post-ontology bump updates (3.0.0+1)

[jahilton]

Collection a48f5033-3438-4550-8574-cdff3263fdfd - All 3 datasets all assay: EFO:0700010

Collection A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics - update CL:0000677 'gut absorptive cell' to cell_type: CL:4030026 (@rachadele please review/confirm & update the title to the Collection ID once published)

Collection edb893ee-4066-4128-9aec-5eb2b03f8287 - Both datasets update EFO:0010183 'single cell library construction' to assay: EFO:0700011

[jahilton]

Collection Human breast cell atlas - replace CL:0011026 (progenitor cell) w/ CL:0009116 (progenitor cell of mammary luminal epithelium)

[jlzamanian]

Collection: Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon Dataset: Single nucleus transcriptomic profiling of human healthy hamstring tendon (only dataset)

Update the tissue ontology of all 4 samples to new term UBERON:8480009

tendon of semitendinosus

The update will go through Lattice.

[EMRutherford]

Collection: Cell Atlas of The Human Fovea and Peripheral Retina Dataset: Amacrine cells of the human fovea and peripheral retina

Replace CL:0000561 (amacrine cell) with CL:4030027 (GABAergic amacrine cell).
Replace CL:1001509 (glycinergic neuron) with CL:4030028 (glycinergic amacrine cell).

[EMRutherford]

Collection: Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration Dataset: Amacrine cells of human eye

For the following group IDs in the processed matrix files: 1.0 - Replace CL:0000561 (amacrine cell) with CL:0004219 (A2 amacrine cell) 5.0 - Replace CL:0000561 (amacrine cell) with CL:4030028 (glycinergic amacrine cell) 11.0 - Replace CL:0000561 (amacrine cell) with CL:0004232 (starburst amacrine cell)

[EMRutherford]

Collection: Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration

Dataset: Retinal ganglion cells of human eye

For the following group IDs in the processed matrix files: 1.0 and 4.0 - Replace CL:0000740 (retinal ganglion cell) with CL:4023033 (OFF retinal ganglion cell) 2.0 and 5.0 - Replace CL:0000740 (retinal ganglion cell) with CL:4023032 (ON retinal ganglion cell)

Dataset: Cone cells of human eye

For the following group IDs in the processed matrix files: 2.0 - Replace CL:0000573 (retinal cone cell) with CL:0003050 (S cone cell)

[jahilton]

Collection: Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia - all datasets - update MONDO:0004298 (stomach disorder) to new_term_tbd (gastric intestinal metaplasia) (should be in the Feb MONDO release)

[jahilton]

Collection: A molecular cell atlas of COVID-19 initiation in human lung - all datasets

• CL:0002144 (capillary endothelial cell) --> CL:4028001 (pulmonary capillary endothelial cell)
• CL:0000669 (pericyte) --> CL:0009089 (lung pericyte)

[jahilton]

Collection: Transcriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programs

• D2-Matrix & D2-Striosome need to be updated to CL:4023029
• D1-Matrix & D1-Striosome need to be updated to CL:4023026

[jahilton]

Collection: A single-cell transcriptomic atlas spanning the adult rhesus macaque brain.

• Update CL:0002319 to CL:4023072 - 3 datasets: all cells, 1.5M subset, vascular cells

[rachadele]

~Collection: A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics~

~- update CL:0002254 to CL:4030026 – 1 dataset~

Addressed in the top comment

[liaanym]

Collection A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

• update UBERON:0000956 (cerebral cortex) to UBERON:8440075 (gustatory cortex) - 1 dataset in collection, Smart-Seq
• update EFO:0010184 (Smart-like). They used SMART-seq4 (SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing), so waiting for a new term to update to SMART-seq4

[jahilton]

Collection ced320a1-29f3-47c1-a735-513c7084d508, self_reported_ethnicity

• update Indian to Singaporean Indian [HANCESTRO:0598]
• update Malaysian to Singaporean Malay [HANCESTRO:0597]

(Lattice will subsequently remove the Ethnicity_Selfreported column)

[jahilton]

• 661a402a-2a5a-4c71-9b05-b346c57bc451 donor_id:GSM4643738 - update to 5 day [MmusDv:0000115]
• 48d354f5-a5ca-4f35-a3bb-fa3687502252 var_time:P7 - update to 7 day [MmusDv:0000117]
• d86517f0-fa7e-4266-b82e-a521350d6d36 Dataset:RomanovDev10x - update to 23 day [MmusDv:0000144]

[jlzamanian]

