A markup language for electrocardiogram data acquisition and analysis (ecgML).

BACKGROUND: The storage and distribution of electrocardiogram data is based on different formats. There is a need to promote the development of standards for their exchange and analysis. Such models should be platform-/ system- and application-independent, flexible and open to every member of the scientific community.
METHODS: A minimum set of information for the representation and storage of electrocardiogram signals has been synthesised from existing recommendations. This specification is encoded into an XML-vocabulary. The model may aid in a flexible exchange and analysis of electrocardiogram information.
RESULTS: Based on advantages of XML technologies, ecgML has the ability to present a system-, application- and format-independent solution for representation and exchange of electrocardiogram data. The distinction between the proposal developed by the U.S Food and Drug Administration and ecgML model is given. A series of tools, which aim to facilitate ecgML-based applications, are presented.
CONCLUSIONS: The models proposed here can facilitate the generation of a data format, which opens ways for better and clearer interpretation by both humans and machines. Its structured and transparent organisation will allow researchers to expand and test its capabilities in different application domains. The specification and programs for this protocol are publicly available.

Background

Electrocardiogram (ECG) data are acquired, stored and analysed using different formats and software platforms. Medical informatics will fully exploit the benefits from its research only when data can be openly shared and interpreted. Therefore, there is a need to develop cross-platform solutions to support biomedical training, decision-making and telemedicine applications [1].

An important goal is to describe these data independently on the number of channels, instrumentation platform or type of experiments. Moreover, an ECG record should also include annotations relating to the acquisition protocols, patient information and analysis results. These data modelling tasks should consist of flexible and inexpensive tools to enhance pattern recognition capabilities.

The development of these systems will depend on the existence of information that clearly specifies domain terminologies, functional hierarchies and decision rules. The availability of such ontological representations [2] will allow the emergence of standards, which will facilitate the integration of information on a global communication infrastructure.

ECG data have been traditionally recorded using flat file formats, such as the MIT-BIH file library [3]. This type of data format lacks the information necessary to support a meaningful analysis, interoperability and integration of multiple resources. Different governmental, academic and private organisations have proposed minimum requirements for the representation and storage of biomedical information, including signals and images [4]. These efforts aimed to promote the application of standards for message exchange and data integration. In 1993, for example, the CEN/TC251 WG3 (Comité Européen de Normalisation European, Committee for Standardisation, Technical Committee 251) reviewed several data exchange formats for healthcare applications. It includes Abstract Syntax Notation (ASN.1) and Health Level Seven (HL7) [5]. The former defines norms to describe an electronic message based on different data types. One of the disadvantages of ASN.1 is that it does not fully support scalable solutions and query processing. HL7 has been a Standards Development Organisation affiliated to the ANSI (American National Standards Organisation) since 1997 and has become the standard for electronic exchange of historical and administrative data in health services worldwide. The next generation of the messaging standard (V3) has been under development since.

CORBAmed, the Healthcare Domain Task Force of the Object Management Group (OMG) [6], deals with interoperability problems between heterogeneous information systems. To facilitate the seamless and automated data exchange between numerous applications, a common interface architecture was developed that serves in a number of today's information systems. Liaisons have been established with other organisations such as HL7.

The Digital Imaging and Communications in Medicine (DICOM) standards committee supports the achievement of data compatibility between imaging systems and other healthcare information at different levels. This standard has been applied by many private organisations, which need to incorporate diverse bio-signals associated to medical imaging. The DICOM standard is a useful resource that also provides guidelines on how to represent ECG features [4].

More recently, the eXtensible Markup Language (XML) [7] has been suggested as a promising approach to representing biomedical data. Developed as a subset of SGML in 1996 to "be straightforwardly usable over the Internet" and published as a first recommendation by the W3C (World Wide Web Consortium) in 1998, XML soon became a ubiquitous syntax for data and data-exchange over the Internet. Since then, XML-based Markup Languages, specified as e.g. Document Type Definitions (DTD) or XML Schemas (XSD) have been emerging in unlimited numbers and in nearly every imaginable domain [8]. Advantages of XML syntax include platform-, vendor- and application independence as well as an easy-to-follow hierarchical data structure and wide support. "XML's greatest advantage is that it is a user-driven, open standard for exchanging data both over corporate networks and between different enterprises, notably over the Internet. XML's biggest potential lies undoubtedly in its ability to mark up mission-critical document elements self-descriptively" [9]. By following a strict separation of content and presentation information, XML technologies increase the re-usability of information in its purest way as access to the original (raw) data is always given. The use of XML syntax for the exchange of electronic patient records was shown in all aspects in Synapses [10] and SynEx [11] project implementations [12-14].

