Closed aclum closed 1 day ago
For the SRA block use library_strategy = AMPLICON library_source = METAGENOMIC library_selection = PCR library_layout = paired platform = ILLUMINA instrument_model = Illumina MiSeq
Blocked by https://github.com/microbiomedata/issues/issues/776 Montana is reviewing Mongo ingest today
This data is in mongo prod now see https://github.com/microbiomedata/issues/issues/812 Study ID is nmdc:sty-11-ev70y104 The data to make the sra records is here /global/cfs/cdirs/m3408/gsharing/ecofab/ecofab_data
@sujaypatil96 this is ready to start work on.
Starting work on this today, 8/7.
This needs to be moved to the next sprint.
Status update:
PRJNA123456
) so if you see that id in the XML know that it will be replaced with the correct NCBI BioProject id once we’ve created it<Action>
blocks:
<Identifier>
tags. For the NEON studies we were populating that field with information from LibraryPreparation.protocol_link.name
but unfortunately we can’t do that for records in this study, so I am simply populating it with Biosample.name
== Biosample.samp_name
== “sample name” from spreadsheetlibrary_construction_protocol
in this comment<Package>
in the BioSample <Action>
blocks which makes it look like this: <Package>MIMS.me.miscellaneous natural or artificial environment.6.0</Package>
Ideally, we would want to use a standard NCBI package name from here: https://www.ncbi.nlm.nih.gov/biosample/docs/packages/<Action>
blocks for BioSample records and 90 blocks for SRA records which are both the expected number of blocksRefer to the squad slack channel for a preview of the XML export file.
ETA: ideally, end of the week/sprint.
Actively in progress but we are still iterating over the code that generates the xml for this new package so moving the next sprint.
We tried to submit this as a test but are having trouble with the bioproject IDs.
We tried to submit this as a test but are having trouble with the bioproject IDs.
@sujaypatil96 any update on the bioproject IDs issue?
The test submission successfully and will submit to production. Move to next sprint and hope it will be done early next week.
The submission to NCBI went through.
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cc @ssarrafan