Application of Extensible Markup Language (XML) in Medical

Research

A Bibliometrical Analysis

Thomas Ostermann, Christa Raak and Marc Malik

Institute of Integrative Medicine, Witten/Herdecke University, Gerhard-Kienle-Weg 4, Herdecke, Germany

Keywords: Extensible Markup Language, Semantic Web, XML, Bibliometric Analysis.

Abstract: One of the most innovative web standards is the Extensible Markup Language (XML) which allows

structured data storage and exchange and the creation of user defined tags for semantic processing. This

bibliometrical analysis aims at describing the application of XML in medical research. Medline/PubMed

was searched for relevant publications from 1997 to 2010 using the search term “XML” in all fields. All

articles were bibliometrically analysed with respect to their year of publication, language, keywords,

MESH-Headings, Impact factor, number of authors, number of pages. We found a total of 932 articles on

XML from 1998 to 2010 mostly published in English (n=891; 95.6%). The mean impact factor was 1.93 

2.75 and increased from 1.78  3.09 before 2005 to 2.12  2.29 after 2005. Analysis of MESH headings led

to the conclusion that XML predominantly is used in lab research while clinical and health services research

only plays a minor role. As a conclusion, publications on XML impressively show that XML has become a

standard for many software-tools and is more and more recognized in handling huge amounts of data.

Applications in the field of health informatics are reasonable to expect in the future.

1 INTRODUCTION

Already in the early years of information technology

in 1988, Gorry et al. pointed out that “the technical

complexities of biomedical research almost always

demand group effort”. They also state that “groups

that wish to prosper must continually improve their

effectiveness, perhaps through the use of advanced

information technology.” (Gorry et al., 1988). They

proposed the development of a “virtual notebook”

which incorporates information resources like

MEDLINE “with user-specified rules and stored in

designated hypertext structures”. Almost at the same

time Sengupta discussed “issues of heterogeneity in

computer systems networks, databases and

presentation techniques, and the problems it creates

in developing integrated medical information

systems” (Sengupta, 1989). Both authors

recommend the development of a comprehensive

strategy to solve these problems by means of

intelligent information-sharing systems.

Up to the early 1990s, the Internet was mainly

used by academic or military institutions for

communication and file transferring when in 1993

providers were permitted to sell internet connections

to individuals. This changed the complete situation

and masses of users went “online” (Doyle et al.,

1996) and a variety of applications like internet

access for community hospital libraries (Rambo &

Fuller, 1993) or web based protein databases

(Lemkin et al., 1995) were suggested. From that

point the internet evolved dramatically and

Hypertext Transfer Protocol (HTTP V1.0) alongside

with Hyper Text Markup Language (HTML V2.0)

as the main markup language for web pages together

with web browsers were invented and applied i.e. to

“open new possibilities for electronic publishing and

electronic journals” (Pallen, 1995).

Parallel to this development the first Working

Draft of an Extensible Markup Language (XML)

specification was published and in 1998 XML 1.0

was recommended by the World Wide Web

Consortium (W3C) (Treese, 1998).

XML documents according to the W3C “are

made up of storage units called entities, which

contain either parsed or unparsed data. Parsed data is

made up of characters, some of which form

character data, and some of which form markup.

Markup encodes a description of the document's

storage layout and logical structure. XML provides a

mechanism to impose constraints on the storage

layout and logical structure” (Bray et al., 1997).

478

Ostermann T., Raak C. and Malik M..

Application of Extensible Markup Language (XML) in Medical Research - A Bibliometrical Analysis.

DOI: 10.5220/0004911804780483

In Proceedings of the International Conference on Health Informatics (HEALTHINF-2014), pages 478-483

ISBN: 978-989-758-010-9

 2014 SCITEPRESS (Science and Technology Publications, Lda.)

Thus, XML can be used to unite structural properties

of databases, web requirements and the demands of

end users. This is mainly done by using eXtensible

Style sheet Language Transformations (XSLT)

which includes XML oriented vocabulary for

specifying the output format of XML. Therefore

XML is often attributed as a main standard in

semantic web technology (Robu et al., 2006).

