Xml in bio medical field

Presented by: Eng. Juman Ghazi
Director: Dr. Eng. Rasha Masood

What is XML?
 XML stands for EXtensible Markup Language.
 XML is a markup language much like HTML.
 XML was designed to describe data and focus on what
data is.
2

eXtensible Markup Language
 Helps information systems share structured data.
 A meta language that gives meaning to data that other
application can use.
 Application and platform independent.
 Allows various types of data.
 Extensible to accommodate new tags and processing methods.
 Allows user-defined tags.
4

Advantages of using XML
 Simpler version of Standard Generalized Markup
Language (SGML).
 Easy to understand and read.
 Supported by large number of platforms.
 Used across open standards.
5

Components of an XML Document
1. Elements: <hello>
2. Attributes: <item id=“33905”>
3. Entities: < (<)
4. Advanced Components
1. CData Sections
2. Processing Instructions
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Example in HTML
7
<html>
<head>
<title>Menu</>
</head>
<body>
<h1>Soup</h1>
<h4>4.99</h4>
</body>
</html>

Example in HTML
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<?xml version=“1.0” ?>
<menu>
<item>
<itemname>soup</itemname>
<cost>4.99</cost>
</item>
</menu>

Declaration:
 First line in document.
 Provides information to the parser.
 Recommended but optional.
 Contains three name-value pairs:
 Version (common).
 Encoding (defaults to UTF-8).
 Standalone (rare).
11

Tags:
 Text in between <and >
 Have start tag and end tag.
 Tags and data stored together.
 Data is self-descriptive and easy to under stand.
12

13
Root
(text) (text) (text)
element element

Elements:
 Basic building blocks of XML file.
 Text between a start tag and end
tag is considered the value of the
element
 Documents contain one root
element.
 Can contain Nested elements.
14

Attributes:
 Provide additional information about
the elements.
 Name-value pairs:
- Single or double quotes to encode
values.
- Attribute names are unique within
the same element.
16

Comments:
 Appear anywhere in document
- Start tag <!--
- End tag --!>
 contents inside comment are not parsed.
17

More in XML:
1. Schemas
2. Parsers
3. Editors
4. Standards
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1. Schemas:
 Describe the structure and content of an XML
document.
 Define a shared vocabulary for application.
 Can be expressed using XML schema languages
such as:
-Document Type Definition (DTD).
-XML Schema (W3C).
19

Industry standards and data exchange:
20

2. Parsers:
 Read and process the content of an XML
document.
 Include push and pull parsers
-Pull parsers: events generated by the application
-Push parsers: events controlled by the parser
 Free XML parsers available, including tools from
IBM.
21

3. Editors:
 Text and graphical editors facilitate the editing
of XML code.
 Benefits of using editors:
coding effort.
-Provide to perform tasks.
22

4. Standards:
 Various types of standards:
- Core standards from the basis of what is expressed
in an XML document.
- Processing standards relate to XML processing by
developers.
- Key vocabularies (applications).
 XML standards influencers include the W3C, ISO and
OASIS.
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XML RuLes:
1. Must Have a Closing Tag.
In HTML, some elements do not
have to have a closing tag:
<p>This is a paragraph
<p>This is another paragraph
In XML, it is illegal to omit the
closing tag.
<p>This is a paragraph</p>
<p>This is another paragraph</p>
2. XML Tags are Case Sensitive.
XML tags are case sensitive. The tag
<Letter> is different from the tag
<letter>.
<Message>This is incorrect</message>
<message>This is correct</message>
"Opening and closing tags"
are often referred to as "Start and
end tags". Use whatever you prefer.
It is exactly the same thing.
25

XML RuLes:
3. Elements Must be Properly
Nested:
In HTML, you might see improperly
nested elements:
<b><i>This text is bold and
italic</b></i>
In XML, all elements must be
properly nested within each other:
<b><i>This text is bold and
italic</i></b>
4. XML Documents Must Have a Root
Element:
XML documents must contain one
element that is the parent of all
other elements. This element is called
the root element.
<root>
<child>
<subchild>.....</subchild>
</child>
< /root>
26

XML RuLes:
XML Attribute Values Must be
Quoted:
XML elements can have attributes
in name/value pairs
< note date=12/11/2007>
< to>Tove</to>
< from>Jani</from>
< /note>
< note date="12/11/2007">
< to>Tove</to>
< from>Jani</from>
< /note> 27
Wrong
Right

XML RuLes:
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5. Entity References
Some characters have a special meaning in XML.
-character like "<" inside an XML element, will
generate an error because the parser interprets it as
the start of a new element.
<message>if salary < 1000 then</message>
<message>if salary < 1000 then</message>

Characters have a special meaning in XML
Characters meanings in XML
Less than
<<
Greater than
>&qt;
ampersand
&&
apostrophe
‘'
Quotation mark"
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tensibleXeXML Elements are
XML elements can be extended to carry more information.
<note>
<to>Tove</to>
<from>Jani</from>
<body>Don't forget me this weekend!</body>
</note>
Added some extra information to it:
<note>
<date>2008-01-10</date>
<to>Tove</to>
<from>Jani</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>
Should the application break or crash?
No. One of the beauties of XML, is that it can be
extended without breaking applications. 31

Examples: 1- book store
<bookstore>
<book category="CHILDREN">
<title>Harry Potter</title>
<author>J K. Rowling</author>
<year>2005</year>
<price>29.99</price>
</book>
<book category="WEB">
<title>Learning XML</title>
<author>Erik T. Ray</author>
<year>2003</year>
<price>39.95</price>
</book>
</bookstore>
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Why XML For -informatics?
 Biology is a complex discipline.
 Wide variety of data resources and repositories.
 Biological data represented in multiple formats. (FASTA
, agp ,gff..)
 No standard protocol:
1-to interrogate biological data stores.
2-for Genomic, Proteonomic, Chemi-informatics.
3-to exchange biological data.
 Difficulties in using and exchanging data.
34

XML in -informatics
1- (Visual Genomics).
2- (ProteoMetrics).
3- (Chemical info. “atomic, crystallographic
info., structures….”).
4- ene ntology onsortium.
35

The Bioinformatics Sequences Markup Language
(BSML)
-The DTD is aimed at representing DNA, RNA, Protein
sequences and their graphic properties.
-Found the structure of the information to be similar to
the one used in the databases.
(http://www.ebi.ac.uk/embl.html)
(http://www.visualgenomics.com/products/index.html)
(http://www.ncbi.nlm.nih.gov; http://www.ddbj.nig.ac.jp) 36

Gene Ontology Consortium
Controlled description for:
1- Molecular function.
2- Biological processes.
3- Cellular locations of gene products.
37

The BIOpolymer Markup Language
(BioML)
- is different to BSML approach.
- BioML Goal (Fenyo, 1999) is “
BioML was designed to mimic the
hierarchical structure of aliving organism.”
- Data integration e.g nucleotide and protein sequences
38

Xml in bio medical field

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