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Biological Dynamics Markup Language

What is BDML/BD5?

  • BDML (Biological Dynamics Markup Language) is an open XML-based format for representing spatiotemporal dynamics of biological objects (quantitative data) from molecules to cells to organisms. BDML covers a wide variety of quantitative data obtained by bioimage informatics techniques and mechanobiological simulation.
  • BD5 is the other open HDF5-based format for representing quantitative data. It enables fast access to the data and fast transfer of large data.

BDML/BD5 Publication

  • Koji Kyoda, Yukako Tohsato, Kenneth H. L. Ho, Shuichi Onami (2015)
    Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data, Bioinformatics, Volume 31, Issue 7, 1 April 2015, Pages 1044–1052, https://doi.org/10.1093/bioinformatics/btu767
  • Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami (2020)
    BD5: An open HDF5-based data format to represent quantitative biological dynamics data, PLOS ONE, Volume 15, Issue 8, August 2020, Pages e0237468, https://doi.org/10.1371/journal.pone.0237468.


OmicsBDML is an open format for representing quantitative omics data, such as gene, protein, and metabolite with spatiotemporal information. OmicsBDML schema can be found here OmicsBDML schema.

Details of BDML/BD5

BDML version 3.0 includes an option to store numerical quantitative data in BD5 binary format. BD5 is based on HDF5 (https://support.hdfgroup.org/HDF5/) which is developed by the HDF Group open source consortium. HDF5 is a data model, library, and file format for storing and managing data. Therefore, all the open source tools available for accessing and retrieving HDF5 are also applicable to BD5. Meta-data are still stored within BDML.

The older version of BDML schema files:

BDML specification