Furthermore the use of the unicode standard enables

xml documents not only to be machine- but also

human-readable (Bray et al., 2008).

Today a huge variety of XML-based applications

like RSS, SOAP have been developed and XML-

based formats have become the standard for many

software-tools like open office. In the context of

medical research, XML applications are applied in a

variety of fields ranging from lab research to

application in health services research. But also web

applications in the field of health information

libraries like semantic bibliographic search engines

make use of the potentials of XML (Ostermann et

al., 2009).

Up to now, information about these applications

has not been analysed systematically. Thus, there is

a basic need to give a bibliometric overview on the

application of XML in medical research. This article

aims at giving such an overview by analysing

articles on XML in journals listed in MEDLINE.

2 MATERIAL AND METHODS

In March 2011 Medline/PubMed was searched for

articles about XML from 1999 until 2010. To get the

broadest possible overview only “XML” was

entered as a search term for all fields. Basic

bibliometrical data from the articles found this way

was directly downloaded from PubMed by using the

csv-download option. This file included PMID,

Title, Authors, Journal, Year, language, and length

of the paper. If available official impact factors were

retrieved from the yearly Journal Citation Reports

and mapped to this data. Finally, MeSH descriptors

from the articles as well as its origin were extracted

from an xml-download and transformed and also

added to the csv-extraction sheet.

Bibliometrical analysis was performed for the

complete dataset and subdivided for the publication

year using publication year’s median as the splitting

cut point. Nominal variables were analyzed using

cross tabulations and Chi-Square-Test statistics

while metrical data was described in terms of Mean

 Std.-Dev. and Median and rank test statistics. All

statistical analyses were carried out using SPSS

Version 19.

3 RESULTS

PubMed search found a total of 923 bibliographical

records from 1999 to 2010. While at the beginning

articles on XML were seldom (1999: 24 articles,

2000: 47 articles) a first peak was reached in 2003

with 102 articles. After a decrease in 2004 with only

85 articles the highest number of articles in Medline

was obtained in 2005 with a total of 109 articles.

From 2005 publication activity decreased again to a

local minimum in 2008 with only 76 articles, which

finally went up to 86 publications in 2010. With

respect to their origin, the majority of publications

came from Europe (n=440; 47.7%) closely followed

by American publications (n=337; 36.5%), while

publications from Asia (n=125; 13.5%) and

Australia (n=21; 2.3%) only play a minor role. No

publications came from Africa. In more detail, the

majority of publications was published by US-

American research groups (n=301; 32.6%, followed

by Germany (n=116;12.6%) the UK (n=102;11.1%),

France (n=49; 5.3%) and Japan (n=47; 5.1%). A

closer look at the chronological development of

percentages reveals that in the early years, American

publications ranged first but after 2000 declined and

only managed to be above Europe in 2007 (Figure

1).

Europe

10 19 34 35 48 44 43 50 36 38 41 42

Americ a

12 23 18 24 42 29 42 29 40 26 31 21

Asia

2 5 6 5 10 9 20 16 16 9 7 20

Aus tralia

000023412333

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

Figure 1: Number of publications on XML subdivided by

their origin and year of publication.

The median number of authors in all years ranged

between 3 and 4 and the number of descriptors

(keywords) ranged between 5 and 8. Number of

pages increased within the course of time from a

median of 6 before 2005 to 7.5 after 2005 (p<0.001;

Mann Whitney U-Test, Table 1).

Even more important than authors and page

numbers is the development of the impact factor and

the fields of research of publications on XML.

ApplicationofExtensibleMarkupLanguage(XML)inMedicalResearch-ABibliometricalAnalysis

479

Table 1: Sample description.

