New Generation Database Systems: XML Databases

IS 257 – Fall 2006 2006.11.28- SLIDE 1

New Generation Database Systems: XML Databases

University of California, BerkeleySchool of Information

IS 257: Database Management

IS 257 – Fall 2006 2006.11.28- SLIDE 2

Lecture Outline• XML and RDBMS• Native XML Databases

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Lecture Outline• XML and DBMS• Native XML Databases

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Standards: XML/SQL• As part of SQL3 an extension providing a

mapping from XML to DBMS is being created called XML/SQL

• The (draft) standard is very complex, but the ideas are actually pretty simple

• Suppose we have a table called EMPLOYEE that has columns EMPNO, FIRSTNAME, LASTNAME, BIRTHDATE, SALARY

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Standards: XML/SQL• That table can be mapped to:

<EMPLOYEE> <row><EMPNO>000020</EMPNO> <FIRSTNAME>John</FIRSTNAME> <LASTNAME>Smith</LASTNAME> <BIRTHDATE>1955-08-21</BIRTHDATE> <SALARY>52300.00</SALARY> </row>

<row> … etc. …

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Standards: XML/SQL• In addition the standard says that

XMLSchemas must be generated for each table, and also allows relations to be managed by nesting records from tables in the XML.

• Variants of this are incorporated into the latest versions of ORACLE

• But what if you want to deal with more complex XML schemas (beyond “flat” structures)?

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XML to Relational Database Mapping

Bhavin Kansara

The following slides are adapted from:

Slide from Bhavin Kansara

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Introduction• XML/relational mapping means data

transformation between XML and relational data models

• XML documents can be transformed to relational data models or vice versa.

• Mapping method is the way the mapping is done


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XML• XML: Extensible Markup Language• Documents have tags giving extra information

about sections of the document– E.g. <title> XML </title> – <slide> Introduction </slide>

• XML has emerged as the standard for representing and exchanging data on the World Wide Web.

• The increasing amount of XML documents requires the need to store and query XML documents efficiently.

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XML vs. HTML

• HTML tags describe how to render things on the screen, while XML tags describe what thing are.

• HTML tags are designed for the interaction between humans and computers, while XML tags are designed for the interactions between two computers.

• Unlike HTML, XML tags tell you what the data means, rather than how to display it

<name><first> abc </first><middle> xyz </middle><last> def </last>

</name>

<html><head><title>Title of page</title></head><body>abc xyz def </body></html>

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XML Technologies

• Schema LanguagesDTDsXML Schemas

• Query LanguagesXPathXQueryXSLT

• Programming APIsDOMSAX

<bib> { for $b in doc("http://bstore1.example.com/bib.xml")/bib/book where $b/publisher = "Addison-Wesley" and $b/@year > 1991 return <book year="{ $b/@year }"> { $b/title } </book> }</bib>

<?xml version="1.0" encoding="ISO-8859-1"?><?xml-stylesheet type="text/xsl" href="simple.xsl"?><breakfast_menu> <food> <name>Belgian Waffles</name> <price>$5.95</price> <description> two of our famous Belgian Waffles </description> <calories>650</calories> </food></breakfast_menu>

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DTD ( Document Type Definition )• DTD stands for Document Type Definition• The purpose of a Document Type

Definition is to define the legal building blocks of an XML document.

• It formally defines relationship between the various elements that form the documents.

• DTD allows computers to check that each component of document occurs in a valid place within the document.


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DTD ( Document Type Definition )


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XML vs. Relational DatabaseCUSTOMERName AgeABC 30

XYZ 40

<customers> <custRec>

<Name type=“String”>ABC</custName> <Age type=“Integer”>30</custAge>

</custRec> <custRec>

<Name type=“String”>XYZ</custName> <Age type=“Integer”>40</custAge>

</custRec> </customers>

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XML vs. Relational Database


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<!ELEMENT note (to+, from, header, message*, #PCDATA)>Slide from Bhavin Kansara

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When XML representation is not beneficial• When downstream processing of the data

is relational • When the highest possible performance is

required• When any normalized data components

have value outside the XML representation or the data need not be retained in XML form to have value

• When the data is naturally tabular


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When XML representation is beneficial• When schema is volatile • When data is inherently hierarchical in

nature • When data represents business objects in

which the component parts do not make sense when removed from the context of that business object

• When applications have sparse attributes • When low-volume data is highly structured


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XML-to-Relational mapping• Schema mapping

Database schema is generated from an XML schema or DTD for the storage of XML documents.

• Data mappingShreds an input XML document into relational tuples and inserts them into the relational database whose schema is generated in the schema mapping phase


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Schema Mapping


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Simplifying DTD


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DTD graph


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Inlined DTD graph• Given a DTD graph, a node is inlinable if and only if it

has exactly one incoming edge and that edge is a normal edge.


