DataHarmonizer

A tool helping metadata collection and validation

Maja Magel

Charlie Pauvert

2024-07-19

DataHarmonizer

• Data and metadata collection can be crucial (e.g., COVID-19)

• DataHarmonizer: a super spreadsheet to help (Gill et al. 2023)

Main features

• Load metadata standards

• Fill the template

• Validate your metadata against the template

• Easy navigation based on:
  • Sections of metadata fields
  • Metadata requirements
• Display expected values

NMDC submission portal

• National (USA) Microbiome Data Collaborative

Leverage DataHarmonizer to lower barriers to collect, study and biosample data

• Not going to use it for data submission but data description!

• Receive guidance on how to meet standards

Submission portal Demo

An otter dataset

• Sample: feces collected in the wild
• Model system: Eurasian river otter (Lutra lutra)

See the “full” methods section in the pad!

Image by Bernard-Boehne from Wikimedia Commons

Exercise/demonstration

Task:

• Go to https://data-sandbox.microbiomedata.org/submission/
• Log with your ORCID and go again to the link above
• Create a new submission using the otter dataset
• Read the methods section in the pad
• Download the XLSX template to help you validate your submission

Download the XLSX solution

your turn!

References

Gill, Ivan S., Emma J. Griffiths, Damion Dooley, Rhiannon Cameron, Sarah Savić Kallesøe, Nithu Sara John, Anoosha Sehar, et al. 2023. “The DataHarmonizer: A Tool for Faster Data Harmonization, Validation, Aggregation and Analysis of Pathogen Genomics Contextual Information.” Microbial Genomics 9 (1). https://doi.org/10.1099/mgen.0.000908.