worzyk fh anhalt telemedizin ws 09/10 xml - 1 xml extensible markup language

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Telemedizin WS 09/10XML - 1

XML

Extensible Markup Language

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XML

• Metalanguage– A Language, which describes languages– Languages describe formats for data

exchange

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Example

Hans MeyerLohmannstrasse 2306366 KöthenDr. Else MüllerBernburger Strasse 5606366 Köthen

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Example

Hans MeyerLohmannstrasse 2306366 Köthen

Dr. Else MüllerBernburger Strasse 5606366 Köthen

<Patient> <Name> <Strasse> <Ort></Patient><Arzt> <Name> <Strasse> <Ort></Arzt>

</Name></Strasse></Ort>

</Name></Strasse></Ort>

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Structure of XML documents

• Prolog– Deklaration of type of dokument– DTD (Document Type Definition)

• Elements

http://www.w3schools.com/xml/default.asp

http://de.selfhtml.org/

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Document Type DefinitionDTD

• It describes the grammar of a XML - document

• It describes permitted elements and attributes– their data type and range of values– their nesting

• An XML – Dokument, that conforms to a DTD is called valid

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Example DTD<?xml version="1.0" encoding="ISO-8859-1"?><!DOCTYPE Personen [ <!ELEMENT Personen (Patient)> <!ELEMENT Patient (#PCDATA)>]><Personen> <Patient> Hans Meyer Lohmannstrasse 23 06366 Köthen </Patient></Personen>

http://www.inf.hs-anhalt.de/~Worzyk/Telemedizin/Beispiele/Patienten1.xml


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Structure of XML documents• DTD describes the characteristics of the

elements• Elements are initiated by a start tag

<Elementname> and are terminated by a closing tag </Elementname>.

• XML tags are case sensitive• Elements can contain Elements.• #PCDATA Parsed character data: The

elements consist of character strings whose characters are part of the defined character set.

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Names of Elements

• Names can contain letters, numbers, and other characters

• Names must not start with a number or punctuation character

• Names must not start with the letters xml (or XML or Xml ..)

• Names cannot contain spaces

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Sequence of Elements

Subordinate elements are separated in the declaration by commas and included in parentheses.

Example:<?xml version="1.0" encoding="ISO-8859-1"?><!DOCTYPE Personen [ <!ELEMENT Personen (Patient,Arzt)> <!ELEMENT Patient (Name,Adresse)> <!ELEMENT Arzt (Name, Adresse)> <!ELEMENT Name (#PCDATA)> <!ELEMENT Adresse (#PCDATA)>]> http://www.inf.hs-anhalt.de/~Worzyk/Telemedizin/Beispiele/Patienten2.xml


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selection list

• Selection of exactly one element: The available elements are seperated by |

• Example:<!DOCTYPE Personen [ <!ELEMENT Personen (Patient|Arzt)> <!ELEMENT Patient

(Name,Adresse,Diagnose)> <!ELEMENT Arzt (Name,

Adresse,Fachgebiet)>



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Multiple occurrence

* The element can appear no time or arbitrarily often

+ The element can appear at least one time or arbitrarily often

? The element can appear no time or at most one time

Datenbanksysteme 2 SS 2004Seite 13 - 13

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Attributes<!ATTLIST element-name attribute-name attribute-type

default-value>

Types of attriutes::CDATA, (en1|en2|..), ID, IDREF, IDREFS, NMTOKEN,

NMTOKENS, ENTITY, ENTITIES, NOTATION, xml:

Defaultvalue:value#REQUIRED, #IMPLIED, #FIXED value


http://www.w3schools.com/xml/xml_attributes.asp


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Comments

Comments are embedded by <!– and -->

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Well-formed XML - File

• The file starts with the XML-declaration, which establish the reference to XML

• It exists at least one data element• It exists exactly one root element, which

contain all other data elements• All required attributes are defined• All elements have the right content• The elements must be nested properly

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Valide XML - File

• The file is well-formed• A DTD is assigned to the file• The content of the file is according

to the assigned DTD

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ParserA parser validates if an XML Document is valide:

<html><body>

<script type="text/javascript">var xmlDoc = new ActiveXObject("Microsoft.XMLDOM")xmlDoc.async="false"xmlDoc.validateOnParse="true"xmlDoc.load("Patienten5.xml")

document.write("<br />Error Code: ")document.write(xmlDoc.parseError.errorCode)document.write("<br />Error Reason: ")document.write(xmlDoc.parseError.reason)document.write("<br />Error Line: ")document.write(xmlDoc.parseError.line)</script>

</body></html>

http://www.inf.hs-anhalt.de/~Worzyk/Telemedizin/Beispiele/Parser.htm

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DTD - Disadvantages

• Few datatypes• specification not in XML – Syntax

– Specification can not be validated with a parser

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XML - Schema

• An XML Schema:• defines elements that can appear in a document • defines attributes that can appear in a document • defines which elements are child elements • defines the order of child elements • defines the number of child elements • defines whether an element is empty or can

include text • defines data types for elements and attributes • defines default and fixed values for elements and

attributes

http://www.w3schools.com/schema/schema_intro.asp

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XML SchemaAdvantages over DTD

• XML Schemas are extensible to future additions

• XML Schemas are richer and more useful than DTDs

• XML Schemas are written in XML • XML Schemas support data types

– xs;date, xs;dateTime, xs:string

• XML Schemas support namespaces – xmlns:xs="http://www.w3.org/2001/XMLSchema“

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Dublin Core Standard

Dublin Core Metadata InitiativeConference in 1995 in Dublin / Ohio

defined a set of describing attributs to categorize documents in the internet

15 core elements are recommended in „Dublin Core Metadata Element Set, Version 1.1 (ISO 15836)“

http://dublincore.org/documents/dces/

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How to create an XML structure

• Create a tree-structure of the data• Convert that structure to a DTD• Add data elements• Test

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ExampleQuarterly billing

• One file consists of exactly one physician and at least one patient

• A phyiscian is either a General Practitioner or a dentist

• A general practitioner has an address and a profession

• A dentist has an address• A patient has an address and no ore

more diagnisis• An address consists of Name, City, Street• A name has a salutation Mr. or Ms.

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ExampleQuarterly billing

billing

Physician Patient

General Practitioner Dentist Address Diagnosis

Address Profession ? Adresse Name City Street

Mr Ms

+

| *

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Example - DTD

<?xml version="1.0" encoding="ISO-8859-1"?><!DOCTYPE Billing [ <!ELEMENT Billing (Physician, Patient+)> <!ELEMENT Physician (General_Practitioner | Dentist)> <!ELEMENT General_Practitioner (Address, Profession?)> <!ELEMENT Dentist (Address)> <!ELEMENT Patient (Address, Diagnosis*)> <!ELEMENT Address (Name, City, Street)> <!ELEMENT Profession (#PCDATA)> <!ELEMENT Diagnosis (#PCDATA)> <!ELEMENT Name (#PCDATA)> <!ELEMENT City (#PCDATA)> <!ELEMENT Street (#PCDATA)> <!ATTLIST Name Salutation (Mr|Ms) "Ms">]>

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Example - Data< Billing > < Physician > < General_Practitioner > <Address> <Name>Dr. Erpel</Name> <City>Entenhausen</City> <Street>Am Krankenhaus 1</Street> </Address> < Profession >Geriatrics</ Profession > </ General_Practitioner > </ Physician > < Patient > <Address> <Name Anrede="Herr">Daniel</Name> <City>Entenhausen</City> <Street>Bahnhofstrasse 3a</Street> </Address> <Diagnose>Bettflucht</Diagnose> </Patient> <Patient> <Address> <Name>Daisy</Name> <City>Entenhausen</City> <Street>Am Stadtpark</Street> </Address> <Diagnosis>Sonnenbrand</Diagnosis> <Diagnosis>Migräne</Diagnosis> </Patient></ Billing >

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Queries to XML - Files

• XPath• XQuery

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XPath

The language XPath serves to address parts of a XML document.

It was designed for the use both in XSLT and in XPointer.