The U.S Food and Drug Administration (FDA) Centre for Drug Evaluation and Research has proposed recommendations for the exchange of time-series data. It includes a hierarchical structure for the representation of signals, including ECG data, which may be encoded as an XML file. This protocol focuses on the acquisition of multiple records from different subjects within a single file [15,16]. The HL7 committee has been actively cooperating with the World Wide Web Consortium (W3C) to define XML guidelines to represent medical information [17]. HL7 has endorsed the Clinical Document Architecture (CDA), which supports the generation and exchange of clinical messages [18]. Other XML-based initiatives for the representation and distribution of biomedical information are: The ASTM E31.25 subcommittee [19], the CEN/TC251 Task Force on XML Applications in Healthcare [20] and the Clinical Data Interchange Standards Consortium (CDISC) [21]. However, these efforts have not focused on ECG data. Some of them place a greater emphasis on the administrative and financial transactions associated with a clinical environment.

Recent advances include I-Med, which is an XML-based format for clinical data [22]. This project consists of a domain-independent interface for exchanging several types of medical information. Its major goal is to provide a unique platform for clinical transactions. These messages can include ECG records, which may be described by basic features, such as QRS duration and text-based interpretations. One major limitation of this solution is that it partially addresses important ECG data content-definitions.

This article introduces a markup language for supporting ECG data exchange and analysis (ecgML). It synthesises key recommendations specified by the initiatives presented above.

Methods

There is a need to harmonise the representation of digital ECG data originating from the full spectrum of devices along with annotations for events, and to include necessary associated information, such as patient identification, interpretation and other clinical data. The hierarchical data tree structures depicted in Figures 1 to 6 are proposed to address such concerns. Tables 1 to 8 describe the elements and attributes defined in this model. In this paper terms written in bold and italic prints represent either XML element or attribute names. Element names should be words concatenated with the first letter of each word capitalised (UpperCamelCase, ). Attribute names satisfy the same rule except for the first word (lowerCamelCase, ).

Figure 1

The tree diagram of ecgML: ECGRecord element

Figure 6

The tree diagram of ecgML: Annotations element

Table 1

The description of ecgML: ECGRecord element

ECGRecord	The root element for XML-based ECG record
Element/attribute	Description/Origin	Required	Values/Data Type	Example
studyID	Unique ID for an ECG record.	Required	string	ECG000001
StudyDate	Study date. To be expressed as YYYY-MM-DD.	Required	date	2002-10-22
StudyTime	Study time. To be expressed as HH:MM:SS.SSS	Required	time	12:01:00
Comment	Comments about the ECG Record	Optional	string	Subject under stress 1 hour after dose.
PatientDemographics	Describes patient demographics	Required	See Table 2
Record	The details for ECG data.	Required	See Table 3
MedicalHistory	Description of the patient's clinical problems and diagnoses.	Optional	string	Ventricular ectopy
Diagnosis	For the latest diagnostic interpretation of the ECG.	Optional	string	Myocardial infarction

