Xml in bio medical field

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XML in Bio- medical field

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Xml in bio medical field

  1. 1. Presented by: Eng. Juman Ghazi Director: Dr. Eng. Rasha Masood
  2. 2. 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
  3. 3. 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
  4. 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
  5. 5. Components of an XML Document 1. Elements: <hello> 2. Attributes: <item id=“33905”> 3. Entities: &lt; (<) 4. Advanced Components 1. CData Sections 2. Processing Instructions 6
  6. 6. Example in HTML 7 <html> <head> <title>Menu</> </head> <body> <h1>Soup</h1> <h4>4.99</h4> </body> </html>
  7. 7. HTML in web browser 8
  8. 8. Example in HTML 9 <?xml version=“1.0” ?> <menu> <item> <itemname>soup</itemname> <cost>4.99</cost> </item> </menu>
  9. 9. XML in web browser 10
  10. 10. 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
  11. 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
  12. 12. 13 Root (text) (text) (text) element element
  13. 13. 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
  14. 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
  15. 15. Comments:  Appear anywhere in document - Start tag <!-- - End tag --!>  contents inside comment are not parsed. 17
  16. 16. More in XML: 1. Schemas 2. Parsers 3. Editors 4. Standards 18
  17. 17. 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
  18. 18. Industry standards and data exchange: 20
  19. 19. 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
  20. 20. 3. Editors:  Text and graphical editors facilitate the editing of XML code.  Benefits of using editors: coding effort. -Provide to perform tasks. 22
  21. 21. 23
  22. 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. 24
  23. 23. 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
  24. 24. 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
  25. 25. 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
  26. 26. XML RuLes: 28 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 &lt; 1000 then</message>
  27. 27. Characters have a special meaning in XML Characters meanings in XML Less than <&lt; Greater than >&qt; ampersand &&amp; apostrophe ‘&apos; Quotation mark&quot; 29
  28. 28. 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
  29. 29. 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> 32
  30. 30. 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
  31. 31. XML in -informatics 1- (Visual Genomics). 2- (ProteoMetrics). 3- (Chemical info. “atomic, crystallographic info., structures….”). 4- ene ntology onsortium. 35
  32. 32. 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
  33. 33. Gene Ontology Consortium Controlled description for: 1- Molecular function. 2- Biological processes. 3- Cellular locations of gene products. 37
  34. 34. 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

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