
TYPE numeric group group group group group group group group group group group group group group group group group group group numeric group group group group group group group group
BM01_16dpp_AAGCAGTGGTAT 12|2 UO_0000035 MBA:000000944 Folium-tuber vermis (VII) BM01 False|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 31 MONDO_0005015|MONDO_0006849 diabetes mellitus|mastitis CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA 1 UO_0000035 MBA:000000302|MBA:000000294|MBA:000000795 Superior colliculus, sensory related|Superior colliculus, motor related|Periaqueductal gray BM01 FALSE NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 31 MONDO_0005709 common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT 24|2 UO_0000035 MBA:000000714|MBA:000000972 BM01 True|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European|British HANCESTRO_0005|HANCESTRO_0462 31 MONDO_0005015|MONDO_0005709 diabetes mellitus|common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_AAGCAGTGGTAT 12|2 UO_0000035 MBA:000000944 Folium-tuber vermis (VII) BM01 False|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 31 MONDO_0005015|MONDO_0006849 diabetes mellitus|mastitis CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA 1 UO_0000035 MBA:000000302|MBA:000000294|MBA:000000795 Superior colliculus, sensory related|Superior colliculus, motor related|Periaqueductal gray BM01 FALSE NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 31 MONDO_0005709 common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT 24|2 UO_0000035 MBA:000000714|MBA:000000972 BM01 True|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry|British HANCESTRO_0005|HANCESTRO_0462 31 MONDO_0005015|MONDO_0005709 diabetes mellitus|common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CGGTAAACCATT 36|3|1 UO_0000035 MBA:000001041 Paraflocculus BM01 True|False|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year HANCESTRO_0005|HANCESTRO_0462 31 MONDO_0005015|MONDO_0006849|MONDO_0005709 diabetes mellitus|mastitis|common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG 0 UO_0000035 MBA:000000909|MBA:000000502 Entorhinal area|Subiculum BM01 FALSE NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 31 MONDO_0000001 disease CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG 0 UO_0000035 MBA:000000909|MBA:000000502 Entorhinal area|Subiculum BM01 FALSE NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 31 MONDO_0000001 disease CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
2 changes: 1 addition & 1 deletion tests/data/annotation/metadata/convention/valid_cell_type__custom_v2.2.1.txt
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NAME disease__time_since_onset disease__time_since_onset__unit organ_region organ_region__ontology_label donor disease__treated species species__ontology_label geographical_region geographical_region__ontology_label library_preparation_protocol library_preparation_protocol__ontology_label organ organ__ontology_label sex is_living organism_age__unit organism_age__unit_label ethnicity__ontology_label ethnicity organism_age disease disease__ontology_label cell_type cell_type__ontology_label donor_id biosample_id biosample_type preservation_method cell_type__custom
TYPE numeric group group group group group group group group group group group group group group group group group group group numeric group group group group group group group group group
BM01_16dpp_AAGCAGTGGTAT 12|2 UO_0000035 MBA:000000944 Folium-tuber vermis (VII) BM01 False|False NCBITaxon_9606 human GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 31 MONDO_0005015|MONDO_0006849 diabetes|mastitis CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh epithelial
BM01_16dpp_AAGCAGTGGTAT 12|2 UO_0000035 MBA:000000944 Folium-tuber vermis (VII) BM01 False|False NCBITaxon_9606 human GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 31 MONDO_0005015|MONDO_0006849 diabetes|mastitis CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh epithelial
BM01_16dpp_TAAGCAGTGGTA 1 UO_0000035 MBA:000000302|MBA:000000294|MBA:000000795 "Superior colliculus, sensory related|Superior colliculus, motor related|Periaqueductal gray" BM01 FALSE NCBITaxon_9606 Homo Sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year white HANCESTRO_0005 31 MONDO_0005709 common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh epithelial
BM01_16dpp_CTAAGCAGTGGT 24|2 UO_0000035 MBA:000000714|MBA:000000972 BM01 True|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year British HANCESTRO_0462 31 MONDO_0005015|MONDO_0005709 diabetes mellitus|common cold CL_0000066 epithelial cell BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh epithelial
BM01_16dpp_CGGTAAACCATT 36|3|1 UO_0000035 MBA:000001041 Paraflocculus BM01 True|False|False NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year HANCESTRO_0462 31 MONDO_0005015|MONDO_0006849|MONDO_0005709 diabetes|breast infection|common cold BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh sub-epithelial
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10 changes: 5 additions & 5 deletions tests/data/annotation/metadata/convention/valid_no_array_synonyms_v2.0.0.txt
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NAME cell_type cell_type__ontology_label organism_age disease disease__ontology_label species species__ontology_label geographical_region geographical_region__ontology_label library_preparation_protocol library_preparation_protocol__ontology_label organ organ__ontology_label sex is_living organism_age__unit organism_age__unit_label ethnicity__ontology_label ethnicity race race__ontology_label donor_id biosample_id biosample_type preservation_method
TYPE group group numeric group group group group group group group group group group group group group group group group group group group group group group
BM01_16dpp_AAGCAGTGGTAT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10x 3' v2 UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10x 3' v2 UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10X 3' v2 UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CGGTAAACCATT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10X 3' v2 sequencing UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG CL_0000066 epithelial cell 31 PATO_0000001 quality NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_AAGCAGTGGTAT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10x 3' v2 UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10x 3' v2 UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10X 3' v2 UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CGGTAAACCATT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0009899 10X 3' v2 sequencing UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG CL_0000066 epithelial cell 31 PATO_0000001 quality NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
10 changes: 5 additions & 5 deletions tests/data/annotation/metadata/convention/valid_no_array_v2.0.0.txt
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NAME cell_type cell_type__ontology_label organism_age disease disease__ontology_label species species__ontology_label geographical_region geographical_region__ontology_label library_preparation_protocol library_preparation_protocol__ontology_label organ organ__ontology_label sex is_living organism_age__unit organism_age__unit_label ethnicity__ontology_label ethnicity race race__ontology_label donor_id biosample_id biosample_type preservation_method
TYPE group group numeric group group group group group group group group group group group group group group group group group group group group group group
BM01_16dpp_AAGCAGTGGTAT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CGGTAAACCATT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG CL_0000066 epithelial cell 31 PATO_0000001 quality NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_AAGCAGTGGTAT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_TAAGCAGTGGTA CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C43862 Norwegian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CTAAGCAGTGGT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CGGTAAACCATT CL_0000066 epithelial cell 31 MONDO_0000001 disease NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
BM01_16dpp_CCGAATTCACCG CL_0000066 epithelial cell 31 PATO_0000001 quality NCBITaxon_9606 Homo sapiens GAZ_00003181 Boston EFO_0008919 Seq-Well UBERON_0001913 milk female yes UO_0000036 year European ancestry HANCESTRO_0005 NCIT_C126538 Scandinavian BM01 BM01_16dpp_r3 PrimaryBioSample_BodyFluid Fresh
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