 2005

> 2005 Total

# of articles

Mean per year

489

434

923

# of authors

Mean

Median

4.3  3.2

5.0  3.7

4.6  3.5

# of pages

Mean

Median

7.0  4.3

8.2  4.5

7.5

7.6  4.5

Origin

Asia

Europe

Australia

233 (47%)

190 (39%)

57 (12%)

9 ( 2%)

207 (47%)

147 (34%)

68 (16%)

12 ( 3%)

440 (47%)

337 (36%)

125 (14%)

21 ( 2%)

Language

English

Others

477 (98%)

12 ( 2%)

405 (93%)

29 ( 7%)

882 (96%)

41 ( 4%)

Impact factor

Mean

Median

% IF-Journals

1.8  3.1

47%

2.1  2.3

1.46

59%

1.9  2.8

0.69

53%

# descriptors

Mean

Median

7.6  3.9

6.9  4.1

7.3  4.0

Impact factor (IF) increased from a mean of 0.8

in 1999 to a mean of 2.65 in 2004 and decreased

again until 2008 where IF reached the maximum of

3.1 (both mean and median) but then decreased

again. Compared to the time before 2005 IF has

significantly increased from 1.8  3.1 to 2.1  2.3

after 2005. One reason for this development is

reflected by the percentage of journals with impact

factor which significantly (p<0.001; Chi-Square-

Test) increased from 47.0% before 2005 to 58.8%

after 2005. Figure 2 shows this development in more

detail.

A more detailed analysis with respect to the

origin of the papers also reveals that there is a small

but significant difference between publications from

Europe (Mean IF=2.00  2.76) and America (IF 2.12

 2.94), which is also reflected in the course of time

(Table 2).

Again US-American publications on XML

cumulated the highest impact (300 publication with

a IF-sum of 626.47).

With the highest IF-mean per publication of 3.52

the UK cumulates to a total sum of 359.23 IF-points

from 102 articles. Only Canada has a comparable IF-

mean with 2.82 from 31 publications, while

Germany only adds 159.62 IF-points from 116

publications and Japan adds 96.72 points out of 47

publications. A more detailed analysis of the

journals XML-articles were published in reveals that

Figure 2: Boxplots of the development of Impact factor of

XML-publications within the course of time.

Table 2: Development of Impact factor subdivided by

origin and year of publication.

Europe America

Year

IF (MSD)

1999 10

1.29  2.81

0.53  0.88

2000 19

0.32  1.24

0.63  1.27

2001 34

1.08  1.43

0.92  1.68

2002 35

1.37  2.14

2.03  2.37

2003 48

2.35  5.14

2.00  2.61

2004 44

2.36  2.91

3.69  4.50

2005 43

1.96  2.48

2.78  4.23

2006 50

2.25  2.21

1.73  2.31

2007 36

1.63  2.15

2.07  2.62

2008 38

3.24  2.07

3.19  2.61

2009 41

2.36  2.44

2.22  2.41

2010 42

2.05  2.08

1.67  2.31

Total

440

2.00  2.76

337

2.12  2.94

four from the Top-10 Journals covering 254 articles

did not have an Impact factor at the time of

publication (Table 3).

In particular, the journal “Studies in health

HEALTHINF2014-InternationalConferenceonHealthInformatics

480

Table 3: Top-20 list of journals with XML-publications

and their Impact factor.

Rank Journal

N % IF Sum

Stud Health Technol

Inform

135 14.6 0.00

Bioinformatics 83 9.0 443.21

AMIA Annu Symp Proc 60 6.5 0.00

BMC Bioinformatics 52 5.6 187.74

Nucleic Acids Res 51 5.5 355.05

Int J Med Inform 33 3.6 54.82

Proc AMIA Symp 33 3.6 0.00

Conf Proc IEEE Eng Med

Biol Soc

26 2.8 0.00

Comput Methods

Programs Biomed

19 2.1 15.52

J Am Med Inform Assoc 19 2.1 50.65

BMC Med Inform Decis

Mak

14 1.5 8.59

J Med Syst 14 1.5 6.38

J Digit Imaging 13 1.4 13.46

Methods Inf Med 13 1.4 15.43

IEEE Trans Inf Technol

Biomed

11 1.2 16.02

Proteomics 11 1.2 53.48

J Chem Inf Model 10 1.1 33.77

Brief Bioinform 7 0.8 16.58

J Med Internet Res 7 0.8 3.59

Med Inform Internet Med 7 0.8 8.47

Total

618 67.0 1282.76

technology and informatics” ranks first in 7 of 12

years. Other journals however from the field of

Medical and Bioinformatics with mean impact

factors greater that three do however compensate

this resulting in a mean IF of 2.08 in the Top-20 list

of journals.