Table 8

The description of ecgML: Annotations element

Annotations	Annotations for each ECG record. Based on FDA XML Data Format Specification (revision C).
Element/attribute	Description/Origin	Required	Values/Data Type	Example
PointNotation	A set of fiducial points with an X and Y position.
PointLabel	Name of the fiducial points.	Required	Based on DICOM waveform list	R peak
XValue	X position of notation. To be expressed as HH:MM:SS.SSS	Required	time or samples	00:27:01
YValue	Y position in mV of notation	Optional	float	0.3
Comment	Comment about the point notation	Optional	string	Paced beat
WaveNotation	Annotations for interval measurements.
Pwave	The annotations of P wave (onset, offset, peak, annotation, comment)	Optional	See Table 9	Normal
QRSwave	The annotations of QRS wave (onset, offset, peak, annotation, comment)	Required	See Table 9	PVC
Twave	The features of T wave (onset, offset, peak, annotation, comment)	Optional	See Table 9	inverted
Uwave	The annotations of U wave (onset, offset, peak, annotation, comment)	Optional	See Table 9	Normal
OtherWave	The annotations for other duration (onset, offset, peak, annotation, comment).	Optional	See Table 9

The tree diagram of ecgML: Record element

The tree diagram of ecgML: ClinicalProtocol element

The tree diagram of ecgML: RecordData element

The tree diagram of ecgML: Waveforms element

Each patient record starts with a root element , which is uniquely identified by its attribute . The and elements represent the latest time record of the study of the ECG recording. contains a text version of the latest diagnostic interpretation of the ECG, while is a description of medical history of patient's clinical problems and disgnoses. There are two main components for each record: one and one or more components. It is worth noting that each record can have only one element, which would be kept updated all the time; while multiple elements are allowed to be held in one patient record. This opens up every opportunity to keep track of the history of the patient's diagnoses.

contains information of general interest concerning the person from whom the recording is obtained, such as demographic data (e.g. , , etc.) and contact information (e.g. , etc.). This component is required in each record.

represents the physical storage for the basic content of an ECG recording. The and attributes specify the acquisition date and time for each record, which makes it possible to include multiple time-related ECG recordings within a file. and are used to identify who is responsible for the recording and where it is acquired. There are three main components: zero-or-one , zero-or-one , and one-or-more . Such flexible structure allows each recording to have its own characteristics.

is an optional element, which describes the device that generated the data. It should support the full spectrum of ECG devices, including standard 12-lead ECGs, Holter monitors, transtelephonic monitors and implanted devices. The main components in this section include , , , and a description of filtering technique used during the ECG acquisition (e.g. and ).

is an optional element, which may include information relating to a patient's clinical report. The attribute of each element is used to describe the measurement unit of each observation. Currently, this section only includes basic clinical dimensions, such as and . However, other variables can be easily added.

is a key ecgML element. There can be multiple elements within a file, which are identified by their element names. The DICOM lead labelling format is recommended for this purpose. includes three main sub-components: , and .

Based on the FDA-recommended PlotGroup format [16], are represented by a series of values along two dimensions X, Y (and ). Based on these values, a plot of voltage vs. time may be generated with a viewer program. The (time) are evenly spaced. represents the initial value. represents the sampling frequency measured in Hz. The duration of a channel signal is represented by the element . ecgML supports three formats to represent : a element, a element (associated with a specified scheme, which may be base64 or hexadecimal), and a to refer to an external file.

The elements and , which are encoded into the elements and , illustrate the beginning and ending values of the corresponding waveform. The associated with indicates how to convert the binary into real values. The element in contains a list of float data separated by delimiters, representing the real value of each sample ECG data.

would typically be used to describe events specific to the corresponding channel. It defines a time point or interval, which can be used for performing the measurements. This consists of a collection of and elements. Each can be specified with a (the name of the specific point, e.g. P wave onset), a (time, expressed as HH:MM:SS.SSS format), (amplitude in mV) and any relevant comment. includes descriptions for basic ECG waves, such as , , , , and other events that can be defined by the user (). Wave descriptions are based on the following five elements: (the beginning value), (the peak value, for a T wave, it is possible to have two values), (the ending value), (annotation for the specified wave, such as "normal" or "abnormal"), and any comments on the annotation are given using the element. The value of , , and can be expressed as either time or sample values.

The element contains a list of (the measurements of each recorded channel). Each element may be associated with a and a measurement .

There are different levels at which a record can define supplementary information. A at the level can be used to indicate additional acquisition information, for example, place and technical conditions of the acquisition process. A at the level may typically be used to define the format of the representation of the , e.g. which delimiter is used. A at the level may be used to describe, for example, whether a measurement is a global average or an instantaneous value.

