odML Format and Terminologies for Automated Handling of (Meta)data
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Ludwig-Maximilians-Universitaet Muenchen, Department Biology II, Germany
For analysis, management, and sharing of experimental data, metadata that provide information about data acquisition and experimental conditions are indispensable. Computer-based analysis and data management requires this meta information to be stored and exchanged in machine-readable form. We propose a simple format, the "Open metaData Markup Language" (odML) for metadata. This format specifies a hierarchical structure for storing arbitrary meta information as extended key-value pairs, so called properties, which can be logically grouped into sections and subsections. The odML defines the format, not the content, so that it is inherently extensible and can be adapted flexibly to the specific requirements of any laboratory. This freedom, however, is in conflict with the goal of data sharing: there, a correct understanding of metadata and data is only possible if the annotations apply the same terms or, if mappings between the terminologies applied by sender and receiver are provided.
To facilitate the usage of a common standard terminology we started to define collections of terms and respective definitions for neurophysiology. A terminology is an odML section, for example, the Subject terminology, which contains the terms to describe an experimental subject. Further terminologies are defined, e.g., to describe cells, stimuli, or the properties and settings of used hardware items. They all define names of metadata items not the contents. These terms are meant to be recommendations which should be used if appropriate, but may also be ignored or extended, if necessary. The odML format, however, does not force the scientist to use the suggested terms. The format further offers two ways of customization to meet individual requirements or tastes: (I) It is possible to define synonyms for properties and sections that can be used instead of the originally defined names, or, (II) through individual terminologies which provide mappings to the standard terminologies, custom sets of terms can be created. In both ways, freedom and flexibility is gained without softening the approach of a common standard. The odML is open source and all resources can be found on www.g-node.org/odml. Especially, for the terminologies community feedback is required and highly appreciated.
To completely describe the conditions that led to a certain dataset requires a vast number of metadata and is thus considered a tedious business. We propose that metadata acquisition should start as early and, as the actual data acquisition, as automated as possible. In order to facilitate this, we provide odML-libraries in some common programming languages that allow easy integration of metadata handling into the laboratory workflow, automatically collecting metadata information where it becomes available.
Acknowledgments: Supported by BMBF grant 01GQ0801.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Poster Presentation
Topic:
Electrophysiology
Citation:
Grewe
J,
Wachtler
T and
Benda
J
(2010). odML Format and Terminologies for Automated Handling of (Meta)data.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00117
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Received:
15 Jun 2010;
Published Online:
15 Jun 2010.
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Correspondence:
Thomas Wachtler, Ludwig-Maximilians-Universitaet Muenchen, Department Biology II, Planegg-Martinsried, Germany, wachtler@bio.lmu.de