ROSMAP metabolomics metadata creation

[avanlinden]

The OG ROSMAP metabolomics data (111 brains run on Biocrates p180 + a bespoke bile acids assay, and 597 serum samples run on Biocrates p180) do not have biospecimen or assay metadata associated with them.

To do:

• [x] check that all specimens from data files have projids that are in the clinical file
• [x] check that specimenIDs from data files have not already been used in the clinical file
• [x] create biospecimen metadata for all specimens from metabolomics data files and append to biospecimen file
• [x] create assay metadata for all specimens from metabolomics data files and upload to Metadata folder

[avanlinden]

Biospecimen and assay metadata for the ROSMAP metabolomics pilot data have been created.

Specimens added to biospecimen file here. New metabolomics assay metadata file here.

For biospecimen metadata:

• the "brain bile acids" assay I renamed as "UPLC-MSMS", which is what it was annotated as. In the biospecimen file, the assay is "UPLC-MSMS" and the specimenIdSource is "University of Hawaii Cancer Center"
• tissue data taken from reports
• need to confirm with Colette if all samples were postmortem -- brains obviously were, but not sure about serum. Individuals related to serum samples are in clinical file so are deceased, but serum may have been collected pre-mortem.

assay metadata:

• metabolite type taken from reports, glycerophospholipids added to dictionary
• need to ask Colette about ionMode
• batch size and batch number were pulled from the Plate.Bar.Code column of data files for the Biocrates data. The bile acid data from U Hawaii does not have any batch info in the data or report
• should consider adding "massSpectrometerType" or something to the assay metadata, to distinguish which samples/batches were run on the FIA vs UPLC mass spec parts of the Biocrates assay

code here: https://github.com/avanlinden/curation-wrangling/blob/main/clean-existing-studies/create-ROSMAP-metabolomics-metadata.R

[avanlinden]

Changed the "UPLC-MSMS" assay to "Biocrates Bile Acids". Closing.