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The Ontology for Experimental Neurophysiology: a first step toward semantic annotations of neurophysiology data and metadata.

Petr Brůha1, Václav Papež1, Anita Bandrowski2, Jan Grewe3, Roman Mouček1, Shreejoy Tripathy4, Thomas Wachtler3 and Yann Le Franc5*
  • 1 University of West Bohemia, Department of Computer Science and Engineering, Czechia
  • 2 The University of California, San Diego, Neuroscience Information Framework, Center for Research in Biological Systems, United States
  • 3 Ludwig-Maximilians Universität München, Department Biologie II, Germany
  • 4 Carnegie Mellon University, Department of Biological Sciences and Center for the Neural Basis of Cognition, United States
  • 5 University of Antwerp, Belgium

Analysis of existing ontological resources reveals a lack of terms for accurately and unambiguously annotating electrophysiological data and metadata. With the development of different resources for describing and sharing this particular type of data, the community needs controlled vocabularies to describe the different types of electrophysiology recording paradigms.

To build such vocabulary, or ontology, we created a dedicated workgroup involving relevant initiatives such as the EEGBase (http://eegdatabase.kiv.zcu.cz/home.html), the G-Node (www.g-node.org), the INCF task force on standards for sharing of electrophysiology data (http://www.incf.org/programs/datasharing/electrophysiology-task-force), NIF (www.neuinfo.org) and Neuroelectro.org (www.neurolectro.org).

As the field of electrophysiology is heterogeneous and multifaceted and the corresponding scope of the ontology considerable, the development of OEN has been separated along two main branches: a branch considering devices and methods, and a branch considering neurophysiological concepts. Here, we describe the first version of the Ontology for Experimental Neurophysiology ( OEN, https://github.com/G-Node/OEN), focused on devices and methodology, and our strategy for the creation of the neurophysiological concepts.

The device branch terminology is built upon existing ontologies related to neurophysiological experiments or investigation, namely the Ontology for Biomedical Investigation (OBI, http://obi-ontology.org/) and the Neural ElectroMagnetic Ontologies, (NEMO, http://purl.bioontology.org/ontology/NEMO). Existing terms describing neurophysiological devices and methods have been imported using the MIREOT format (Courtot et al., 2011) and the web service Ontofox (http://ontofox.hegroup.org/). The granularity of the ontology has been extended using the odML terminology (http://www.g-node.org/projects/odml/terminologies) and terms from the EEGBase.
To test our ontology, we created a simple knowledge base to describe the content of the EEGBase database. We are showing here some preliminary results and the infrastructure to transform EEGBase into semantic EEGBase.

In parallel we are developing a terminology to describe neurophysiological concepts such as action potential. This work is done in collaboration with other relevant ontologies such as the Phenotypic Quality Ontology (PATO, http://obofoundry.org/wiki/index.php/PATO:Main_Page) and the Gene Ontology, (GO, http://www.geneontology.org). To gather the feedback of the community, we are using Neurolex and web-based surveys to gather and assess the diversity of definitions.

Acknowledgements

This work is supported by the German INCF Node (BMBF grant 01GQ0801) and the European Regional Development Fund (ERDF), Project "NTIS - New Technologies for Information Society", European Centre of Excellence, CZ.1.05/1.1.00/02.0090.

References

Courtot M., Gibson F., Lister A.L., Malone J., Schober D., Brinkman R.R., Ruttenberg A., MIREOT: The minimum information to reference an external ontology term, 2011, J. Appl. Ontol., 6(1):23-33

Keywords: ontology, Neurophysiology, metadata, annotation, OWL

Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.

Presentation Type: Poster

Topic: General neuroinformatics

Citation: Brůha P, Papež V, Bandrowski A, Grewe J, Mouček R, Tripathy S, Wachtler T and Le Franc Y (2013). The Ontology for Experimental Neurophysiology: a first step toward semantic annotations of neurophysiology data and metadata.. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00026

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Received: 23 Apr 2013; Published Online: 11 Jul 2013.

* Correspondence: Dr. Yann Le Franc, University of Antwerp, Wilrijk, 2610, Belgium, ylefranc@gmail.com