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ODS, EDF, EAV& GlobalTypes
Christoph Fuchs12.02.2014
Operational Data StoreEuropean Data Format
Entity-attribute-value modelGlobalTypes
Christoph Fuchs12.02.2014
ODSOperational Data Store
Operational Data Store
● integrates data from multiple sources
Operational Data Store
“An operational data store is a subject-oriented, integrated, volatile, current-valued, detailed-only collection of data in support of an
organization's need for up-to-the-second, operational, integrated, collective information.”
Operational Data Store
“An operational data store is a subject-oriented, integrated, volatile, current-valued, detailed-only collection of data in support of an
organization's need for up-to-the-second, operational, integrated, collective information.”
Bill Inmon
Operational Data Store
● integrates data from multiple sources
● “on-thy-fly”
Operational Data Store
● integrates data from multiple sources
● “on-thy-fly”
● implemented in Data Warehouses
ODS / Data Warehouse
Operational Data Store
● integrates data from multiple sources
● “on-thy-fly”
● implemented in Data Warehouses
ODS - Software?
● Eclipse BIRT Project● RapidMiner● SpagoBI● R● KNIME● TACTIC
Source: http://en.wikipedia.org/wiki/Business_intelligence_tools#Open_source_free_products
ODS - Software?
● Eclipse BIRT Project● RapidMiner● SpagoBI● R● KNIME● TACTIC
Source: http://en.wikipedia.org/wiki/Business_intelligence_tools#Open_source_free_products
EDFEuropean Data Format
European Data Format
● standard file format for exchange and storage of medical time series
European Data Format
● standard file format for exchange and storage of medical time series
● open and non-proprietary
Source: https://groups.yahoo.com/neo/groups/EDF/info
European Data Format
● standard file format for exchange and storage of medical time series
● open and non-proprietary
● published in 1992 Electroencephalography and Clinical Neurophysiology (82: 391-393)Full specification: http://www.edfplus.info/specs/edf.html
European Data Format+
● extension published in 2003
● a few additional specifications
● only minor changes
Full specification: http://www.edfplus.info/specs/edfplus.html
European Data Format+
● “Any space inside the hospital code [...] must be replaced by a different character … ”
● 'Digital maximum' must be larger than 'Digital minimum'
Full specification: http://www.edfplus.info/specs/edfplus.html
EDF Example (Hypnogram)
EDF Example (Hypnogram)● Header contains:
○ startdate○ enddate○ patient data
(age, etc.)● Body contains:
○ binary readings
Source: B van Sweden, B Kemp, HAC Kamphuisen, EA van der Velde. Alternative electrode placement in (automatic) sleep scoring (Fpz-Cz / Pz-Oz versus C4-A1 / C3-A2). Sleep 13(3):279-283 (1990).
EDF Example (Reading)● Header contains:
○ startdate○ enddate○ patient data
EEG/EOG/EMG information
○ body temp, electrodes, ...
Source: B van Sweden, B Kemp, HAC Kamphuisen, EA van der Velde. Alternative electrode placement in (automatic) sleep scoring (Fpz-Cz / Pz-Oz versus C4-A1 / C3-A2). Sleep 13(3):279-283 (1990).
EDF Example (Reading)● Body again contains
binary information
Source: B van Sweden, B Kemp, HAC Kamphuisen, EA van der Velde. Alternative electrode placement in (automatic) sleep scoring (Fpz-Cz / Pz-Oz versus C4-A1 / C3-A2). Sleep 13(3):279-283 (1990).
Companies using EDF
● 92 companies listed, from all over the world
Companies using EDF
● 92 companies listed, from all over the world
○ Guger Technologies, Austria, Europe. Their EEG software reads EDF.
○ The Siesta Group, Austria, Europe. Their web-based sleep scoring and multi-center research reads and writes EDF and EDF+.
EAVEntity-attribute-value model
Entity-attribute-value model
“data model to describe entities where the number of attributes [...] is potentially vast, but the number that will actually apply to a
given entity is relatively modest”
Entity-attribute-value model
“data model to describe entities where the number of attributes [...] is potentially vast, but the number that will actually apply to a
given entity is relatively modest”=
“Sparse Matrix”
Entity-attribute-value model
● Also known as:
○ object-attribute-value model
○ vertical database model
○ open schema
Entity-attribute-value model
Caution!
● can be an anti-pattern
Entity-attribute-value model
Caution!
● can be an anti-pattern
● longer development times● poor use of DB resources● more complex queries
Entity-attribute-value model
Data is recorded as three columns:
● entity
● attribute (or parameter)
● value
Entity-attribute-value model
Example
(<patient XYZ, 1/5/98 9:30 AM>, <Temperature in degrees Fahrenheit>, "102" )
(<patient XYZ, 1/5/98 9:30 AM>, <Presence of Cough>, "True" )
(<patient XYZ, 1/5/98 9:30 AM>, <Type of Cough>, "With phlegm, yellowish,
streaks of blood" )
(<patient XYZ, 1/5/98 9:30 AM>, <Heart Rate in beats per minute>, "98" )
...
Entity-attribute-value model
Looks familiar?
Entity-attribute-value model
Data is recorded as three columns:
● subject
● predicate
● object
Entity-attribute-value model
RDF is an EAV
Entity-attribute-value model
● medical data is a good use-case
○ many possible data points
○ every patient only “uses” a few of these data points
Entity-attribute-value model
● medical data is a good use-case
● However, EDF and EDF+ don’t seem to be an EAV model per se
GlobalTypesaka complexType
GlobalTypes (complexType)
● complex types in XSD(XML Schema definition language)
● A complex type element is an XML element that contains other elements and/or attributes.
GlobalTypes (complexType)<complexType
id=IDname=NCNameabstract=true|falsemixed=true|falseblock=(#all|list of (extension|restriction))final=(#all|list of (extension|restriction))any attributes
>
(annotation?,(simpleContent|complexContent|((group|all|choice|sequence)?,((attribute|attributeGroup)*,anyAttribute?))))
</complexType>
GlobalTypes (complexType)
Source: http://www.w3schools.com/schema/el_complextype.asp
complexType Example
GlobalTypes (complexType)
● complexType in XSD
● can be used for modeling medical data
● the problem is, as always, agreeing on an ontology
SummaryODS, EDF, EAV, GlobalTypes
Summary● ODS Operational Data Store
○ business data integration “on-thy-fly”
● EDF European Data Format○ standard for medical data
● EAV Entity-attribute-value model○ e.g. RDF (subject-predicate-object)
● GlobalTypes aka XSD complexType○ define complex types in XSD
Thank youQuestions?