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Inlined DTD graph


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Generated Database Schema


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Data Mapping• XML file is used to insert

data into generated database schema

• Parser is used to fetch data from XML file.


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Summary• Simplify DTD• Create DTD graph from simplified DTD• Create inlined DTD graph from DTD graph• Use inlined DTD graph to generate

database schema• Insert values from XML file into generated

tables


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Issues• So, we can convert the XML to a relational

database, but can we then export as an XML document?– This is equally challenging

• But MOSTLY involves just re-joining the tables• How do you store and put back the wrapping tags

for sets of subelements?• Since the decomposition of the DTD was

approximate, the output MAY not be identical to the input

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Lecture Outline• XML and RDBMS• Native XML Databases

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Native XML Database (NXD) • Native XML databases have an XML-based

internal model– That is, their fundamental unit of storage is XML

• However, different native XML databases differ in What they consider the fundamental unit of storage– Document vs element or segment

• And how that information or its subelements are accessed, indexed and queried– E.g., SQL vs. Xquery or a special query language

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Database Systems supporting XQuery• The following database systems offer XQuery

support: – Native XML Databases:

• Berkeley DB XML• eXist• MarkLogic• Software AG Tamino• Raining Data TigerLogic• Documentum xDb (X-Hive/DB)

– Relational Databases (also support SQL): • IBM DB2• Microsoft SQL Server• Oracle

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Anatomy of a Native XML database• The next set of slides (available on the

class web site) come from George Feinberg of SleepyCat Software– SleepyCat is now part of Oracle

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Further comments on NXD• Native XML databases are most often

used for storing “document-centric” XML document– I.e. the unit of retrieval would typically be the

entire document and not a particular node or subelement

• This supports query languages like Xquery– Able to ask for “all documents where the third

chapter contains a page that has boldfaced word”

– Very difficult to do that kind of query in SQL

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XML-Based IR - Cheshire II• I thought I would take a little time to talk about

how the Cheshire system (that I have been working for nearly 20 years) uses XML, since it has some similarities (and many differences) to XML database systems

• Cheshire II (and Cheshire 3) are document-centric and involve parsing the XML for the purposes of indexing (and sometimes for retrieval of partial documents)

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Cheshire II SGML/XML Support• Underlying native format for all data is SGML or

XML• The DTD defines the file format for each file• Full SGML/XML parsing• SGML/XML Format Configuration Files define

the database• USMARC DTD and MARC to SGML conversion

(and back again)• Access to full-text via special SGML/XML tags

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SGML/XML Support• Example XML record for a DL document

<ELIB-BIB><BIB-VERSION>ELIB-v1.0</BIB-VERSION><ID>756</ID><ENTRY>June 12, 1996</ENTRY><DATE>June 1996</DATE><TITLE>Cumulative Watershed Effects: Applicability of Available Methodologies to the Sierra Nevada</TITLE><ORGANIZATION>University of California</ORGANIZATION><TYPE>report</TYPE><AUTHOR-INSTITUTIONAL>USDA Forest Service</AUTHOR-INSTITUTIONAL><AUTHOR-PERSONAL>Neil H. Berg</AUTHOR-PERSONAL><AUTHOR-PERSONAL>Ken B. Roby</AUTHOR-PERSONAL><AUTHOR-PERSONAL>Bruce J. McGurk</AUTHOR-PERSONAL><PROJECT>SNEP</PROJECT><SERIES>Vol 3</SERIES><PAGES>40</PAGES><TEXT-REF>/elib/data/docs/0700/756/HYPEROCR/hyperocr.html</TEXT-REF><PAGED-REF>/elib/data/docs/0700/756/OCR-ASCII-NOZONE</PAGED-REF></ELIB-BIB>

