DATABASE OF EEG/ERP EXPERIMENTS

Petr Ježek and Roman Mouček

Department of Computer Science and Engineering, University of West Bohemia

Univerzitní 8, 306 14 Pilsen, Czech Republic

Keywords: Electroencephalography (EEG), Event related potentials (ERP), EEG/ERP data, Metadata, Relational

database, Web interface, Spring framework, Hibernate, Semantic web technologies, Data conversion.

Abstract: The article deals with the database of EEG/ERP experiments and its developed prototype. Storage,

download and interchange of EEG/ERP data and metadata through the web interface is possible, various

user roles are defined. The requirements specification including the system context, scope, basic features,

data formats and metadata structures is presented. The system architecture, used technologies and the final

realization are described. Additional tools and structures as converters of data formats and generated

ontology are mentioned. The possible users of the database are specified.

1 INTRODUCTION

Our research group at Department of Computer

Sciences and Engineering, University of West

Bohemia in cooperation with other partner

institutions (e.g. Czech Technical University in

Prague, University Hospital in Pilsen, Škoda Auto

Inc, ... ) specializes in the research of attention,

especially attention of drivers and seriously injured

people. With regard to our research we widely use

the methods of electroencephalography (EEG) and

event related potentials (ERP). Within our partner

network we are responsible for technical and

scientific issues, e.g. EEG/ERP laboratory operation,

development of advanced software tools for

EEG/ERP research, or analysis and proposal of

signal processing methods.

EEG and ERP experiments take usually long

time and produce a lot of data. With the increasing

number of experiments carried out in our laboratory

we had to solve their long-term storage and

management. Looking for a suitable data store for

EEG/ERP data and metadata we encountered series

of problems:

 There is no widely spread and generally used

standard for EEG/ERP data files within the

community.

 Results (interpretations) of EEG/ERP

experiments are usually more important than

obtained data (some researchers even declare

that experimental data have a low value when

they are interpreted).

 There is no reasonable and easily extensible

tool for long-term EEG/ERP data (metadata)

storage and management (the general practice

is to organize data and metadata in common

file directories).

 There is no practice to share and interchange

data between EEG/ERP laboratories

(EEG/ERP data are supposed to be secret or

unimportant to share them).

2 SPECIFICATION OF EEG/ERP

DATABASE

2.1 System Context

Because of hard manual work with large amount of

EEG/ERP data and metadata and in face of

difficulties mentioned in Introduction part, we

decided to design and implement own software tool

suitable for EEG/ERP data and metadata storage and

management.

The developed EEG/ERP data store (called

simply the system in the following text) pursues not

only our local research but in general it contributes

to advancements in human brain understanding. In

addition, we believe that such advanced software

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Ježek P. and Moucek R. (2010).

DATABASE OF EEG/ERP EXPERIMENTS.

In Proceedings of the Third International Conference on Health Informatics, pages 222-227

DOI: 10.5220/0002698102220227

 SciTePress

tools increase both the efficiency and the

effectiveness of neuroscientific research.

2.2 Requirements Specification

The specification of requirements originated from

experience of our laboratory, co-workers from

cooperating institutions, books describing principles

of EEG/ERP design and data recording (e.g. Luck,

2005) and numerous scientific papers describing

specific EEG/ERP experiments. It also corresponds

to the effort of International Neuroinformatics

Coordinating facility (INCF) (Pelt, 2007) in the field

of development and standardization of databases in

neuroinformatics.

2.2.1 System Users

The system prototype is dedicated for department

users and collaborative partners as well as for

a limited group of researchers interested in

EEG/ERP research. The system is supposed to be

widely tested to guarantee the safety of personal

information, availability of EEG/ERP resources and

their usability for people interested in this research

field.

2.2.2 Project Scope and System Features

EEG/ERP database enables clinicians and various

community researchers to store, update and

download data and metadata from EEG/ERP

experiments. System is developed as a standalone

product (integration with the software for EEG/ERP

experimental design is not a task of this project).

The database access is available through a web

interface. We need a web server supporting open

source (Java and XML) technologies and a database

system, which is able to process huge EEG/ERP

data. The system is easily extensible and can serve

as an open source.

The system essentially offers the following set of

features (the number of accessible features depends

on a specific user role):

 User authentication

 Storage, update, and download of EEG/ERP

data and metadata

 Storage, update and download of EEG/ERP

experimental design (experimental

scenarios)

 Storage, update and download of data

related to testing subjects

The crucial user requirement is the possibility to

add an additional set of metadata required by

a specific EEG/ERP experiment. The complete

overview of the system features and user roles (use

case diagram) is available in (Pergler, 2009).

