My short course about XML and bioinformatics. January 2013.

1. <XML>
Pierre Lindenbaum
http://plindenbaum.blogspot.com
@yokofakun(http://twitter.com/yokofakun)
INSERM-UMR1087 Nantes
January 2013
https://github.com/lindenb/courses/tree/master/about.xml

2. Extensible Markup Language

3. Machine Readeable

4. Human Readeable

5. DOM

6. ... not always
artOfLineage></rdf:Description><rdf:Description
g/taxonomy/12292"><rdf:typerdf:resource="http:/
ankrdf:resource="http://purl.uniprot.org/core/S
ttp://www.w3.org/2001/XMLSchema#boolean">true</
><scientificName>Nicotianavelutinamosaicvirus</
commonName><hostrdf:resource="http://purl.unipr
ClassOfrdf:resource="http://purl.uniprot.org/ta
datatype="http://www.w3.org/2001/XMLSchema#bool
escription><rdf:Descriptionrdf:about="http://pu
df:typerdf:resource="http://purl.uniprot.org/co
p://purl.uniprot.org/core/Species"/><scientific
me><rdfs:subClassOfrdf:resource="http://purl.un
fLineagerdf:datatype="http://www.w3.org/2001/XM
eage></rdf:Description><rdf:Descriptionrdf:abou

7. Just a format

8. *.txt
PMID- 16381885
OWN - NLM
STAT- MEDLINE
DA - 20051229
DCOM- 20060228
LR - 20091118
IS - 1362-4962 (Electronic)
IS - 0305-1048 (Linking)
VI - 34
IP - Database issue
DP - 2006 Jan 1
TI - From genomics to chemical genomics: new developments in KEGG.
PG - D354-7
AB - The increasing amount of genomic and molecular information is the basis for
understanding higher-order biological systems, such as the cell and the orga
and their interactions with the environment, as well as for medical, industr
and other practical applications. The KEGG resource (http://www.genome.jp/ke
provides a reference knowledge base for linking genomes to biological system
categorized as building blocks in the genomic space (KEGG GENES) and the che
space (KEGG LIGAND), and wiring diagrams of interaction networks and reactio
networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally a
to the KEGG suite of databases. This reflects our attempt to computerize
functional interpretations as part of the pathway reconstruction process bas
the hierarchically structured knowledge about the genomic, chemical and netw
spaces. In accordance with the new chemical genomics initiatives, the scope

9. *.xml
<?xml version="1.0"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2008//EN
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation Status='MEDLINE' Owner='NLM'>
<PMID Version='1'>16381885</PMID>
<DateCreated>
<Year>2005</Year>
<Month>12</Month>
<Day>29</Day>
</DateCreated>
<DateCompleted>
<Year>2006</Year>
<Month>02</Month>
<Day>28</Day>
</DateCompleted>
<DateRevised>
<Year>2009</Year>
<Month>11</Month>
<Day>18</Day>
</DateRevised>
<Article PubModel='Print'>
<Journal>
<ISSN IssnType='Electronic'>1362-4962</ISSN>
<JournalIssue CitedMedium='Internet'>

10. *.json
{ "header": { "type": "efetch.pubmed", "version":
"0.3" }, "result": [ { "medlinecitation": { "pmid"
: { "version": "1", "value": "17284678" }, "datecr
eated": { "year": "2007", "month": "03", "day": "0
2" }, "datecompleted": { "year": "2007", "month":
"04", "day": "05" }, "daterevised": { "year": "200
9", "month": "11", "day": "18" }, "article": { "jo
urnal": { "issn": { "issntype": "Print", "value":
"1088-9051" }, "journalissue": { "citedmedium": "P
rint", "volume": "17", "issue": "3", "pubdate": [
"2007", "Mar" ] }, "title": "Genome research", "is
oabbreviation": "Genome Res." }, "articletitle": "
Sequencing and analysis of chromosome 1 of Eimeria
tenella reveals a unique segmental organization."
, "pagination": [ "311-9" ], "abstract": { "abstra
cttexts": [ { "value": "Eimeria tenella is an intr
acellular protozoan parasite that infects the inte
stinal tracts of domestic fowl and causes coccidio
sis, a serious and sometimes lethal enteritis. Eim
eria falls in the same phylum (Apicomplexa) as sev
eral human and animal parasites such as Cryptospor
idium, Toxoplasma, and the malaria parasite, Plasm
odium. Here we report the sequencing and analysis
of the first chromosome of E. tenella, a chromosom
e believed to carry loci associated with drug resi

