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XML Technology - what is it ?

XML (Extensible Markup Language) is THE new format for exchange of information within the business world. Whereas until recently, exchange of information (whether it be data, documents, etc..) was plagued by the existence of thousands of differents formats, XML has in very short time become the "defacto" new standard for electronic information exchange. You may not realise it, but when you shop on the internet, use a search engine, or check all the possible train connections between Basel and Berlin, information streams are in XML.

Why has XML taken such a high flight in such a short time ? There are some simple reasons:

• XML is human readable. Take a look at the following XML-file and try to find out what it is about. You don't have to be an expert in pharmaceutics ! You do not need a special program to actually read the contents of the file.
• As you see the document is self-describing. The metadata (the data about the data) are included in the file, viz. in the tags (e.g. <Information_item>).
• XML is in Unicode. The Unicode characterset includes al the characters of almost all the written languages in the world. So you can have the same document in German, French or Italian, but also in Greek, Russian, Korean, Japanese or any other written language.
• XML is hierarchical data. This facilitates exchange of the information. For example a tools store can have its full inventory into one or more XML-files. If the shop owner has agreed on a (partial or complete) common data structure with his supplier (the tools factory), an XML file(s) can be used by the factory to supply enough tools just-in-time. The common data structure is usually implemented as a Document Type Definition (DTD) or as an XML-Schema.
• XML is machine-independend. Sick and tired of having trouble to exchange data between Windows, Unix and McIntosh ? XML is the answer.
• XML separates content from presentation. XML itself is purely content, whereas the content can be presented in several ways, e.g. in HTML, in WAP, in Word, in Excel, and even in PDF etc. The presentation is usually performed by using a stylesheet. One such a stylesheet can then be used to present different XML-files which have the same data structure.
• Results from SQL queries into databases can easily be converted to self-describing XML. See our goodies page for examples. XML files can also easily be stored into databases. The major database manufacturers even base their database technology on XML and Java.

When exchanging information, people can agree on the format. Unfortunately, thousands of formats exist. This misery is over when using XML. For many applications, it may be useful to agree on a common datastructure. Such a datastructure is described in either a DTD or in an XML-Schema. These describe how the data is organised and what its hierarchy is. We will here not go into technical details, but we can say that many communities have already agreed upon a common data structure. As such, many XML-extensions have seen the light in the recent years, e.g. MathML (Mathematical XML), CML (Chemical XML), BSML (Bioinformatics Sequence Markup Languegae), GEML (Gene Expression Markup Language), Real Estate Transaction Information XML, FpML (Financial products Markup Language), and many many others (see e.g. The XML Cover Pages). They all enable the exchange of information between members in a community (e.g. all the mathematicians in the world, all the real-estate brokers in the US, etc..

XML-Schema

The successor of DTD is XML-Schema. DTDs have several disadvantages:

• DTDs are not written in XML, which means that developers must learn to work with yet another technology and language
• Data typing in DTDs is weak. Essentially this means, that everything is declared as text, so for example, using a DTD you cannot define that the contents of the element <Patient_Number> should be a non-zero, positive number

But now there is XML-Schema, with the following advantages: Furthermore, XML-Schema has very strong datatyping: a large number of primitive data types have been defined in advance, ranging from integers, boolean to dates (ISO-format) to something like a "QName". A full list of the primitive datatypes can be found at the W3C website.

• XML-Schema is written ... in XML. This means that the same technology can be used for reading and processing an XML-Schema as for any other XML file.
  
• These datatypes can then further be restricted (e.g. one can state that the positive non-zero number should be between 10001 and 99999) or combined. Also one can use so-called "patterns": for example the datatype "DateTime" (of which 2003-01-03T09:23:58+06:00 is an example) can also be defined by the pattern:
  "[0-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](\.[0-9]+)?((\+|-)[0-2][0-9]:[0-5][0-9]"
• XML-Schemas can easily be transformed into Java Objects (Java classes), using a technology named "Java Architecture for XML Binding" (JAXB). This means that when reading an XML-Schema, it is possible to derive all the necessary Java classes (with the correct datatype !) automatically. Of course, this makes life easy for the application developer when developing software to work with XML data.

Examples of recent XML-Schemas for use in Life Sciences and Pharma are:

• CDISC-Lab XML-Schema. You can find the XML-Schema here
• XML-Signature, the new way of signing any electronic document, especially ... XML-documents. The Signature itself is in XML
• Furthermore, CDISC is preparing the 1.2 version of the Operational Data Model (ODM), which will have an XML-Schema instead of a DTD. XML4Pharma has also contributed to this new standard (by giving suggestions - e.g. using XML-Signature - and testing)
• Agave: Genomic Annotation
• Many other standards for which DTDs exist are currently transforming these to XML-Schema

XML separates content from presentation. The owner of the content can prepare his/her work using a word processor, or an XML-editor such as XMLSpy or XMLNotePad or Liquid XML Studio (there are many others).

Using XMLNotePad to generate XML Content

The content manager does not have to bother how the data will be presented later. He/She doesn't have to know or understand about presentation anyway. Think about those long painful days where a content manager and a computer specialist were sitting together to put al this information in good-looking HTML pages !

The computer specialist can concentrate on building the presentation, not being bothered by ever changing content. He/She just builds up an ever-reusable stylesheet (XSL stylesheet) that can also be used when the content changes and when another document with the same structure is generated.

Constructing stylesheets is a real specialism. However the learning curve is well-worth going through. Once the skill mastered, the company will save many expensive working hours (time is money) and profit from the reusability of both XML and XSL. An example of an XSL stylesheet can be found here. This stylesheet makes it possible to view an XML-file directly in MS Internet Explorer. Another example, using the CDISC-ODM standard, is also available.
Other stylesheets can be constructed to transform the XML document to WAP, to HTML, to PDF. The transformation is usually performed at the server side.

For one set of XML-files (e.g. having the same DTD), yet-existing or not-yet-existing (e.g. as they are generated by a database querie), one can develop several stylesheets, e.g. one (or more) for presentation on a web page, one for WAP, one for generation of Adobe PDF files, one for generating a Word document. One can even think about a stylesheet that works in a package for developing layouts on packaging cartons ! Such software packages usually work on Apple MacIntosh computers, but due to the portability of XML this does not create any problem.
For example, the above stylesheet presents the XML data (patient information) onto a web page. The same stylesheet is used for generating (automatically) the English, German, French, Italian or any other language web page. The presented stylesheet is an extremely simple one.

Another stylesheet can be used to transform the Spirig Nosedrops data to a PDF-file. The stylesheet can be found here. The transformation to PDF needs a special processing engine, which resides on the server.
Transformation to PDF is especially important as PDF documents cannot be manipulated, can be provided with electronic signatures, and PDF is the common format for submission to regulatory authorities.

A much more complicated example of transformation to PDF : a CDISC-ODM example (Clinical data report).

Stylesheets can also be used to filter information, add information, add images, links, JavaScript, Java applets, and many many more. The essence is: the pure data in the XML file, all presentation in the XSL file.

XML4Pharma, Katzelbachweg 18, 8052 Thal, Austria