2.2.3 User Roles

Since the system is thought to be finally open to the

whole EEG/ERP community there is necessary to

protect EEG/ERP data and metadata, and especially

personal data of testing subjects stored in the

database from an unauthorized access. Then

a restricted user policy is applied and user roles are

introduced.

On the basis of activities that a user can perform

within the system the following roles are proposed:

 Anonymous user has the basic access to the

system (it includes essential information

available on the system homepage and the

possibility to create his/her account by filling

the registration form).

 Reader has already his/her account in the

system and can list through and download

experimental data, metadata and scenarios

from the system, if they are made public by

their owner. Reader cannot download any

personal data or store his/her experiments into

database.

 Experimenter has the same rights as Reader;

in addition he/she can insert his/her own

experiments (data and metadata including

experimental scenarios) and he/she has the full

access to them. This user role cannot be

assigned automatically, a user with the role

reader has to apply for it and the new role

must be accepted by supervisor.

 Supervisor has an extra privilege to

administer user accounts and change their user

roles according to the policy.

2.2.4 Data Formats

There exists a variety of data formats for storing

EEG/ERP data. The more spread formats and

formats used in our laboratory include European

Data Format (EDF and EDF+) (“EDF”, n.d.), Vision

Data Exchange Format (VDEF) (“VDEF”, n.d.),

Attribute-Relation File Format (ARFF) (“ARFF”,

n.d.), and KIV format (Kučera, 2008).

European Data Format (EDF) contains an

uninterrupted digitized EEG record stored in one file

(a header record is followed by data records). The

header content has a variable length. It identifies

a testing subject and specifies the technical

characteristics of recorded EEG signal. The data part

contains consecutive fixed-duration epochs of the

record. Despite its drawback this data format has

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been probably the most hopeful attempt to

standardize description of EEG data.

Vision Data Exchange Format (VDEF) is used

by the technical equipment in our laboratory. EEG

record is divided into three files: a header file,

a marker file and a data file. The header file based

on Windows INI format describes recorded data and

provides a limited set of corresponding metadata as

the attribute-value pairs. The marker file contains

information about markers (their types and timing)

in EEG signal. The data file contains raw EEG data.

Attribute-Relation File Format (ARFF) is used in

our laboratory as the interface to WEKA software

(“WEKA”, n.d.). Data and metadata are stored in

one ASCII file consisting of two sections. The

header section provides a limited set of metadata and

it is followed by the data part.

KIV data format is a modification of simple

ASCII format of EEG signal, where metadata (file

header in ASCII) are stored in XML file and data

from electrodes are stored in separate binary files.

The users’ requirement on the system is to accept

at least three formats mentioned above. An optional

requirement is to provide users with conversion tools

between these formats.

Standardization of EEG/ERP data format we are

also working on (with INCF support) is out of scope

of this article.

2.2.5 Definition of Metadata

The data obtained from EEG/ERP experiments are

senseless if they are not supported by more detailed

description of testing subjects, experimental

scenarios, laboratory equipment etc. Metadata are

also necessary for an interpretation of performed

experiment and for data search and manipulation.

Metadata are organized in several semantic groups:

 Scenario of experiment (name, length,

description, …)

 Experimenters and testing persons (given

name, surname, contact, experiences,

handicaps, …)

 Used hardware (laboratory equipment,

type, description, …)

• Actual surrounding conditions (weather,

temperature, …)

• Description of raw data (format, sampling

frequency, …)

There is important that only a small predefined

set of metadata is optional to fill in. In addition,

a user with the role experimenter has the right to

define his/her own metadata.

2.2.6 System Sustainability

The system purpose is not only to serve as a local

managing tool for our EEG/ERP research but to

serve as a system, which enables sharing and

interchange of data between various research groups.

Nowadays EEG and ERP data are provided by

diverse groups of not only medical communities but

scientists or universities as well. The system is

therefore developed as open source accepting INCF

recommendations. It will be offered as a free

managing tool and source of EEG/ERP data within

collection of other neuroinformatics data sources.

2.2.7 System Security

The system database contains personal data, which

are necessary for interpretation of experiment or for

contact with testing subject. Only experimenter has

access to personal data of testing persons who took

part in his/her experiment. Collection of personal

data and their storage are managed according to law.

2.2.8 System Performance

The system database has to work with long

EEG/ERP records (usually tens of megabytes) in

reasonable time. The main limiting factor is a user

internet connection, not the database performance.

3 SYSTEM DESIGN AND

REALIZATION

3.1 System Architecture

The system is based on three layer architecture. This

architectonic style is supported by selection of

programming tools and technologies. We used Java

and XML technologies to ensure a high level of

abstraction (system extensibility) as well as a long

term existence of the system as open source.