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<USMARC Material="BK" ID="00000003"><leader><LRL>00722</LRL><RecStat>n</RecStat> <RecType>a</RecType><BibLevel>m</BibLevel><UCP></UCP><IndCount>2</IndCount> <SFCount>2</SFCount><BaseAddr>00229</BaseAddr><EncLevel> </EncLevel> <DscCatFm></DscCatFm><LinkRec></LinkRec><EntryMap><FLength>4</Flength><SCharPos> 5</SCharPos><IDLength>0</IDLength><EMUCP></EMUCP></EntryMap></Leader> <Directry>001001400000005001700014008004100031010001400072035002000086035001700106100001900123245010500142250001100247260003200258300003300290504005000323650003600373700002200409700002200431950003200453998000700485</Directry><VarFlds> <VarCFlds><Fld001>CUBGGLAD1282B</Fld001><Fld005>19940414143202.0</Fld005> <Fld008>830810 1983 nyu eng u</Fld008></VarCFlds> <VarDFlds><NumbCode><Fld010 I1="Blank" I2="Blnk"><a>82019962 </a></Fld010> <Fld035 I1="Blank" I2="Blnk"><a>(CU)ocm08866667</a></Fld035><Fld035 I1="Blank" I2="Blnk"><a>(CU)GLAD1282</a></Fld035></NumbCode><MainEnty><Fld100 NameType="Single" I2=""><a>Burch, John G.</a></Fld100></MainEnty><Titles><Fld245 AddEnty="Yes" NFChars="0"><a>Information systems :</a>theory and practice /<c>John G. Burch, Jr., Felix R. Strater, Gary Grudnitski</c></Fld245></Titles><EdImprnt><Fld250 I1="Blank" I2="Blnk"><a>3rd ed</a></Fld250><Fld260 I1="" I2="Blnk"><a>New York :</a>J. Wiley,<c>1983</c></Fld260></EdImprnt><PhysDesc><Fld300 I1="Blank" I2="Blnk"><a>xvi, 632 p. :</a>ill. ;<c>24 cm</c></Fld300></PhysDesc><Series></Series><Notes><Fld504 I1="Blank" I2="Blnk"><a>Includes bibliographical references and index</a></Fld504></Notes><SubjAccs><Fld650 SubjLvl="NoInfo" SubjSys="LCSH"><a>Management information systems.</a></Fld650> ...

SGML Support

• Example SGML/MARC Record

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SGML Support• Mini-TREC document…

<DOC><DOCNO>FT931-3566</DOCNO><PROFILE>_AN-DCPCCAA3FT</PROFILE><DATE>930316</DATE><HEADLINE>FT 16 MAR 93 / Italy's Corruption Scandal: Magistrates hold key tounlocking Tangentopoli - They will set the investigation agenda</HEADLINE><BYLINE> By ROBERT GRAHAM</BYLINE><TEXT>OVER the weekend the Italian media felt obliged to comment on a non-event.No new arrests had taken place in any of the country's ever more numerouscorruption scandals which centre on the illicit funding of political parties...</TEXT><XX> …

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…Companies:-</XX><CO>Ente Nazionale Idrocarburi. Ente Nazionale per L'Energia Electtrica. Ente Partecipazioni E Finanziamento Industria Manifatturiera. IRI Istituto per La Ricostruzione Industriale.</CO><XX>Countries:-</XX><CN>ITZ Italy, EC.</CN><XX>Industries:-</XX><IN>P9222 Legal Counsel and Prosecution. P91 Executive, Legislative and General Government. P13 Oil and Gas Extraction. P9631 Regulation, Administration of Utilities. P6719 Holding Companies, NEC.</IN><XX>Types:-</XX> …

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…

<TP>CMMT Comment & Analysis.

GOVT Legal issues.

</TP>

<PUB>The Financial Times

</PUB>

<PAGE>

London Page 4

</PAGE>

</DOC>

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SGML/XML Support

• Configuration files for the Server are also SGML/XML:– They include tags describing all of the data

files and indexes for the database.– They also include instructions on how data is

to be extracted for indexing and how Z39.50 attributes map to the indexes for a given database.

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Cheshire Configuration Files<DBCONFIG><DBENV>/projects/is240/GroupX/indexes </DBENV>



<FILEDEF TYPE=SGML>

<DEFAULTPATH>/projects/is240/GroupX </DEFAULTPATH>

<FILETAG> trec </FILETAG>

<FILENAME> /projects/is240/ft </FILENAME>

<CONTINCLUDE> /projects/is240/ft.CONT </CONTINCLUDE>

<FILEDTD> /projects/is240/TREC.FT.DTD </FILEDTD><ASSOCFIL> ft.assoc </ASSOCFIL>

<HISTORY> cheshire_index/TESTDATA.history </HISTORY>…

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<INDEXES>

<INDEXDEF ACCESS=BTREE EXTRACT=KEYWORD NORMAL=NONE PRIMARYKEY=IGNORE><INDXNAME> cheshire_index/trec.docno.index </INDXNAME><INDXTAG> docno </INDXTAG>

<INDXMAP><USE> 12 </USE><struct> 1 </struct> </INDXMAP>



<INDXKEY><TAGSPEC><FTAG>DOCNO </FTAG></TAGSPEC> </INDXKEY> </INDEXDEF>…

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<INDEXDEF ACCESS=BTREE EXTRACT=KEYWORD_PROXIMITY NORMAL=STEM><INDXNAME> cheshire_index/trec.topic.index </INDXNAME><INDXTAG> topic </INDXTAG>