12. XML namespace
<my-database> <my-database
<record> xmlns="http://mydatabase.org"
<title>Record1</title> xmlns:h="http://www.w3.org/1999/xhtml">
<html> <record>
<head> <title>Record1</title>
<title>hello</title> <h:html>
</head> <h:head>
<body> <h:title>hello</title>
<h1>Hello</h1> </h:head>
</body> <h:body>
</html> <h:h1>Hello</h:h1>
</record> </h:body>
</my-database> </h:html>
</record>
</my-database>

13. xmllint

14. xsltproc

15. Parsing

16. DOM
Element root = document.getDocumentElement();
for (Node item=root.getFirstChild();
item!=null;
item=item.getNextSibling()){
if (item.getNodeType()==Node.ELEMENT_NODE)
{
System.out.println(
((Element)item).getAttribute("id"));
}
}

17. StAx
public interface XMLStreamReader {
public int next();
public boolean hasNext() ;
public String getText();
public String getLocalName();
public String getNamespaceURI();
// ...other methods not shown
}

18. SAX
public interface ContentHandler
{
public void startDocument () ;
public void endDocument();
public void startElement(String name, Attri
public void endElement (String name);
public void characters (char ch[], int star
}

19. XPath
<?xml version="1.0" encoding="UTF-8"?> $ xmllint -xpath
<genes> '/genes/gene[1]/name[2]/text()'
<gene id="1"> genes1.xml
<name>Gene1</name>
<name>gene-1</name> gene-1
<sequence>ATAATGCTAGCTAGCTATCGAATG</sequence>
</gene> $ xmllint -xpath
<gene id="2"> '/genes/gene[1]/name[2]'
<name>Gene2</name> genes1.xml
<name>gene-2</name>
<sequence>AATTGCGATTCATCGATGCTATA</sequence> <name>gene-1</name>
</gene>
</genes> $ xmllint -xpath
'count(/genes/gene)'
genes1.xml
2
$ xmllint -xpath
'/genes/gene[@id='2']/name[1]/text()'
genes1.xml
Gene2

20. XInclude
<?xml version="1.0" encoding="UTF-8"?>
<genes xmlns:xi="http://www.w3.org/2001/XInclud
<gene id="1">
<name>Gene1</name>
<name>gene-1</name>
<sequence><xi:include
href="sequence.txt"
parse="text"
/></sequence>
</gene>
<xi:include
href="gene2.xml"
parse="xml"/>
</genes>

21. XHTML

22. SVG
<svg
xmlns="http://www.w3.org/2000/svg"
width='300px' height='300px'>
<circle
cx='120' cy='150' r='60' style='fill: gold;'
/>
<polyline
points='120 30, 25 150, 290 150'
stroke-width='4' stroke='brown'
style='fill: none;' />
<polygon
points='210 100, 210 200, 270 150'
style='fill: lawngreen;' />
<text x='60' y='250'
fill='blue'>Hello, World!</text>
</svg>

23. XSL-FO
<?xml version="1.0" encoding="ISO-8859-1"?>
<fo:root xmlns:fo="http://www.w3.org/1999/XSL/Format">
<fo:layout-master-set>
<fo:simple-page-master master-name="A4">
<!-- Page template goes here -->
</fo:simple-page-master>
</fo:layout-master-set>
<fo:page-sequence master-reference="A4">
<!-- Page content goes here -->
</fo:page-sequence>
</fo:root>

