Ods, edf, eav & global types

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?