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
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: