ontology updates w/ 5.2.0

[jahilton]

• 48d354f5-a5ca-4f35-a3bb-fa3687502252
  • obs.var_time:P7 - update to 7 day [MmusDv:0000117]
• d86517f0-fa7e-4266-b82e-a521350d6d36
  • obs.Dataset:RomanovDev10x - update to 23 day [MmusDv:0000144]
  • obs.Dataset: Mickelsen10x - update to 4wk [MmusDv:0000149]
  • obs.Dataset: Flynn10x - update to 4wk [MmusDv:0000149]
  • obs.SRA_ID:SRR5164436 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164437 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164438 - update to 4wk [MmusDv:0000149]
• 613f5480-4957-4f80-b804-0e2b85ac454c
  • obs['age'] = P4 - update to 4 day [MmusDv:0000114]
  • obs['age'] = P7 - update to 7 day [MmusDv:0000117]
• 4828d33d-fb26-42e7-bf36-18293b0eec85
  • obs['donor_id'] = 'pooled_Control_P5' - update to 5 day [MmusDv:0000115]
  • obs['donor_id'] = 'pooled_Deprived_P5' - update to 5 day [MmusDv:0000115]
  • obs['donor_id'] = 'pooled_Control_P7' - update to 7 day [MmusDv:0000117]
  • obs['donor_id'] = 'pooled_Deprived_P7' - update to 7 day [MmusDv:0000117]

[jychien]

• 398e34a9-8736-4b27-a9a7-31a47a67f446
  • kit should be used to update EFO:0008913 (single-cell RNA sequencing) to appropriate assay (PIPseq, Aasteria scRNA-seq, and HIVE CLX). New terms are still at waiting to be assigned at EFO: https://github.com/EBISPOT/
• 1e313b15-4aca-4e5a-94a3-1093c4c42abd
  • 'assay_ontology_term_id' should be updated to 3' STRT-seq after new term ID has been assigned at EFO: New term request for modified version of STRT-seq EBISPOT/efo#2251
• 350fe77e-cc64-482e-a42a-18bec9e4a629
  • For "Stromal cells" subset: ‘Early Theca’ needs to be updated from 'stromal cell of ovary' (CL:0002132) to whatever CL term ID that eventually gets assigned for ‘pre-theca cell’: [NTR] pre-theca cell obophenotype/cell-ontology#2527
• 964581c3-b5ac-494d-9bd4-0dcb6fb058da
  • salivary glandular cell types can be made more specific after CL terms have been looked through: [NTR-cxg] Add children to CL:1001596 (salivary gland glandular cell) obophenotype/cell-ontology#2524

[corismall]

• Private collection: HiPSC-derived retinal organoid subpopulations from healthy and POAG donors

  • all obs - update to adult stage [HsapDv:0000258]

• Private collection: HiPSC-derived retinal pigmented epithelium from healthy and AMD-GA donors

  • all obs - update to adult stage [HsapDv:0000258]

[corismall]

Private collection: A non-canonical lymphoblast in refractory childhood T-cell acute leukaemia

• for all datasets, all obs - update to pediatric stage [HsapDv:0000264]

[jahilton]

Not related to new terms, but recently found to be needing updates so we'll leverage migration, given the size of the Datasets

• c114c20f-1ef4-49a5-9c2e-d965787fb90c - all Datasets, all obs --> EFO:0030028 (sci-RNA-seq3)
• 45d5d2c3-bc28-4814-aed6-0bb6f0e11c82 - all Datasets, all obs --> EFO:0030028 (sci-RNA-seq3)

[jahilton]

Across-the-corpus replace CL:4023070 with CL:4023064
From CL...

Comments: [‘caudal ganglionic eminence derived GABAergic interneuron\nand caudal ganglionic eminence derived interneuron are the same cell type. \nThe two must be merged and one needs to be defined as obsolete. \nWe decided to deprecate the entity with the more specific term and redundant qualities \nin the label. See comments in issue 2357.’]

[jychien]

Private collection:

• "A longitudinal single-cell atlas of pediatric high-grade glioma.":
  • Request for new MONDO term for "pediatric high-grade glioma" has been accepted: Request for new term [pediatric high-grade glioma] monarch-initiative/mondo#8126

[jahilton]

These were either completed during the migration to 5.2 or carried to #1023 for the next migration