ReDU metadata

[lamccue]

Looking at the ReDU metadata requirements

ReDU is the system for metadata collection and storage for GNPS2, the web-based mass spectrometry analysis platform developed and maintained by the Mingxun Wang's group at UC Riverside.

Metedata are collected by ReDU in an online template spreadsheet.

JGI metabolomics projects plan to use ReDU.

ReDU spreadsheet elements

There are color-coded sections of the spreadsheet for the types of metadata fields supported.

• red: MassiveID and filename
• blue: sample metadata
• yellow: mass spectrometry metadata
• gray: additional mixed bag of metadata fields

Relation of the ReDU mass spec fields (yellow category) with NMDC schema elements

1. YearOfAnalysis
   • ReDU (e.g, 2021)
   • NMDC doesn't have an overarching date for the analysis
   • MaterialProcessing classes generally have slots for start_date and end_date
2. SampleCollectionMethod
   • this appears to be a mix of sample metadata and identification of a processed sample, for example:
     • this allowed term refers to Sample metadata collection: "lumbar puncture"
     • this allowed term refers to processed sample generation: "extract, solid phase extraction (C18)"
3. SampleExtractionMethod
   • ReDU provides a list of specific extraction mixtures (e.g., methanol-water (9:1)) to choose from
   • NMDC uses MaterialProcessing Class: Extraction
     • Extraction has several slots to specify the solvents, their mass and volume, and extraction target (DNA, RNA, metabolite, protein, lipid), as well as slots to specify input (Sample) and output (ProcessedSample)
     • NMDC valid example
4. InternalStandardsUsed
   • ReDU provides a list of chemical compounds (e.g., sulfadimethoxine)
   • NMDC does not capture an internal standard
   • rather, we capture information about how the run was calibrated, which varies depending on type of mass spectrometry (GC-MS, LC-MS, FTICR, etc), this is in Class: CalibrationInformation
5. MassSpectrometer
   • ReDU provides a list of Thermo Fisher instruments and Ontobee identifiers (e.g., Q Exactive|MS:1001911)
   • NMDC uses MaterialEntity Class: Instrument which has separate slots for vendor and model, these slots have enums
6. IonizationSourceAndPolarity
   • ReDu provides a list of descriptors for combined ionization source and the polarity (e.g., electrospray ionization (positive))
   • NMDC uses the Class: MassSpectrometryConfiguration, which is a subclass of DataGeneration Class: MassSpectrometry
     • MassSpectrometryConfiguration has 6 slots to capture specific info for: acquisition strategy, resolution, mass analyzer, ionization source, collection mode, polarity mode
7. ChromatographyAndPhase
   • ReDU provides a list of types of chromatography (e.g., reverse phase (C18))
   • NMDC uses the Class: ChromatographyConfiguration, which is a subclass of DataGeneration Class: MassSpectrometry
     • ChromatographyConfiguration has 4 slots to capture specific info for: liquid, gas or solid phase, the stationary_phase, mobile phase and temperature

@mslarae13 @aclum this is information I gathered for the Metadata meeting. I started it as a discussion, as a place to gather information, thoughts and guide discussion.

I am not the expert in mass spec. Comments and corrections from @kheal are welcome.

[kheal]

Thanks @lamccue for gathering this information.

I think ReDu's "YearOfAnalysis" is more akin to the MassSpectrometry class's start_date. Otherwise I think these mappings to NMDC fields are accurate.

I would also note that all of the mass spec ReDu metadata are not required, while much/most of the NMDC versions are required.