XPath models a XML document as a tree, which consists of knots.

http://www.informatik.hu-berlin.de/~obecker/obqo/w3c-trans/xpath-de-20010702/

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Example<?xml version="1.0" encoding="ISO-8859-1"?>

<bookstore>

<book category="COOKING"> <title lang="en">Everyday Italian</title> <author>Giada De Laurentiis</author> <year>2005</year> <price>30.00</price></book>

<book category="CHILDREN"> <title lang="en">Harry Potter</title> <author>J K. Rowling</author> <year>2005</year> <price>29.99</price></book>

<book category="WEB"> <title lang="en">XQuery Kick Start</title> <author>James McGovern</author> <author>Per Bothner</author> <author>Kurt Cagle</author> <author>James Linn</author> <author>Vaidyanathan Nagarajan</author> <year>2003</year> <price>49.99</price></book>

<book category="WEB"> <title lang="en">Learning XML</title> <author>Erik T. Ray</author> <year>2003</year> <price>39.95</price></book>

</bookstore>

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Queries with XPath

Select all titles: /bookstore/book/title

Select the title of the first book/bookstore/book[1]/title

Select all the prices/bookstore/book/price/text()

Select price nodes with price>35/bookstore/book[price>35]/title

http://www.w3schools.com/xpath/xpath_examples.asp

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XQuery

• Querylanguage for XML data• Uses Xpath expression• Analogy to SQL

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Xquery Example<?xml version="1.0" encoding="ISO-8859-1"?>

<bib>

<book year="1994">

<title>TCP/IP Illustrated</title>

<author><last>Stevens</last><first>W.</first></author>

<publisher>Addison-Wesley</publisher>

<price>65.95</price>

</book>

<book year="1992">

<title>Advanced Programming in the Unix environment</title>

<author><last>Stevens</last><first>W.</first></author>

<publisher>Addison-Wesley</publisher>


</book>

<book year="2000">

<title>Data on the Web</title>

<author><last>Abiteboul</last><first>Serge</first></author>

<author><last>Buneman</last><first>Peter</first></author>

<author><last>Suciu</last><first>Dan</first></author>

<publisher>Morgan Kaufmann Publishers</publisher>


</book>

<book year="1999">

<title>The Technology and Content for Digital TV</title>

<editor>

<last>Gerbarg</last><first>Darcy</first>

<affiliation>CITI</affiliation>

</editor>

<publisher>Kluwer Academic Publishers</publisher>


</book>

</bib>

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Xquery Example

Query:

doc("books.xml")/bib/book[price<50]

results:

<book year="2000">

<title>Data on the Web</title>

<author><last>Abiteboul</last><first>Serge</first></author>

<author><last>Buneman</last><first>Peter</first></author>

<author><last>Suciu</last><first>Dan</first></author>

<publisher>Morgan Kaufmann Publishers</publisher>


</book>

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FLWOR

For, Let, Where, Order by, Return

for $x in doc("books.xml")/bib/bookwhere $x/price>50order by $x/titlereturn $x/title

Results:<title>Advanced Programming in the Unix

environment</title><title>TCP/IP Illustrated</title><title>The Technology and Content for Digital TV</title>

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XML – Documents in Databases

XML – Documents can be• Focussed on data• Focussed on text• Semi-structured

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Alternatives to store XML Documents

• Storage as a whole• Storage within the XML-Structure• Transformation to structures of the

database

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Storage of XML documents as a whole

Original will be stored in a file system or as CLOB in a database

full-text indexStrukturindex

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Example<hotel url=“http://www.hotel-huebner.de“ id=“h0001“ erstellt-am=“03/02/2003“ Autor=“Hans Müller“> <hotelname>Hotel Hübner</hotelname> <kategorie>4</kategorie> <adresse> <plz>18199</plz> <ort>Warnemünde</ort> <strasse>Seestraße</strasse> </adresse> <telefon>0381 / 5434-0</telefon> <fax> 0381 / 5434-444</fax> <anreisebeschreibung>Aus Richtung Rostock kommend ... </anreisebeschreibung></hotel>

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full-text index

Begriff Verweis

hotel * * *

Warnemünde *

Rostock *

ort * *

<hotel url=“http://www.hotel-huebner.de“ id=“h0001“ erstellt-am=“03/02/2003“ Autor=“Hans Müller“> <hotelname>Hotel Hübner</hotelname> <kategorie>4</kategorie> <adresse> <plz>18199</plz> <ort>Warnemünde</ort> <strasse>Seestraße</strasse> </adresse> <telefon>0381 / 5434-0</telefon> <fax> 0381 / 5434-444</fax> <anreisebeschreibung>Aus Richtung Rostock kommend ... </anreisebeschreibung></hotel>

