ontology updates w/ 5.3.0

[jahilton]

Carried over from #958

• 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: NTR: PIPseq, Asteria single-cell RNA-seq, and HIVE CLX EBISPOT/efo#2244
• 1e313b15-4aca-4e5a-94a3-1093c4c42abd
  • 'assay_ontology_term_id' should be updated to EFO:0022845 [modified/3' STRT-seq]
• 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
• 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]

The following donors in the following Collections will need to have development_stage updated to 90yr+ once the term is available - obophenotype/developmental-stage-ontologies#77

• 4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e - donor_id values MMD_22_20137, A23_5566, 19-D011, D018-13, 19-D006
• 8f126edf-5405-4731-8374-b5ce11f53e82 - donor_id values S00006, S00063

[jychien]

Private collection: "Single Nuclei Atlas of Innervated and Denervated Mouse Muscle" have the following NTRs at CL:

• type IIx muscle cell ("Type IIX" in author_cell_type): [NTR-cxg]type IIx muscle cell obophenotype/cell-ontology#2673
• neuromuscular junction ("NMJ" in author_cell_type): [NTR-cxg] neuromuscular junction obophenotype/cell-ontology#2678
• myotendinous junction ("MTJ" in author_cell_type): [NTR-cxg] myotendinous junction obophenotype/cell-ontology#2676

[jychien]

Private collection: "Cyclin replacement hijacks the cell cycle's genetic regulatory program to orchestrate multiciliogenesis" will need to following:

• CL:0000065 (“ependymal cell”) in both cell_type_ontology_term_id and tissue_ontology_term_id will need to be updated to CL:4052001 ("multiciliated ependymal cell")

[jychien]

Private collection: "Mouse Post-Flu Time Series" will need the following update:

• CL:0002503 ("adventitial cell") in cell_type_ontology_term_id will need to be updated to CL:4052030 ("adventitial fibroblast")