ElVisML: an open data format for the exchange and storage of electrophysiological data in ophthalmology

PurposeThe ISCEV standards and recommendations for electrophysiological recordings in ophthalmology define a set of protocols with stimulus parameters, acquisition settings, and recording conditions, to unify the data and enable comparability of results across centers. Up to now, however, there are no standards to define the storage and exchange of such electrophysiological recordings. The aim of this study was to develop an open standard data format for the exchange and storage of visual electrophysiological data (ElVisML).MethodsWe first surveyed existing data formats for biomedical signals and examined their suitability for electrophysiological data in ophthalmology. We then compared the suitability of text-based and binary formats, as well as encoding in Extensible Markup Language (XML) and character/comma-separated values.ResultsThe results of the methodological consideration led to the development of ElVisML with an XML-encoded text-based format. This allows referential integrity, extensibility, the storing of accompanying units, as well as ensuring confidentiality and integrity of the data. A visualization of ElVisML documents (ElVisWeb) has additionally been developed, which facilitates the exchange of recordings on mailing lists and allows open access to data along with published articles.ConclusionsThe open data format ElVisML ensures the quality, validity, and integrity of electrophysiological data transmission and storage as well as providing manufacturer-independent access and long-term archiving in a future-proof format. Standardization of the format of such neurophysiology data would promote the development of new techniques and open software for the use of neurophysiological data in both clinic and research.

[1]  J. Oberg,et al.  Why the Mars probe [accident investigation] , 1999 .

[2]  Arnaud Delorme,et al.  EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis , 2004, Journal of Neuroscience Methods.

[3]  Gunnar Lotz.  Design and implementation of reading center software for multi-center clinical trials , 2011 .

[4]  Scott Boag,et al.  XQuery 1.0 : An XML Query Language , 2007 .

[5]  Vaegan,et al.  ISCEV Standard for Clinical Electro-oculography (EOG) 2006 , 2006, Documenta Ophthalmologica.

[6]  Michael Bach,et al.  Erratum to: ISCEV Standard for clinical electro-oculography (2017 update) , 2017, Documenta Ophthalmologica.

[7]  Nona Wesley.  A Little Less Conversation , 2011 .

[8]  Steven J. DeRose,et al.  XML Path Language (XPath) , 1999 .

[9]  Barbara Catania,et al.  XML Data Stores: Emerging Practices , 2005, IEEE Internet Comput..

[10]  Paul J. Walmsley,et al.  XML Schema Part 0: Primer Second Edition , 2004 .

[11]  E. Troeger,et al.  An integrated software solution for multi-modal mapping of morphological and functional ocular data , 2010, 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology.

[12]  Alois Schlögl.  An overview on data formats for biomedical signals , 2009 .

[13]  Miles A. Whittington,et al.  Minimum Information about a Neuroscience Investigation (MINI): Electrophysiology , 2008 .

[14]  F. Cremers,et al.  Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial , 2014, The Lancet.

[15]  Chris D. Nugent,et al.  An XML Format for storing Body Surface Potential Map recordings , 2009, 2009 36th Annual Computers in Cardiology Conference (CinC).

[16]  Artur V. Cideciyan,et al.  Leber congenital amaurosis due to RPE65 mutations and its treatment with gene therapy , 2010, Progress in Retinal and Eye Research.

[17]  Jessy D. Dorn,et al.  The Argus II epiretinal prosthesis system allows letter and word reading and long-term function in patients with profound vision loss , 2013, British Journal of Ophthalmology.

[18]  David Beech,et al.  XML-Schema Part 1: Structures Second Edition , 2004 .

[19]  Eberhart Zrenner,et al.  Erg explorer: a software for post-processing, analysing, and reporting of electrophysiological data , 2008 .

[20]  Michael Bach,et al.  ISCEV Standard for full-field clinical electroretinography (2015 update) , 2014, Documenta Ophthalmologica.

[21]  Donald C. Hood,et al.  ISCEV standard for clinical multifocal electroretinography (mfERG) (2011 edition) , 2012, Documenta Ophthalmologica.

[22]  E. Kerty,et al.  Multimodal evoked potentials, EEG and electroretinography in patients with dystrophia myotonica , 1988, Acta neurologica Scandinavica.

[23]  Olaf Dössel,et al.  Present your research to the world! Preface , 2009 .

[24]  Donald E. Eastlake,et al.  XML-Signature Syntax and Processing , 2001, RFC.

[25]  P. Greenberg,et al.  Retinal implants: a systematic review , 2014, British Journal of Ophthalmology.

[26]  A. El-Osta,et al.  Gene name errors are widespread in the scientific literature , 2016, Genome Biology.

[27]  Alfred Stett,et al.  Subretinal electronic chips allow blind patients to read letters and combine them to words , 2010, Proceedings of the Royal Society B: Biological Sciences.

[28]  Eberhart Zrenner,et al.  ElVisML: A little less conversation. Experiences with the Electrophysiology of Vision Markup Language in clinical routine and in a multi‐center trial , 2011 .

[29]  Fahad I Al-Saikhan,et al.  The gene therapy revolution in ophthalmology. , 2013, Saudi journal of ophthalmology : official journal of the Saudi Ophthalmological Society.

[30]  Michael Bach,et al.  ISCEV standard for clinical visual evoked potentials: (2016 update) , 2016, Documenta Ophthalmologica.

[31]  Mary A. Johnson,et al.  ISCEV standard for clinical pattern electroretinography (PERG): 2012 update , 2007, Documenta Ophthalmologica.

[32]  Bob Kemp,et al.  European data format ‘plus’ (EDF+), an EDF alike standard format for the exchange of physiological data , 2003, Clinical Neurophysiology.

[33]  D. Eastlake,et al.  XML Encryption Syntax and Processing , 2003 .

[34]  T Penzel,et al.  Standards for biomedical signal databases. , 2001, IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society.

[35]  Arvind Malhotra,et al.  XML Schema Part 2: Datatypes Second Edition , 2004 .

[36]  Michael Bach,et al.  Guidelines for calibration of stimulus and recording parameters used in clinical electrophysiology of vision , 2004, Documenta Ophthalmologica.

[37]  Florence Debarre,et al.  The Availability of Research Data Declines Rapidly with Article Age , 2013, Current Biology.

[38]  Haiying Wang,et al.  A markup language for electrocardiogram data acquisition and analysis (ecgML) , 2003, BMC Medical Informatics Decis. Mak..

[39]  C J McDonald,et al.  Units of measure in clinical information systems. , 1999, Journal of the American Medical Informatics Association : JAMIA.

[40]  Wojciech Zareba,et al.  New Era for Digital ECG: FDA Requires Digital ECG Submission for Tested Drugs , 2001, Annals of noninvasive electrocardiology : the official journal of the International Society for Holter and Noninvasive Electrocardiology, Inc.

[41]  Alois Schlögl.  GDF - A general dataformat for BIOSIGNALS , 2006, ArXiv.