drcc metadata template for data submission: metadata ...• the taxonomic definition of species,...
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DRCC metadata template fordata submission:
Metadata description & examples
NIH metabolomics data sharing policy
• Please review the complete data sharing plan for the NIH common fund metabolomics program available at:
http://www.metabolomicsworkbench.org/nihmetabolomics/datasharing.html
NIH metabolomics data sharing policy: Highlights
• Start date for data sharing:Data sharing as described in this plan for all grants supported by NIH Common Fund Metabolomics Program will be applicable from the beginning of the grant award.
• Definition of metabolomics data to be shared:Data to be shared includes four general data types: 1. the raw data generated by the metabolomics laboratory, 2. the analytical metadata, 3. the associated biological and clinical data in compliance with HIPPA guidelines and 4. the final result matrix with quantitative or semi-quantitative metabolite values and appropriate substance identifiers.
Raw data includes:• The spectrometric, spectrographic and chromatographic data as
created by the instrument software.• A description of the platform and vendor software version used
to generate and analyze raw data files.
An open exchange format submission is encouraged, as long as the raw data and exchange format contain the same level of information. File names should use identifiers that can be linked to the final result matrix of an experiment.
Analytical metadata includes:• Details on how samples were obtained at the biological or
clinical laboratory• Sample storage conditions.• Sample preparation and extraction protocols,• Analytical methods including the instrument and analytical
methods with enough detail to allow for an independent replication of the experiment.
Biological metadata includes:• The taxonomic definition of species, organs, cell types or cell
line information that was used in in-vivo and in-vitro experiments.
• Submission of more detailed metadata is highly encouraged, including animal husbandry, dietary information, or important human subject metadata such as age, body mass index, gender, co-morbidities, fasting state, medication and other anonymized information.
NIH metabolomics data sharing policy: Highlights
Metabolites x sample ID, including a list of all known and, where appropriate, unknown metabolites for each given experimental sample:
• The final data results matrix must contain the same local sample identifiers specified in the accompanying metadata file(s) and raw data file(s) in order to ensure an unambiguous relationship between experimental metadata, results and raw data.
• The results matrix may consist of measurements for known and/or unknown (unidentified) metabolites.
• In the case of known metabolites, the InChIKey and/or PubChem compound ID (if these are available) should be provided. Other compound identifiers (e.g. KEGG ID, ChemSpider ID) will be translated to the corresponding InChIKey and PubChem compound ID using the RefMet, a Reference list of Metabolites names.
• In the case of unknown metabolites, the local identifier and other annotations such as measured m/z value, retention index and type should be provided in order to track these metabolites across different experiments.
• The results matrix must contain the units of measurement (pmol/ml, ng/sample, MS peak height, MS peak area, etc).
NIH metabolomics data sharing policy: Highlights
• Embargo times:Investigators who collect the data have a legitimate interest in benefiting from their investment of time and effort. Data should be shared no later than the acceptance for first publication of the findings from the data set. The embargo time for data sharing will expire one year from the end of the active grant. In the case of grant renewal the data sharing embargo time will expire with the end of the funding period for the renewed grant. Data can be released in a tiered manner by the PIs, but no later than the expiration of embargo time to the public.
NIH metabolomics data sharing policy: Highlights
*The metabolomics standards initiative (MSI). Metabolomics (2007) 3:249–256
DRCC metadata concepts:Metabolomics standards initiative* (MSI)
Project
Sample A Sample B Sample…
Treatment X Treatment Y Treatment …
Collection C Collection D Collection …
Sampleprep E Sampleprep F Sampleprep …
Study ID: STXXXXX
Treatment ID: TRXXXXX
Collection ID: COXXXXX
Sampleprep ID: SPXXXXX
Analysis ID: ANXXXXX Analysis I Analysis J Analysis …
Sample ID: SAXXXXX
Study 1 Study 2 Study …
DRCC metadata
DRCC metadata template
• Metadata template data description
• Filling in metadata template for data submission: Metadata examples
DRCC metadata template
• Metadata template data categories & data fields– Project
– Study
– Study Design
– Subjects
– Treatments
– Collection
– SamplePrep
– Chromatography
– Analysis
– MS
– NMR
• Filling in metadata template for data submission: Metadata examples
Metadata template: Project data
Metadata example: Project data
Metadata example: Project data
Metadata example: Project data
Metadata template: Study data
Metadata example: Study data
Metadata example: Study data
Metadata example: Study data
Metadata example: Study data
Metadata template: Study Design data
Metadata example: Study Design data
Metadata example: Study Design data
Metadata example: Study Design data
Metadata example: Study Design data
Metadata template: Subjects data
Metadata template: Subjects data
Metadata example: Subjects data
Metadata example: Subjects data
Metadata example: Subjects data
Metadata template: Treatments data
Metadata template: Treatments data
Metadata template: Treatments data
Metadata example: Treatments data
Metadata example: Treatments data
Metadata example: Treatments data
Metadata template: Collection data
Metadata example: Collection data
Metadata template: SamplePrep data
Metadata example: SamplePrep data
Metadata example: SamplePrep data
Metadata example: SamplePrep data
Metadata template: Chromatography data
Metadata template: Chromatography data
Metadata example: Chromatography data
Metadata template: Analysis data
Metadata template: Analysis data
Metadata example: Analysis data
Metadata example: Analysis data
Metadata example: Analysis data
Metadata template: MS data
Metadata template: MS data
Metadata template: MS data
Metadata example: MS data
Metadata template: NMR data
Metadata template: NMR data
Metadata example: NMR data
Metadata example: NMR data
The End