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odML

odml

odML (open metadata Markup Language) is a file format for storing arbitrary metadata. The underlying data model offers a way to store metadata in a structured human- and machine-readable way. Well organized metadata management is a key component to guarantee reproducibility of experiments and to track provenance of performed analyses.

python-odml is the python library for reading and writing odml metadata files. It is a registered research resource with the RRID:SCR_001376 .

APIs

Viewer/Editor

  • odml-ui: Graphical editor
  • odmlTables Spreadsheet interface (by INM-6 FZ JÛlich) for odml files.

Terminologies

odML facilitates and encourages standardization by providing terminologies. An odml-file can be based on such a terminology. In that case one does not need to provide definitions since they are part of the linked terminology.


Getting started

Installation

python-odml is most conveniently installed via pip.

pip install odml

Tutorial and examples

Python convenience scripts

The Python installation features two convenience commandline scripts.

  • odmlconversion: Converts odML files of previous file versions into the current one.
  • odmltordf: Converts odML files to the supported RDF version of odML.

Both scripts provide detailed usage descriptions by adding the help flag to the command.

odmlconversion -h
odmltordf -h

Support

If you experience problems using odml feel free to join our IRC channel #gnode at FreeNode or write an email to dev@g-node.org. If you find a bug please report it using the project issue tracker.

License

This project is open source published under an MIT license-like see license file for details.


Citing

If you use odml, it would be much appreciated if you would cite it in publications with its identifier RRID:SCR_001376 and/or the reference:

Grewe J., Wachtler T., and Benda J. (2011). A bottom-up approach to data annotation in neurophysiology. Front. Neuroinform. 5:16, doi:10.3389/fninf.2011.00016

Referenced By