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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.

  1. BioSignalML Putting biosignals onto the Semantic Web David Brooks

  2. Background • Biosignal -- time series data resulting from a biological process.

  3. 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.

  4. 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, …

  5. 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.

  6. Background • A lot of file formats: – manufacturer; research; regulatory; … BDF 24 bit version of EDF EDF European Data Format EDF+ European Data Format plus FDAXML FDA standard for ECG GDF General Data Format (an EDF derivative) MFER Medical waveform Format Encoding Rules (ISO) SCP Standard Communication Protocol for ECG (CEN) WFDB WaveForm DataBase

  7. Background • A lot of file formats: – manufacturer; research; regulatory; … BDF 24 bit version of EDF • Often developed for a EDF European Data Format specific problem domain. EDF+ European Data Format plus FDAXML FDA standard for ECG GDF General Data Format (an EDF derivative) MFER Medical waveform Format Encoding Rules (ISO) SCP Standard Communication Protocol for ECG (CEN) WFDB WaveForm DataBase

  8. Background • A lot of file formats: – manufacturer; research; regulatory; … BDF 24 bit version of EDF • Often developed for a EDF European Data Format specific problem domain. EDF+ European Data Format • All generally good at plus storing time series data. FDAXML FDA standard for ECG GDF General Data Format (an EDF derivative) MFER Medical waveform Format Encoding Rules (ISO) SCP Standard Communication Protocol for ECG (CEN) WFDB WaveForm DataBase

  9. Background • A lot of file formats: – manufacturer; research; regulatory; … BDF 24 bit version of EDF • Often developed for a EDF European Data Format specific problem domain. EDF+ European Data Format • All generally good at plus storing time series data. FDAXML FDA standard for ECG GDF General Data Format (an • Metadata format is file EDF derivative) specific. MFER Medical waveform Format Encoding Rules (ISO) SCP Standard Communication Protocol for ECG (CEN) WFDB WaveForm DataBase

  10. Background • A lot of file formats: – manufacturer; research; regulatory; … BDF 24 bit version of EDF • Often developed for a EDF European Data Format specific problem domain. EDF+ European Data Format • All generally good at plus storing time series data. FDAXML FDA standard for ECG GDF General Data Format (an • Metadata format is file EDF derivative) specific. MFER Medical waveform Format Encoding Rules • Metadata content tends to (ISO) be domain specific. SCP Standard Communication Protocol for ECG (CEN) WFDB WaveForm DataBase

  11. Difficulties • Polysomnography: – “Currently, digital data from most PSG systems can only 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.

  12. Difficulties • Polysomnography: – “Currently, digital data from most PSG systems can only 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.

  13. Difficulties • Polysomnography: – “Currently, digital data from most PSG systems can only 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: µ V, 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.

  14. Semantic Web • Web content that is meaningful to computers. – Knowledge representation, ontologies, reasoning, intelligent agents, …

  15. Semantic Web • 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, …

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

  17. BioSignalML • Abstract common elements of storage formats.

  18. BioSignalML • Abstract common elements of storage formats. • Use Semantic Web standards/technologies. – Objects have web identifiers. – Ontologies define terms, properties, relationships.

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

  20. BioSignalML as RDF • Core concepts: – Recordings – Signals – Events and Annotations.

  21. BioSignalML as RDF • Core concepts: – Recordings – Signals – Events and Annotations. • RDF graph:

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

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

  24. BioSignalML implementation • Biosignal repository: Abstraction Layer Python API Signal Recordings Metadata WFDB HDF5 EDF Triple Store

  25. BioSignalML implementation • Biosignal repository: • Web based with HTTP Internet Web endpoints: Browsers – File import/export – RDF metadata RDF HTML Raw Files Stream – Data streamed via RESTful Web Services web-sockets. Abstraction Layer Python API Signal Recordings Metadata WFDB HDF5 EDF Triple SPARQL Query Store

  26. BioSignalML implementation • Biosignal repository: • Web based with HTTP Applications Internet Web endpoints: and Tools Browsers – File import/export – RDF metadata RDF HTML Raw Files Stream – Data streamed via RESTful Web Services web-sockets. • C client (plus Python, Abstraction Layer Python Javascript, …) API Signal Recordings Metadata WFDB HDF5 EDF Triple SPARQL Query Store

  27. BioSignalML clients • Web browser:

  28. BioSignalML clients • Web browser: • RDF browser:

  29. BioSignalML clients • Python code: import bi import biosignalml import bi import 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 or data in da datasource: si sig.a .append(data) rec.c rec .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

  30. BioSignalML clients • CellML modelling:

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

  32. 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.

  33. Thank you

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