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full-text - andStructurindex

Begriff Verweis Element

Warnemünde * *

Seestrasse * *

Rostock * *

<hotel url=“http://www.hotel-huebner.de“ id=“h0001“ erstellt-am=“03/02/2003“ Autor=“Hans Müller“> <hotelname>Hotel Hübner</hotelname> <kategorie>4</kategorie> <adresse> <plz>18199</plz> <ort>Warnemünde</ort> <strasse>Seestraße</strasse> </adresse> <telefon>0381 / 5434-0</telefon> <fax> 0381 / 5434-444</fax> <anreisebeschreibung>Aus Richtung Rostock kommend ... </anreisebeschreibung></hotel>

Element Ver weis

Ord nung

Vor gänger

hotel * 1

adresse * 2 *

ort * 3 *

strasse * 3 *

anreise bschreibung

* 2 *

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Queries

Volltextindexhotel AND warnemünde(hotel OR pension) AND (rostock OR warnemünde)

Volletxt- und Strukturindexhotel.adresse.ort CONTAINS (“warnemünde“) ANDhotel.freizeitmoeglichkeit CONTAINS (“swimming pool“)

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Characteristics full-text index

Description of Schema Not required

Reconstruction of document

The document remains in the original form

Queries - Information Retrieval - SQL

further characteristics The evaluation of the structure is possible

Use Document-centered applications

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generic storage Storage within the XML-

Structure

All Informationen of the XML-Dokument will be stored– simple generic Storage– Document Object Model

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BeispielDocID Element

nameID Vor

gängerOrdnung

Wert

h0001 hotel 101 1h0001 hotelname 102 101 1 Hotel Hübnerh0001 kategorie 103 101 2 4h0001 adresse 104 101 3h0001 plz 105 104 1 18119h0001 ort 106 104 2 Warnemünde...

DocID Attributname

ID Element Wert

h0001 url 101 101 http://www.hotel-huebner.de

h0001 id 102 101 h0001...

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Document Object Model

The structure of the tree will be transformed to a class hierarchy

Storage in objectrelational or objektoriented databases

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Queries

• XPath• QXuery• XQL

– Abfragesprache der Software AG

• SQL

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Characteristics Generic Storage

Description of Schema Not required

Reconstruction of document possible, but expensive

Queries - XQuery, XQL - QL considers the storage

structures further characteristics Queries anb Updates possible with

DOM Use for documents

- Focussed on data - Focussed on text - Semi-structured

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Transformation to Structures of databasesDTD or Schema must be availableAutomatic or userdriven proceduresTransformtion to

relationalobjectrelationalobjectoriented

Databases

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Transformation XML - Information Datenbankiformation Element Root - Element Relation XML - Element Attribut of a Relation Sequence of Elementen Attribute of a Relation Alternative of Elementen Attribute of a Relation Element with Qualifizierer ? Attribut, nullvalue possible Element with Qualifizierer +

or * SET oder LIST

komplex strukturiertes Element

ROW

Attribut XML - Attribut Attributof a Relation #IMPLIED Nullvalue not allowed #REQUIRED Nullvalue not allowed Defaultwert Defaultvalue

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ExampleHotelname url id erstellt-am autor kate

gorie fax anreisebeschreibung

Hotel Hübner

http:// h0001 03/02/2003 Hans Müller

4 0381 Aus Richtung Rostock

id plz ort strasse nummer

h0001 18119 Warnemünde Seestrasse

12

id telefon Ordnung

h0001 0381 / 5434 - 0 1

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Queries

• SQL with– Joins– Aggregatfunktionen– Queryoptimizing– Update

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Characteristics Structures of databases

Description of Schema required

Reconstruction of document

only partly possible

Queries - SQL und XML

further characteristics Keeps the order of elements with additional attributs

Use For data-centered applications

worzyk fh anhalt telemedizin ws 09/10 xml - 1 xml extensible markup language

Documents

xml data

xml document

xml dokument

letters xml

xml metalanguage

xml tags

storage of xml documents

databases xml documents