This research applies the DICOM recommendation for defining ECG channel names, fiducial point markers and waveform encoding details. Moreover, it applies the Unified Code for Units of Measure (UCUM) scheme for defining measurement units, such as cm for and mV for [24] when appropriate.

This specification has been encoded into an XML-based data protocol. Additional files 1 and 2 are the DTD and XSD files for ecgML respectively. Additional file 3 is an ECG record, which has been generated using ecgML.

Results

Evaluation of the model

It is fundamental to demonstrate the system-, application- and format-independence of ECG data when using ecgML. Special importance should be given to illustrate the autonomy of content from its presentational scheme, e.g. printed graphs, tabular data to be imported into data mining systems for further analysis or audio files. Figure 7 illustrates the distinction separation of the five important components in XML publishing. Based on advantages of XML technologies, ecgML exhibits a remarkable advantage over existing systems where every information system has its own internal information-model and information is merged and intertwined with its representation format. Figure 8 exemplifies a scenario where the raw ECG data is kept in an ecgML data file and therefore independently from possible presentation information. Various XSLT transformations (stored as XSL files and applied on the fly, transparent to the user) convert the ecgML source into user- and/or application-specific data formats, such as MPEG (audio), MatLab (text) and SVG/PNG (graphics). The centralised storage of the ECG record and dynamic creation of data representations avoids redundancy.

Figure 7

Publication Model

Figure 8

Dynamic transformation of ecgML data

The FDA, together with a number of other institutions, has developed and published an XML vocabulary [16] to represent collected time-series data. However, there are some significant differences between the FDA proposal and ecgML. The FDA proposal is intended to represent collected biological data, including ECG, electroencephalogram (EEG), or other time series data such as temperature, pressure and oxygen saturation. The main goal is to facilitate the submission of the biological data and to make sure that accuracy and consistency of the measurements made from the collected biological data is achieved. It is important for the FDA to view the biological data in an appropriate way. Thus, the data model (specified in a DTD) includes some presentation information, such as elements MinorTickInterval, MajorTickInterval and LogScale. On the other hand, the purpose of ecgMLis to develop anopen and transparent way of representing, exchanging and mining ECG data. Therefore, ecgML not only consists of basic components, which may be used to perform knowledge discovery in ECG data (e.g. , and ) but also follows the principle of separating content and presentation information, which will exhibit great advantages when using ecgML in combination with inter-media transformation.

Accompanying tools

A series of tools are being developed to assist users in exploiting ecgML-based applications. These include an XML-based ECG record generator, ECG parser and ECG viewer. The generator will automatically produce XML-based ECG records from existing ECG databases, e.g. the MIT-BIH database [3]. The ECG parser allows the user reading the ECG records and access their contents and structure, whereas the ECG viewer provides onscreen display of the required waveform data (Figure 9). It shows all annotation information of the individual waveform. The hierarchical structure of the XML-based ECG record is displayed. It can be expanded and shrunk at any level. This interface can also show individual episodes of the ECG waveform chosen from the ecgML structure. The viewer tool graphically locates boundaries (i.e. beginning, peak, and end) of the P, QRS and T waveforms for each selected QRS complex.

Figure 9

Screenshot of ECG viewer

Conclusions

ecgML will enable the seamless integration of ECG data into electronic patient records (EPRs) and medical guidelines. This protocol can support data exchange between different ECG acquisition and visualisation devices. Similarly, it may enable data mining using heterogeneous software platforms and applications. The data and metadata contained in an ecgML record may be useful to improve pattern recognition in ECG applications. It would also aid the implementation of automated decision support models such as case-based reasoning. Figure 10 illustrates the utilisation of map files to convert "raw" ecgML files into customised output formats, which will be imported into data mining systems for further analysis. ecgML may also be significant for problems such as future proof storage, context-sensitive (textual) search of patterns in ECG data, and its native inclusion into medical guidelines. Further research will address the following issues.

Figure 10

Converting XML-based ECG record into tabular data using map files. Notations for all tree diagrams are illustrated as follows. Lines of descriptive text outside an element box indicate attributes that the element should have. Default value is shown underlined.