3.1.1 Persistence Layer

Persistence layer uses Hibernate framework. It

means that relational database and object – relational

mapping are supported. Oracle 11g database server

is used to ensure the processing of large data files.

ERA model of relational database is available in

Figure 1; all tables describing metadata extension

are omitted to keep the model understandable.

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Figure 1: Database structure – ERA model.

3.1.2 Application and Presentation Layer

Application and presentation layers are designed and

implemented using Spring technology. This

framework supports MVC architecture, Dependency

injection and Aspect Oriented Programming.

Integration of both frameworks, Hibernate and

Spring MVC, was without difficulties. Spring

Security framework is used to ensure management

of authentication and user roles.

User access to the relational database is realized

through the web interface. Majority of users are

familiarized with web applications and they do not

need any additional software except a web browser.

User interface is divided into several parts (main

menu, second level menu, header, footer, and

content part). The main menu includes e.g. the

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following sections:

 Home – system introduction, registration,

 Experiments – management of EEG/ERP

experiments

 Scenarios – management of experimental

EEG/ERP designs

 People – management of people in the

system

Figure 2 presents a user interface preview.

Figure 2: User interface preview.

Input data are validated. Error messages are

presented using special marks in JSP views and by

definition of CSS styles for corresponding input

fields.

Storage/download of raw EEG/ERP files is

universal; there is possible to store/download any

allowed file type.

3.2 Semantic Web Technologies

Registration of the system as a recognized data

source occasionally requires providing data and

metadata structures in the form of ontology in

accordance with ideas of semantic web. We also

started to work on the representation of data and

metadata structures using semantic web

technologies. Nowadays there is possible to generate

and provide data and metadata structures using

Ontology Web Language (OWL). The details will be

presented in a separate paper.

3.3 Conversions Between Data Formats

Converters between data formats mentioned in

Section 2.2.4 were implemented. These converters

can be downloaded and used locally; no conversion

is performed during data upload/download.

4 CONCLUSIONS

The presented system combines research in

EEG/ERP and informatics fields as well as

application of informatics in neuroscience. Our

research group designed and implemented the

prototype of experimental EEG/ERP database for

storage, download and interchange of EEG/ERP

experiments. The database preserves EEG/ERP raw

data together with the corresponding metadata. The

currently developed prototype is prepared for

extensive testing carried out by our department,

cooperating institutions and a limited number of

people interested in EEG/ERP research and its

applications.

Advanced Java technologies (Hibernate, Spring,

and Spring security frameworks) were used to

ensure a high level of abstraction and further

maintenance and extensibility of the system as the

open source software.

In addition, converters between various data

formats and database ontology in OWL are provided

for experienced users.

We hope that EEG/ERP database can also

provide useful data and metadata to research groups,

which do not perform their own experiments, but

which are interested e.g. in signal processing or data

mining.

As the next big step we prepare a progressive

change of EEG/ERP experimental database to

EEG/ERP portal offering e.g. advanced software

tools, which can help researchers with difficulties of

EEG/ERP experimental design, and set of methods

for signal processing.

We also plan to register our system as a data

source within large world known projects in

neuroinformatics, e. g. Neuroscience Information

Framework (“NIF”, n. d.).

ACKNOWLEDGEMENTS

The work was supported by the Ministry of

Education, Youth and Sport of the Czech Republic

under the grant ME 949.

REFERENCES

Luck, S. J., 2005. An Introduction to the Event-Related

Potential technique, MIT Press. Cambridge.

Pelt, J. van, Horn J. van, 2007. Workshop report. 1st INCF

Workshop on Sustainability of Neuroscience

Databases. Stockholm.

Pergler, J., 2009. Database of ERP experiments – business

and presentation layer (Databáze ERP experimentů -

aplikační a prezentační vrstva). Thesis (in Czech).

University of West Bohemia. Pilsen.

European Data Format (EDF). (n.d.). Retrieved from

http://www.edfplus.info/

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Vision Data Exchange Format (VDEF). (n.d.). In Brain

Vision Recorder Manual. Retrieved from http://

biomag.uni-

muenster.de/EEGlab/docs/VisionRecorderManual.doc

Attribute Relation File Format (ARFF). (n.d.). Retrieved

from http://weka.wiki.sourceforge.net/ARFF

Kučera, J., 2008. Software for ERP processing, data

reading and presentation (Software pro zpracování

ERP, načítání a zobrazení dat). Thesis. (in Czech).

University of West Bohemia. Pilsen.

Weka 3 - Data Mining with Open Source Machine

Learning Software in Java (WEKA). (n.d.). Retrieved

from http://www.cs.waikato.ac.nz/~ml/weka/

Neuroscience Information Framework (NIF). (n. d.).

Retrieved from http://www.neuinfo.org/

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