Example script for creating openMINDS metadata for TVB data uploads in JSON-LD format

What can I find here?

• a Jupyter Python notebook with code and commentaries for creating openMINDS metadata version 1.0 in JSON-LD format for ingestion of TVB-ready data in KnowledgeGraph
• Direct link to notebook
• openMINDS metadata can be directly ingested by EBRAINS' KnowledgeGraph
• it allows to annotate neuroscientific data (e.g. MRI) with metadata that specifies properties of the data in a structured manner and that allows better finding and reuse of the data.
• For more information, please visit the main openMINDS repository: https://github.com/HumanBrainProject/openMINDS
• Note: openMINDS is under ongoing development. The provided notebook was successfully used to create valid metadata sets, however, this may change if the standard changes.

Further information

• openMINDS metadata is required for curation of a data set for publication in EBRAINS' KnowledgeGraph

• This Collab is one of "The Virtual Brain at EBRAINS" cloud services for brain simulation and imaging data processing:

  • Brain network simulation:
    wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain
  •  

  Connectome construction:
  wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline

  •  

  Multiscale co-simulation with spiking networks: 
  wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale
  wiki.ebrains.eu/bin/view/Collabs/co-simulation-tvb-and-nest-high-computer/

  • High-performance simulation: 
    wiki.ebrains.eu/bin/view/Collabs/fast-tvb

  • Bayesian Virtual Epileptic Patient:
    wiki.ebrains.eu/bin/view/Collabs/bayesian-virtual-epileptic-patient
  • TVB Mouse Brains:
    wiki.ebrains.eu/bin/view/Collabs/tvb-mouse-brains
    wiki.ebrains.eu/bin/view/Collabs/mouse-stroke-brain-network-model

Authors

• Roopa Pai
• Michael Schirner
• Lyuba Zehl
• Petra Ritter

Contact

Petra Ritter <petra.ritter@charite.de>