• How does ecgML affect storage capacity?

• Does on-the-fly compression (as used by HTTP 1.1) make a difference in terms of transmission speed?

• Is it feasible to use ecgML in applications such as 24 hour monitoring?

• Does ecgML data contain all the significant information required for ECG analysis?

Competing interests

None declared.

Authors' contributions

HW co-designed and implemented ecgML (DTD and XSD files), developed support tools and drafted the manuscript. FA conceived the study, participated in the design of the model and drafted the manuscript. BJ helped to refine ecgML, brought expertise in XML and EPRs, and help to draft the paper. NB participated in the coordination of this study and contributed to the preparation of this manuscript. All authors read and approved the final manuscript.

Pre-publication history

The pre-publication history for this paper can be accessed here:

Additional File 1

A DTD file for ecgML

Click here for file

Additional File 2

An XML schema for ecgML

Click here for file

Additional File 3

A sample file using ecgML

Click here for file

Table 2

The description of ecgML: PatientDemorgraphics element

PatientDemographics	Describes patient demographics
Element/attribute	Description/Origin	Required	Values/Data Type	Example
patientID	Patient Data (Based on SCP-ECG).	Optional	string	1532948
DOB		Optional	Date	1965-04-05
Sex		Optional	-Male -Female -Unknown -Unspecified	Male
Race		Optional	string	African
Phone	Phone number	Optional	string	00442890368197
Fax	Fax number	Optional	string	00440289036
Email	Email address	Optional	string	hy.wang@ulst.ac.uk
Address	Patient address. Based on HL7's PRA and I-Med recommendation
StreetAddress	Street address	Optional	string	24 Shore Road
State	State or province	Optional	string	N. Ireland
PostalCode	Zip or postal code	Optional	string	BT37 0QB
City	City name	Optional	string	Belfast
Country	Country name	Optional	string	UK
Name	Patient name. Based on IMed DTD
FirstName	Patient firstname	Optional	string	Frank
MiddleName	Patient middle name	Optional	string	J
LastName	Patient lastname	Optional	string	Smith

Table 3

The description of ecgML: Record element

Record	The element for the details of ECG data
Element/attribute	Description/Origin	Required	Values/Data Type	Example
investigatorID	A text description of the referring physician	Optional	string	Dr. John
siteID	A text description of the place where the ECG data was acquired.	Optional	string	Loyal Hosptial
AcquisitionDate	Acquisition date of the recording. To be expressed as YYYY-MM-DD	Optional	date	2002-10-20
AcquisitionTime	Acquisition time of the recording. To be expressed as HH:MM:SS.SSS	Optional	time	11:05:32.00
RecordingDevice	Description of the device that made the recording	Optional	See Table 4
ClinicalProtocol	Additional patient clinical information	Optional	See Table 5
RecordData	Ecg data for each channel.	Required	See Table 6

Table 4

The description of ecgML: RecordingDevice element

RecordingDevice	Description of the device that made the recording. Based on FDA XML Data Format Specification (revision C) and SCP-ECG.
Element/attribute	Description/Origin	Required	Values/Data Type	Example
deviceID	ID number of recording device.	Optional	string	35
Type	Type of recording device.	Optional	string	12-lead ECG
Manufacturer	Manufacture of recording device.	Optional	string	GE Medical Systems
Model	Model of recording device.	Optional	string	MAC 500
SerialNumber	Serial number of recording device	Optional	string	023001236
BaselineFilter	High cut off in Hz. Based on SCP-ECG acquisition data.	Optional	float	0.5
LowpassFilter	Low cut off in Hz. Based on SCP-ECG acquisition data.	Optional	float	120
FilterBitMap	Other filters. Based on SCP-ECG acquisition data.	Optional	-60 Hz notch filter -50 Hz notch filter -Artifact filter -Baseline filter -Undefined	60 Hz notch filter