<INDXMAP><USE> 29 </USE><POSIT> 3 </posit> <struct> 6 </struct> </INDXMAP><INDXMAP><USE> 29 </USE><RELAT> 102 </RELAT><POSIT> 3 </posit> <struct> 6 </struct> </INDXMAP>…<STOPLIST> cheshire_index/topicstoplist </STOPLIST><INDXKEY><TAGSPEC><FTAG>HEADLINE </FTAG><FTAG>DATELINE </FTAG><FTAG>BYLINE </FTAG><FTAG>TEXT </FTAG></TAGSPEC> </INDXKEY> </INDEXDEF>

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Cluster Definitions

<CLUSTER><clusname> classcluster </clusname><cluskey normal=CLASSCLUS>

<tagspec><FTAG>FLD950 </FTAG> <s> â </s>

</tagspec></cluskey><stoplist> /usr3/cheshire2/data2/clasclusstoplist </stoplist><clusmap>

<from> <tagspec><ftag>FLD245</ftag><s>^[ab]</s><ftag>FLD440</ftag><s>â</s><ftag>FLD490</ftag><s>â</s><ftag>FLD830</ftag><s>â</s><ftag>FLD740</ftag><s>â</s>

</tagspec></from><to> <tagspec>

<ftag>titles</ftag> </tagspec></to><from> <tagspec>

<ftag>FLD6..</ftag><s>^[abcdxyz]</s> </tagspec></from><to> <tagspec>

<ftag>subjects</ftag> </tagspec></to><summarize> <maxnum> 5 </maxnum>

<tagspec> <ftag>subjsum</ftag></tagspec></summarize>

</clusmap></CLUSTER>

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Component Definitions<COMPONENTS><COMPONENTDEF><COMPONENTNAME> TESTDATA/COMPONENT_DB1 </COMPONENTNAME><COMPONENTNORM>NONE</COMPONENTNORM><COMPSTARTTAG> <TAGSPEC> <FTAG>mainenty </FTAG> <FTAG>titles </FTAG> </TAGSPEC></COMPSTARTTAG><COMPENDTAG> <TAGSPEC><FTAG>Fld300 </FTAG></TAGSPEC></COMPENDTAG><COMPONENTINDEXES><INDEXDEF ACCESS=BTREE EXTRACT=KEYWORD NORMAL=NONE><INDXNAME> TESTDATA/comp1index1.author…</INDEXDEF></COMPONENTDEF></COMPONENTS>

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Result Formatting (Display)<DISPOPTIONS>KEEP_ENTITIES</DISPOPTIONS>

<DISPLAY> <FORMAT NAME="B" OID="1.2.840.10003.5.105" DEFAULT> <convert function="TAGSET-G"> <clusmap> <from> <tagspec> <ftag>DOCNO</ftag> </tagspec></from> <to> <tagspec> <ftag>28</ftag> </tagspec></to> <from> <tagspec> <ftag>#DOCID#</ftag> </tagspec></from> <to> <tagspec> <ftag>5</ftag> </tagspec></to> </clusmap> </convert></FORMAT></DISPLAY>

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Indexing• Any SGML/XML tagged field or attribute can be

indexed:– B-Tree and Hash access via Berkeley DB (Sleepycat)– Stemming, keyword, exact keys and “special keys”– Mapping from any Z39.50 Attribute combination to a

specific index– Underlying postings information includes term

frequency for probabilistic searching.– SGML may include address of full-text for indexing

• New indexes can be easily added, or old ones deleted

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Database Storage • All data stored as SGML/XML flat text files

plus optional linked full-text files • File format is defined though SGML/XML

DTD (also flat text file)• “Associator” files provide indexed direct

access to each record in SGML/XML files.– Contain offset and record length for each

“record”– Associators can be built to index any

conformant document in a directory sub-tree

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Database Storage

AssociatorFile

Page DataFile

SGML/XMLFile

HistoryFile

DTDFileCluster

File

PostingsFile

IndexFile

IndexFile

RemoteRDBMS

ConfigFile

IndexFile

AssociatorFileProx

data File

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Client/Server Architecture• Server Supports:

– Database storage– Indexing – Z39.50 access to local data– Boolean and Probabilistic Searching– Relevance Feedback– External SQL database support

• Client Supports:– Programmable (Tcl/Tk – Python soon) Graphical User

Interface– Z39.50 access to remote servers– SGML & MARC formatting

• Combined Client/Server CGI scripting via WebCheshire

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Z39.50 Overview

UI

UI

MapQuery

Internet

MapResults

MapQuery

MapResults

MapQuery

MapResults

SearchEngine

New Generation Database Systems: XML Databases

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