add geomx template - draft

[allaway]

This PR is to address #428 .

-I created a GeoMX specific template because it doesn't need a lot of the sequencing related terms, as it is a probe-based transcription assay. I tried to map from HTAN's data model for this, though it seems like most of the details are captured in libraryPrep and libraryPreparationMethod (just more granular/more attributes in HTAN model).

-I didn't include a value (e.g. Synapse ID of GeoMx DSP PKC File,) it doesn't appear to be something that is available on GEO. I'm not sure if this is a nice to have or required for data re-use. We should ask the data contributors.

-I also added RCC file format and did some general meaning -> source cleanup in the FileFormat component.

Remaining questions that should be addressed before merging: the HTAN template includes four values for the assay that are possible (GeoMx DSP Assay Type,The assay type which was used for the GeoMx DSP pipeline.,"RNA nCounter, Protein nCounter, Protein NGS, RNA NGS",,,TRUE,Spatial Transcriptomics,,,). Currently the Assay is just "spatial transcriptomics". Should we deprecate this and add more detailed terms? Or, alternatively, is this more accurately described or captured byplatform metadata with the way we currently scope this term?

[github-actions[bot]]

PR Preview Action v1.4.7 :---: Preview removed because the pull request was closed. 2024-04-23 14:24 UTC

[github-actions[bot]]

Test Suite Report

Template Generation

template	result	link
AnimalIndividualTemplate	:smile:	template link
BiospecimenTemplate	:smile:	template link
ClinicalAssayTemplate	:smile:	template link
EpigeneticsAssayTemplate	:x:
FlowCytometryTemplate	:smile:	template link
GenomicsAssayTemplate	:smile:	template link
GenomicsAssayTemplateExtended	:x:
HumanCohortTemplate	:smile:	template link
ImagingAssayTemplate	:smile:	template link
LightScatteringAssayTemplate	:smile:	template link
MethylationArrayTemplate	:smile:	template link
MRIAssayTemplate	:smile:	template link
PharmacokineticsAssayTemplate	:smile:	template link
PlateBasedReporterAssayTemplate	:smile:	template link
ProcessedAlignedReadsTemplate	:smile:	template link
ProcessedExpressionTemplate	:smile:	template link
ProcessedVariantCallsTemplate	:smile:	template link
ProteomicsAssayTemplate	:smile:	template link
ProtocolTemplate	:smile:	template link
RNASeqTemplate	:x:
ScRNASeqTemplate	:smile:	template link
UpdateMilestoneReport	:smile:	template link
WESTemplate	:x:
WGSTemplate	:smile:	template link

Manifest Validation

manifest	result	expectation
GenomicsAssayTemplate_0.csv	:smile:	Lists can be blank if attr not required using ‘list like’ rule
GenomicsAssayTemplate_1.csv	:smile:	Mixing blanks and regular list values works
GenomicsAssayTemplate_2.csv	:smile:	Conditional validation for attributes is currently not supported
ScRNASeqTemplate_0.csv	:smile:	Single list val works by using ‘list like’ rule
ScRNASeqTemplate_1.csv	:x:	Fail because of missing data in required field libraryStrand

[allaway]

Also requesting feedback from @adamjtaylor if you have any. I hope you don't mind me butchering/retrofitting the HTAN data model to fit ours. :)

[allaway]

This seems to indicate the PKC file is required. https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-configuration-files/

We could just archive all of them on Synapse.... Maybe HTAN has already done this.

[allaway]

Closing b/c I misunderstood the data and need to make some changes!