Collection: 9d63fcf1-5ca0-4006-8d8f-872f3327dbe9 Brain matters: Unveiling the Distinct Contributions of Region, Age, and Sex to Glia diversity and CNS Function

datasets: white matter - all cells c05e6940-729c-47bd-a2a6-6ce3730c4919 white matter - oligodendroglia 12194ced-8086-458e-84a8-e2ab935d8db1

Update the cell_type_ontology_term_id for author cell types COP_A COP_B COP_C

to CL:4023059 differentiation-committed oligodendrocyte precursor

[jahilton]

• [x] Collection a48f5033-3438-4550-8574-cdff3263fdfd - All 3 datasets all assay: EFO:0700010
• [x] Collection A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics - update CL:0000677 'gut absorptive cell' to cell_type: CL:4030026
• [x] Collection edb893ee-4066-4128-9aec-5eb2b03f8287 - Both datasets update EFO:0010183 'single cell library construction' to assay: EFO:0700011
• [x] Collection Human breast cell atlas - replace CL:0011026 (progenitor cell) w/ CL:0009116 (progenitor cell of mammary luminal epithelium)
• [x] Collection: Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon - Update the tissue ontology of all 4 samples to new term UBERON:8480009 (tendon of semitendinosus)
• [x] Collection: Cell Atlas of The Human Fovea and Peripheral Retina. Dataset: Amacrine cells of the human fovea and peripheral retina. Replace CL:0000561 (amacrine cell) with CL:4030027 (GABAergic amacrine cell). Replace CL:1001509 (glycinergic neuron) with CL:4030028 (glycinergic amacrine cell).
• [x] Collection: Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Dataset: Amacrine cells of human eye. For the following group IDs in the processed matrix files:. Replace CL:0000561 (amacrine cell) with CL:0004219 (A2 amacrine cell), CL:4030028 (glycinergic amacrine cell), CL:0004232 (starburst amacrine cell)
• [x] Collection: Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Dataset: Retinal ganglion cells of human eye. For the following group IDs in the processed matrix files: Replace CL:0000740 (retinal ganglion cell) with CL:4023033 (OFF retinal ganglion cell), CL:4023032 (ON retinal ganglion cell)
• [x] Collection: Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Dataset: Cone cells of human eye. 2.0 - Replace CL:0000573 (retinal cone cell) with CL:0003050 (S cone cell)
• [x] Collection: Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia - all datasets - update MONDO:0004298 (stomach disorder) to new_term_tbd (gastric intestinal metaplasia)
• [x] Collection: A molecular cell atlas of COVID-19 initiation in human lung - all datasets. CL:0002144 (capillary endothelial cell) --> CL:4028001 (pulmonary capillary endothelial cell). CL:0000669 (pericyte) --> CL:0009089 (lung pericyte)
• [x] Collection: Transcriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programs. D2-Matrix & D2-Striosome need to be updated to CL:4023029. D1-Matrix & D1-Striosome need to be updated to CL:4023026
• [x] Collection: A single-cell transcriptomic atlas spanning the adult rhesus macaque brain. Update CL:0002319 to CL:4023072 - 3 datasets: all cells, 1.5M subset, vascular cells
• [x] Collection A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. update UBERON:0000956 (cerebral cortex) to UBERON:8440075 (gustatory cortex) & 1 dataset in collection, Smart-Seq. update EFO:0010184 (Smart-like) to SMART-seq4
• [x] Collection: 9d63fcf1-5ca0-4006-8d8f-872f3327dbe9 , datasets: white matter - all cells c05e6940-729c-47bd-a2a6-6ce3730c4919, white matter - oligodendroglia 12194ced-8086-458e-84a8-e2ab935d8db1. Update the cell_type_ontology_term_id for author cell types: COP_A, COP_B, COP_C to CL:4023059

From ontologies not in this update...

• ced320a1-29f3-47c1-a735-513c7084d508, self_reported_ethnicity. update Indian to Singaporean Indian [HANCESTRO:0598]. update Malaysian to Singaporean Malay [HANCESTRO:0597]
• 661a402a-2a5a-4c71-9b05-b346c57bc451 donor_id:GSM4643738 - update to 5 day [MmusDv:0000115]
• 48d354f5-a5ca-4f35-a3bb-fa3687502252 var_time:P7 - update to 7 day [MmusDv:0000117]
• d86517f0-fa7e-4266-b82e-a521350d6d36 Dataset:RomanovDev10x - update to 23 day [MmusDv:0000144]

[jahilton]

Verified that all non HANCESTRO/Dv updates were completed during migration. The rest were carried over to #605