Endpoint to automate data sankey

[shirey]

Create an endpoint to generate the csv needed by the data sankey diagram. Diagram here example csv here

The values for the Assay column will need to be mapped based on a scheme that @pecan88 will provide. Example mapping:

System-derived	Corrected
hubmap-uflorida-tmc	University of Florida TMC
hubmap-northwestern-rt	Northwestern RTI
hubmap-vanderbilt-tmc	Vanderbilt TMC
hubmap-stanford-tmc	Stanford TMC
hubmap-caltech-tmc	California Institute of Technology TMC
hubmap-ucsd-tmc		University of California San Diego TMC
LC-MS Top Down 		LC-MS
Untargeted LC-MS 	LC-MS
TMT LC-MS  LC-MS
Targeted Shotgun / FlowLC-MS
snRNAseq (SNARE-seq2SNARE-seq
snATACseq (SNARE-seqSNARE-seq
scRNA-seq (10x Genomisc/sn/sciRNA-seq
snRNA-seq (10x Genomisc/sn/sciRNA-seq
snRNA-seq (10x Genomisc/sn/sciRNA-seq
scRNA-seq (10x Genomisc/sn/sciRNA-seq
sciRNA-seq sc/sn/sciRNA-seq
sciATAC-seq sc/sn/sciATAC-seq
snATAC-seq sc/sn/sciATAC-seq

[pecan88]

There were no comments or changes from the PIs re: the co

System-derived Corrected
hubmap-uflorida-tmc University of Florida TMC
hubmap-northwestern-rti Northwestern RTI
hubmap-vanderbilt-tmc Vanderbilt TMC
hubmap-stanford-tmc Stanford TMC
hubmap-caltech-tmc California Institute of Technology TMC
hubmap-ucsd-tmc University of California San Diego TMC
LC-MS Top Down LC-MS
Untargeted LC-MS LC-MS
TMT LC-MS LC-MS
Targeted Shotgun / Flow-injection LC-MS LC-MS
snRNAseq (SNARE-seq2) SNARE-seq2 (RNA & ATAC)
snATACseq (SNARE-seq2) SNARE-seq2 (RNA & ATAC)
scRNA-seq (10x Genomics v3) sc/sn/sciRNA-seq
snRNA-seq (10x Genomics v3) sc/sn/sciRNA-seq
snRNA-seq (10x Genomics v2) sc/sn/sciRNA-seq
scRNA-seq (10x Genomics v2) sc/sn/sciRNA-seq
sciRNA-seq sc/sn/sciRNA-seq
sciATAC-seq sc/sn/sciATAC-seq
snATAC-seq sc/sn/sciATAC-seq
scRNA-seq (10x Genomics v3),snATAC-seq sc/sn/sciRNA- & ATAC-seq

I suspect we will need to change the last one to "multiomic seq" however I don't have any confirmation there - just based on two wave 3 TMCs that appear to be submitting it (but it's not SNARE-seq).

[DerekFurstPitt]

@pecan88 I'm having a little trouble understanding the last line. Is it saying that the system derived value would be "scRNA-seq (10x Genomics v3),snATAC-seq" all one value? And that its corrected value would be "sc/sn/sciRNA- & ATAC-seq"?

For the sake of generating this via the api, should I use "sc/sn/sciRNA- & ATAC-seq" or "multiomic seq"?

[pecan88]

Hi @DerekFurstPitt - here is the most current list which I will seek to keep updated: https://docs.google.com/spreadsheets/d/1J6prGhbcffhokVFPynFxKeecz7CPsLHTnulW6LgJnOQ/edit#gid=0

In answer to your question, it would be "Multiome (RNA, ATAC)"