Table 5

The description of ecgML: ClinicalProtocol element

ClinicalProtocol	Additional patient clinical information
Element/attribute	Description/Origin	Required	Values/Data Type	Example
DiastolicBP	Diastolic blood pressure in mmHg. Based on SCP-ECG patient data.	Optional	unsignedInt	72
SystolicBP	Systolic blood pressure in mmHg. Based on SCP-ECG patient data.	Optional	unsignedInt	120
HeartRate	Heart rate in BPM.	Optional	unsignedInt	75
Height	Height in cm. Based on SCP-ECG patient data.	Optional	float	172
Weight	Weight in Kg. Based on SCP-ECG patient data.	Optional	float	120
Pale	Abnormal-looking skin on the face, or tongue	Optional	Yes/No	Yes
Sweaty	Abnormal reaction to heat	Optional	Yes/No	No
Smoker	Smoking?	Optional	string	A pack
Alcohol	Drinking alcohol	Optional	string	seldom
Hypertension	A disorder characterised by high blood pressure	Optional	Unknown/Yes/No	Yes
Diabetes	A disease marked by elevated levels of sugar in the blood.	Optional	Yes/No	No
OtherProtocol	Other clinical symptom	Optional	string	SOB(short of breath)
Medication	Drugs. Based on SCP-ECG drug information.	Optional	string	Digoxin

Table 6

The description of ecgML: RecordData element

RecordData	Ecg data for each channel
Element/attribute	Description/Origin	Required	Values/Data Type	Example
Channel	Lead identifier	Required	Base on DICOM lead labelling scheme	Lead I
Waveforms	A description of ECG waveform	Optional	See Table 6
Annotations	A collection of annotations	Optional	See Table 7
Measurements	A collection of each channel measurements	Optional	See Table 8

Table 7

The description of ecgML: Waveforms element

Waveforms	A 2-D plot with an X and Y axis is used to display the ECG waveform data. Refer to FDA XML Data Format Design Specification (revision C).
Element/attribute	Description/Origin	Required	Values/Data Type	Example
XValues	Describe the X-axis domain
XOffset	Offset from the StartTime.	Required	time	00:23:10
Duration	Duration of the each record.	Required	time	00:00:10
SampleRate	Sample rate in Hz for ECG records.	Required	unsignedInt	500
YValues	Describe the Y-axis domain.
unit	Name of base unit for Y-axis.	Required	Use UCUM when appropriate.	mV
FileLink	A reference to an external file storing ECG data.	Optional	string
RealValue	A list of actual value of ECG data
From	Offset from the origin of the x axis to the beginning of waveform	Required	time or samples	20:00:00
To	Offset from the origin of the x axis to the ending of waveform	Required	time or samples	21:00:04
Data	The list of Y values separated by white space	Required	A list of float values	1.25 2.23 3.2
Comment	Comments on the format, e.g. separated by a specific delimiter	Optional	string	separated by white spaces
Binary Data	Binary representation of ECG data
encoding	Encoding scheme for embedding the binary data within XML document	Required	Base64/Hexidecimal	Base64
From	Offset from the origin of the x axis to the beginning of waveform	Required	time or samples	00:00:00
To	Offset from the origin of the x axis to the ending of waveform	Required	time or samples	12:00:04
Scale	Scale factor to use to convert a binary data into a real value	Required	float	1.0
Data	Encoded binary ECG data	Required	string	A923B420

Table 9

The description of ecgML: Measurements element

Measurements	Measurements of each recorded lead
Element/attribute	Description/Origin	Required	Values/Data Type	Example
Values	The each measurement.	Required	float	20
label	Based on SCP-ECG the lead measurements.	Required	string	P-duration
unit	Name of base unit for the each measurement.	Required	Use UCUM when appropriate.	ms
Comment	Comments on a measurement.	Optional	string	normal

Table 10

The description of ecgML: subelements for elements Pwave, QRSwave, Twave, Uwave and OtherWave

Element/attribute	Description/Origin	Required	Values/Data Type	Example
Onset	Beginning value of the wave in time or samples	Required	Time/samples	00:00:12.000
Peak	Peak value of the wave in time or samples	Required	Time/samples	00:00:12.600
Offset	Ending value of the wave in time or samples	Required	Time/samples	00:00:13.002
Annotation	Annotation of the wave	Optional	string	Normal
Comment	Any comments on the annotation	Optional	string