4 CONCLUSIONS

This articles aimed at summarizing the development

of publications on XML in the medical literature

from 1999-2010. Based on our findings the main

period of visibility and productivity can be identified

in the year 2004. At that time the second edition of

XML 1.1 was initially published (Bray et al., 1997).

While XML 1.1 is not widely implemented, XML

1.0 has been developed further to its fifth edition

which came out in 2008 (Bray et al., 2008). This

year denotes the second high peak in publications

and Impact factors. Although versions of XML have

changed in the course of time, its applications are

still given in knowledge transfer in the life science

(Murray-Rust, 2000) and the creation of interfaces

for related web-based information systems (Badard

and Richard, 2001). The application of XML in

Materials and Hospital Management however only

plays a minor role although Katehakis et al. (2001)

quite early have pointed out the importance of XML

for health services research: “XML provides the

appropriate technology and makes up the most

convenient vehicle towards a common format for

delivering and presenting information content.

Elaboration of the standard DTD logical structure

and related XML infrastructure will make

information personalization flexible and generic

enough to adapt to various types of users and client

devices.” In particular with the upcoming research in

individualized and personalized medicine at that

time (Ginsburg and McCarthy, 2001) XML has

managed to become a standard in clinical laboratory

procedures (Saadawi and Harrison, 2003) but its

way into patient care still seems to be far behind the

possibilities XML is offering: XML-based electronic

medical records may i.e. be used to extract

experiential clinical knowledge. Abidi & Manickam

(2002) proposed “an automated approach to generate

cases for medical case-based reasoning systems”

using XML.

Another field of application is the development

of XML-based search engines. Finding information

in the World-Wide Web is still a crucial matter in

clinical and health services research. Already in the

beginning of XML Butler reported on sophisticated

and specialized search technologies like natural

language processing to assist researchers in finding

information. Meanwhile several XML-based search

engines and tools have been developed in a variety

of fields like Complementary Medicine (Ostermann

et al., 2004), E-Health documents (Gaudinat, 2006),

Proteins and Protenomics (Keller et al., 2005).

Moreover the bibliometric analysis on XML

publications also shows a widespread use of this

technology all over the world. More than 44 nations

including Saskatchewan, Jamaica, Ecuador and

Malaysia underpin the international importance

XML has gained since 1999. However, most of the

publications origin from the main player nations in

the field of information technology namely the US,

Germany and the UK.

ApplicationofExtensibleMarkupLanguage(XML)inMedicalResearch-ABibliometricalAnalysis

481

As a limitation of this review, it has to be noted

that it only focusses on XML as one of many

concepts of the semantic web. Apart from XML

many data representation and communication

standards have been developed in the last two

decades. One of the most important standards is

given by Resource Description Frameworks (RDF).

While XML is a document format for writing and

exchanging information on the Web RDF is a model

for describing semantics and reasoning about

information on the Web (Patel-Schneider & Siméon,

2002).

Already two year earlier than Patel-Schneider

and Siméon, Decker et al. argued that semantic

interoperability should be achieved by exploiting

RDF as a metadata data model (Decker et al., 2000).

Some authors even argue that RDF will be the

universal exchange language of future healthcare

due to its self-describing structure which is easy to

generate (Booth et al., 2013). Moreover RDF might

be more powerful in “large-scale information

integration and vocabulary evolution problems”.

Although the argumentation is straight and RDF

gains more and more attention, it must be noted that

articles on RDF in contrast to XML are quite rare.

Thus, we decided to focus on XML for this current

review which does not imply a voting for XML as a

solitary standard of the semantic web.

Future development according to a recent

position paper of Baclawski & Schneider (2009), is

going to develop information infrastructures based

on Open Ontology Repositories (OOR) combining

existing ontologies with innovative information

technology architectures and standards. XML in this

vision is one but not the only leading standards that

may foster collaborative administration of

knowledge and metadata.

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