24. RDF
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF (...)>
<rdf:Description rdf:about="http://…/isbn/20203
<f:titre xml:lang="fr">Le palais des mirroi
<f:original rdf:resource="http://…/isbn/000
</rdf:Description>
</rdf:RDF>

25. RDF

26. SOAP
<?xml version="1.0" encoding="UTF-8"?>
<SOAP-ENV:Envelope (...)>
<SOAP-ENV:Body>
<r:queryPathwaysForReferenceIdentifiers>
<r:referenceIdentifiers>
<soapenc:string>Q9Y266</soapenc:string>
<soapenc:string>P17480</soapenc:string>
<soapenc:string>P2048</soapenc:string>
</r:referenceIdentifiers>
</r:queryPathwaysForReferenceIdentifiers>
</SOAP-ENV:Body>
</SOAP-ENV:Envelope>

27. WSDL
(...)
<wsdl:message name="getEvsData">
<wsdl:part element="tns:getEvsData" name="p
</wsdl:part>
</wsdl:message>
<wsdl:message name="getEvsDataResponse">
<wsdl:part element="tns:getEvsDataResponse"
</wsdl:part>
</wsdl:message>
<wsdl:portType name="DataQuery">
<wsdl:operation name="getEvsData">
<wsdl:input message="tns:getEvsData" name
</wsdl:input>
<wsdl:output message="tns:getEvsDataRespo

28. WSDL
$ wsimport
"http://evs.gs.washington.edu/wsEVS/EVSDataQue
parsing WSDL...
Generating code...
Compiling code...

29. WSDL
$ more ./edu/washington/gs/evs/webservice/Locus.java
package edu.washington.gs.evs.webservice;
(...)
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "locus", propOrder = {
"geneName",
"chromosome",
"strand",
"mrnaAccession",
"geneId",
"txStart",
"txEnd",
"keggPathwayIds"
})
public class Locus {
protected String geneName;
protected String chromosome;
protected String strand;
protected String mrnaAccession;
protected int geneId;
protected int txStart;
protected int txEnd;
@XmlElement(nillable = true)
(...)

30. Well formed..<a><b>c</a></b>

31. Validated (DTD)
$ cat genes1.dtd
<!ELEMENT genes (gene+)>
<!ELEMENT gene ((name+),sequence)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT sequence (#PCDATA)>
<!ATTLIST gene id CDATA #REQUIRED>
$ xmllint --dtdvalid genes1.dtd genes1.xml

32. DTD/JAXB : no need to create a parser
$ xjc genes1.xsd
$ xjc -dtd genes1.dtd
parsing a schema...
compiling a schema...
generated/Gene.java
generated/Genes.java
generated/Name.java
generated/ObjectFactory.java

33. Validated (XSD)
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
>
<xsd:complexType name="Genes">
<xsd:sequence>
<xsd:element name="gene"
type="Gene"
maxOccurs="unbounded"
/>
</xsd:sequence>
</xsd:complexType>
<xsd:complexType name="Gene">
<xsd:sequence>
<xsd:element name="name" maxOccurs="unbounded" type="xsd:string"/>
<xsd:element name="sequence" type="xsd:string"/>
</xsd:sequence>
<xsd:attribute name="id" use="required" type="xsd:int"/>
</xsd:complexType>
<xsd:element type="Genes" name="genes"/>
</xsd:schema>

34. Validated (XSD)
$ xmllint --noout
--schema genes1.xsd
genes1.xml
genes1.xml validates

35. XSD/JAXB : no need to create a parser
$ xjc genes1.xsd
parsing a schema...
compiling a schema...
generated/Gene.java
generated/Genes.java
generated/ObjectFactory.java

