BioSignalML Putting biosignals onto the Semantic Web David Brooks - - PowerPoint PPT Presentation

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BioSignalML Putting biosignals onto the Semantic Web David Brooks - - PowerPoint PPT Presentation

Mar 23, 2024 335 likes •684 views

BioSignalML Putting biosignals onto the Semantic Web David Brooks Background Biosignal -- time series data resulting from a biological process. Background Biosignal -- time series data resulting from a biological process.

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BioSignalML

Putting biosignals onto the Semantic Web David Brooks

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Background

  • Biosignal -- time series data

resulting from a biological process.

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Background

  • Biosignal -- time series data

resulting from a biological process.

  • Sampled, usually at a

regular rate, which is usually much greater than the highest frequency of interest.

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Background

  • Biosignal -- time series data

resulting from a biological process.

  • Sampled, usually at a

regular rate, which is usually much greater than the highest frequency of interest.

  • Electrical, pressure,

concentration, …

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Background

  • Biosignal -- time series data

resulting from a biological process.

  • Sampled, usually at a

regular rate, which is usually much greater than the highest frequency of interest.

  • Electrical, pressure,

concentration, …

  • Simulation time series data.
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Background

  • A lot of file formats:

– manufacturer; research; regulatory; …

WaveForm DataBase WFDB Standard Communication Protocol for ECG (CEN) SCP Medical waveform Format Encoding Rules (ISO) MFER General Data Format (an EDF derivative) GDF FDA standard for ECG FDAXML European Data Format plus EDF+ European Data Format EDF 24 bit version of EDF BDF

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Background

  • A lot of file formats:

– manufacturer; research; regulatory; …

  • Often developed for a

specific problem domain.

WaveForm DataBase WFDB Standard Communication Protocol for ECG (CEN) SCP Medical waveform Format Encoding Rules (ISO) MFER General Data Format (an EDF derivative) GDF FDA standard for ECG FDAXML European Data Format plus EDF+ European Data Format EDF 24 bit version of EDF BDF

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Background

  • A lot of file formats:

– manufacturer; research; regulatory; …

  • Often developed for a

specific problem domain.

  • All generally good at

storing time series data.

WaveForm DataBase WFDB Standard Communication Protocol for ECG (CEN) SCP Medical waveform Format Encoding Rules (ISO) MFER General Data Format (an EDF derivative) GDF FDA standard for ECG FDAXML European Data Format plus EDF+ European Data Format EDF 24 bit version of EDF BDF

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Background

  • A lot of file formats:

– manufacturer; research; regulatory; …

  • Often developed for a

specific problem domain.

  • All generally good at

storing time series data.

  • Metadata format is file

specific.

WaveForm DataBase WFDB Standard Communication Protocol for ECG (CEN) SCP Medical waveform Format Encoding Rules (ISO) MFER General Data Format (an EDF derivative) GDF FDA standard for ECG FDAXML European Data Format plus EDF+ European Data Format EDF 24 bit version of EDF BDF

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Background

  • A lot of file formats:

– manufacturer; research; regulatory; …

  • Often developed for a

specific problem domain.

  • All generally good at

storing time series data.

  • Metadata format is file

specific.

  • Metadata content tends to

be domain specific.

WaveForm DataBase WFDB Standard Communication Protocol for ECG (CEN) SCP Medical waveform Format Encoding Rules (ISO) MFER General Data Format (an EDF derivative) GDF FDA standard for ECG FDAXML European Data Format plus EDF+ European Data Format EDF 24 bit version of EDF BDF

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Difficulties

  • Polysomnography:

– “Currently, digital data from most PSG systems can

  • nly be viewed if one utilizes the system with which it

was collected.” [1] – “Unfortunately, not much has happened since … no consensus for data sharing has taken root.” [2]

[1] D. Rapoport, I. Ayappa, R. Norman, and S. Herman, “NPSG data interchange-dealing with the Tower of Babel.” Sleep,

  • vol. 29, no. 5, p. 599, 2006.

[2] D. M. Rapoport, email correspondence, November 2011.

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Difficulties

  • Polysomnography:

– “Currently, digital data from most PSG systems can

  • nly be viewed if one utilizes the system with which it

was collected.” [1] – “Unfortunately, not much has happened since … no consensus for data sharing has taken root.” [2]

  • Metadata terms:

– Different groups may have different meanings for a term.

[1] D. Rapoport, I. Ayappa, R. Norman, and S. Herman, “NPSG data interchange-dealing with the Tower of Babel.” Sleep,

  • vol. 29, no. 5, p. 599, 2006.

[2] D. M. Rapoport, email correspondence, November 2011.

