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chanzuckerberg / single-cell-curation

Code and documentation for the curation of cellxgene datasets
MIT License
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post-ontology bump updates #205

Closed jahilton closed 1 year ago

jahilton commented 2 years ago

The 2 methylation (snmC-seq) datasets here: ae1420fe-6630-46ed-8b3d-cc6056a66467 update to: EFO:0030027 (snmC-Seq2)

The 3 datasets here: 00109df5-7810-4542-8db5-2288c46e0424 update to: EFO:0030026 (sci-Plex)

All of the datasets here: 8e880741-bf9a-4c8e-9227-934204631d2a & "Spatial transcriptomic maps of whole mouse embryos reveal principles of neural tube patterning" update to: EFO:0030062 (Slide-seqV2)

The '10x technology' cells in this dataset: "UCSD WashU HuBMAP KPMP" update to: EFO:0030059 (10x multiome)

jahilton commented 2 years ago

CL:0000115 [endothelial cell] cells in the dataset here: 32f2fd23-ec74-486f-9544-e5b2f41725f5 update to: CL:0009095 [endothelial cell of uterus]

jahilton commented 2 years ago

2 cell populations in the dataset here: 6f6d381a-7701-4781-935c-db10d30de293 From Lisa Sikkema... 1: Our annotation: EC aerocyte capillary. Your ontology version: capillary endothelial cell. Newest ontology version: alveolar capillary type 2 endothelial cell 2: Our annotation: EC general capillary. Your ontology version: capillary endothelial cell. Newest ontology version: alveolar capillary type 1 endothelial cell

jychien commented 2 years ago

For HTAN Broad breast cancer collection: HTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironment

jychien commented 2 years ago

For Slide-seq collection: "Spatially mapping T cell receptors and transcriptomes", the assay_ontology_term_id needs to be updated to EFO:0030062 (Slide-seqV2). The one thing to consider is that these are Slide-TCR-seq datasets. There is no EFO term for this assay, but we have yet to determine how to handle TCR/BCR data and if there is some minimum metadata required in order for the assay to be TCR/BCR. Also, have yet to determine if Slice-TCR-seq is different enough from Slide-seqV2 to be considered it's own assay.

jahilton commented 2 years ago

Collection 93eebe82-d8c3-41bc-a906-63b5b5f24a9d

Dataset c05fb583-eb2f-4e3a-8e74-f9bd6414e418, assay should be EFO:0700003 [BD Rhapsody Whole Transcriptome Analysis]

The other 3 Datasets d3566d6a-a455-4a15-980f-45eb29114cab, b3a5a10f-b1cb-4e8e-abce-bf345448625b, cd4c96bb-ad66-4e83-ba9e-a7df8790eb12, assay should be EFO:0700004 [BD Rhapsody Targeted mRNA]

rachadele commented 2 years ago

collection private '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 new CL term requested for BEST4+ cells https://github.com/obophenotype/cell-ontology/issues/1695

jychien commented 2 years ago

Collection a48f5033-3438-4550-8574-cdff3263fdfd

All 3 datasets will need assay updated to EFO:0700010 'TruDrop' (https://github.com/EBISPOT/efo/issues/1759). I don't think this will make schema 3.0.0 pinned ontologies, though.

jahilton commented 2 years ago

Collection 1ca90a2d-2943-483d-b678-b809bf464c30 All datasets have HANCESTRO:0306 [admixed ancestry] that will need to be updated to multiethnic

jahilton commented 2 years ago

Not in pinned ontology - will need to be transferred to the next ontology bump ticket

jahilton commented 1 year ago

All that can be updated are updated The remaining 2 have been carried over to #373