36. XSLT

37. XSLT (text)
<?xml version='1.0' encoding="ISO-8859-1"?>
<xsl:stylesheet $ xsltproc genes2txt.xsl
xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
version='1.0'
>
>id:1|Gene1
<xsl:output method='text'/>
ATAATGCTAGCTAGCTATCGAATG
<xsl:template match="/">
<xsl:apply-templates select="genes"/>
</xsl:template>
>id:2|Gene2
<xsl:template match="genes">
AATTGCGATTCATCGATGCTATA
<xsl:apply-templates select="gene"/>
</xsl:template>
<xsl:template match="gene">
<xsl:text>&gt;id:</xsl:text>
<xsl:value-of select="@id"/>
<xsl:text>|</xsl:text>
<xsl:value-of select="name[1]"/>
<xsl:text>
</xsl:text>
<xsl:value-of select="sequence"/>
<xsl:text>
</xsl:text>
</xsl:template>
</xsl:stylesheet>

38. XSLT (html)
<?xml version='1.0' encoding="ISO-8859-1"?>
<xsl:stylesheet $ xsltproc
xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
version='1.0'
>
genes2html.xsl
<xsl:output method='html'/> genes1.xml
<xsl:template match="/">
<html><body>
<xsl:apply-templates select="genes"/>
</body></html>
<html><body>
</xsl:template>
<h1>2 genes</h1>
<xsl:template match="genes">
<h1> <h2>&gt;id:1|Gene1</h2>
<xsl:value-of select="count(gene)"/> genes
</h1>
<xsl:apply-templates select="gene"/>
<pre>ATAATGCTAGCTAGCTATCG
</xsl:template>
<h2>&gt;id:2|Gene2</h2>
<xsl:template match="gene">
<h2> <pre>AATTGCGATTCATCGATGCT
<xsl:text>&gt;id:</xsl:text>
<xsl:value-of select="@id"/>
<xsl:text>|</xsl:text>
</body></html>
<xsl:value-of select="name[1]"/>
</h2>
<pre>
<xsl:value-of select="sequence"/>
</pre>
</xsl:template>

39. XSLT Embedded
<?xml-stylesheet type="text/xsl" href="genes2html.xsl"?>

40. XSLT (xml)
<?xml version='1.0' encoding="ISO-8859-1"?>
<xsl:stylesheet
xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
xmlns="http://www.w3.org/2000/svg"
xmlns:math="http://exslt.org/math"
version="1.0"
>
<xsl:output method='xml'/>
<xsl:template match="/">
<svg width="500" height="500" version='1.0'>
<xsl:apply-templates select="genes"/>
</svg>
</xsl:template>
<xsl:template match="genes">
<xsl:apply-templates select="gene[1]"/>
</xsl:template>
<xsl:template match="gene">
<text x="250" y="250">
<xsl:value-of select="name[1]"/>
</text>
<xsl:call-template name="drawseq">
<xsl:with-param name="i" select="number(1.0)"/>
<xsl:with-param name="s" select="sequence"/>
</xsl:call-template>
</xsl:template>
<xsl:template name="drawseq">
<xsl:param name="i"/>
<xsl:param name="s" />
<xsl:variable name="L" select="string-length($s)"/>
<text>
<xsl:variable name="angle" select="$i * ( (2.0*3.14159) div $L )"/>
<xsl:attribute name="x"><xsl:value-of select="250+200*math:cos( $angle )"/></xsl:attribute>
<xsl:attribute name="y"><xsl:value-of select="250+200*math:sin( $angle )"/></xsl:attribute>
<xsl:value-of select="substring($s,$i,1)"/>
</text>
<xsl:if test="$i+1 &lt;= $L">
<xsl:call-template name="drawseq">
<xsl:with-param name="i" select="1 + $i"/>
<xsl:with-param name="s" select="$s"/>
</xsl:call-template>
</xsl:if>
</xsl:template>
</xsl:stylesheet>

42. END

43. Photos from wikipedia and W3C.