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Difficulties

  • Polysomnography:

– “Currently, digital data from most PSG systems can

  • nly be viewed if one utilizes the system with which it

was collected.” [1] – “Unfortunately, not much has happened since … no consensus for data sharing has taken root.” [2]

  • Metadata terms:

– Different groups may have different meanings for a term. – Units: µV, uV, V×10-6 ??

[1] D. Rapoport, I. Ayappa, R. Norman, and S. Herman, “NPSG data interchange-dealing with the Tower of Babel.” Sleep,

  • vol. 29, no. 5, p. 599, 2006.

[2] D. M. Rapoport, email correspondence, November 2011.

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  • Web content that is meaningful to computers.

– Knowledge representation, ontologies, reasoning, intelligent agents, …

Semantic Web

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  • Web content that is meaningful to computers.

– Knowledge representation, ontologies, reasoning, intelligent agents, …

  • http://www.w3.org/standards/semanticweb/

– Resource Description Framework (RDF) – RDFS, OWL, SPARQL, …

Semantic Web

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  • Web content that is meaningful to computers.

– Knowledge representation, ontologies, reasoning, intelligent agents, …

  • http://www.w3.org/standards/semanticweb/

– Resource Description Framework (RDF) – RDFS, OWL, SPARQL, …

  • Linking Open Data

Semantic Web

Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/

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BioSignalML

  • Abstract common elements of storage formats.
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BioSignalML

  • Abstract common elements of storage formats.
  • Use Semantic Web standards/technologies.

– Objects have web identifiers. – Ontologies define terms, properties, relationships.

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http://repository.biosignal.org/recording3/signal/4

BioSignalML

  • Abstract common elements of storage formats.
  • Use Semantic Web standards/technologies.

– Objects have web identifiers. – Ontologies define terms, properties, relationships.

  • Time series data is in native format; everything

else is available as RDF metadata.

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BioSignalML as RDF

  • Core concepts:

– Recordings – Signals – Events and Annotations.

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BioSignalML as RDF

  • Core concepts:

– Recordings – Signals – Events and Annotations.

  • RDF graph:
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BioSignalML as an ontology

  • Classes, terms, properties, relationships:
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BioSignalML as an ontology

  • Classes, terms, properties, relationships:
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Metadata Signal Recordings Abstraction Layer Python API EDF WFDB HDF5 Triple Store

BioSignalML implementation

  • Biosignal repository:
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Internet

Metadata Signal Recordings Abstraction Layer Python API EDF WFDB HDF5 Triple Store

SPARQL Query

RESTful Web Services

RDF HTML Raw Files Stream Web Browsers

BioSignalML implementation

  • Biosignal repository:
  • Web based with HTTP

endpoints: – File import/export – RDF metadata – Data streamed via web-sockets.

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Internet

Metadata Signal Recordings Abstraction Layer Python API EDF WFDB HDF5 Triple Store

SPARQL Query

RESTful Web Services

RDF HTML Raw Files Stream

Applications

and Tools Web Browsers

BioSignalML implementation

  • Biosignal repository:
  • Web based with HTTP

endpoints: – File import/export – RDF metadata – Data streamed via web-sockets.

  • C client (plus Python,

Javascript, …)

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BioSignalML clients

  • Web browser:
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BioSignalML clients

  • Web browser:
  • RDF browser:
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BioSignalML clients

import import bi biosignalml import import bi biosignalml.u .units as units repo repo = = bi biosignalml.R .Repository(‘ht http://demo.bi biosignalml.o .org’) rec rec = = re repo.ne new_recording(‘ht http://ex example.org/recording/test’) sig sig = = re rec.ne new_signal(i (id=‘a1 a1’, , units=un units.mi millivolt) for

  • r data in da

datasource: si sig.a .append(data) rec rec.c .close() sig sig = = re repo.ge get_signal(‘ht http://ex example.org/recording/test/signal/a1’) print print si sig.ur uri, , si sig.l .label, si sig.u .units start = 0.0 start = 0.0 end = 10.0 end = 10.0 duration = 1.0 duration = 1.0 while start < end: while start < end: interval = interval = si sig.r .recording.interval(start, duration) for data in for data in si sig.r .read(interval): print data # print data # Si SignalSegment st start += duration

  • Python code:
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BioSignalML clients

  • CellML modelling:
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$ ./bwfilter http://devel.biosignalml.org/recording/physiobank/nifecgdb/ecgca102/signal/3

BioSignalML clients

  • CellML modelling:
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Ongoing work

  • Interfacing with simulation tools (OpenCOR,

SED/ML) – real world applications.

  • Adding a Semantic Web layer to PhysioBank.
  • Integrate Units of Measurement Expressions:

– http://www.sbpax.org/uome/index.html – Ontology to derive units from other units. – An extensible way to automate units validation and conversion.

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Thank you