1. Scientific Applications of XML Arvind Hulgeri, Shantanu Godbole aru@cse.iitb.ernet.in shantanu@it.iitb.ernet.in

2. MathML Math Markup Language

3. MathML Objectives Encode mathematical material for teaching and scientific communication Encode both mathematical notation and mathematical meaning Facilitate conversion to and from other math formats, both presentational and semantic. e.g., Tex, braille Allow the passing of information intended for specific renderers and applications Provide for extensibility Be human legible, and simple for software to generate and process

4. Presentation and Content Markup Presentation markup Captures notational structure Facilitate rendering to various media Content markup Captures mathematical structure Facilitate the assignment of mathematical meaning to an expression Can be mixed together

5. Example: a + b Presentation: a + b Content: a b

6. Example: (a + b) 2 Presentation: a + b 2 Content: a b 2

7. Annotations t  0 dx x ∫ 0 t ⅆ x x Presentation

8. Annotations x 0 t 1 x Content t  0 dx x

9. Annotations Content encoding Presentation encoding

10. Why Two Markups? Same notation may represent several mathematical ideas x i = x power i = i th element of vector x Same mathematical idea often has several notations n C m

11. CML Chemical Markup Language

12. CML – What it does Universal, platform and application independent format for storing and exchanging chemical information Publishing, querying, communicating chemical information for both humans and machines Facilitate conversion to and from legacy formats used by popular chemical editing and display programs

13. CML – The need Absence of mechanisms in HTML for directly handling chemical information e.g. molecular structures and spectra Difficulties in automatically recognizing and extracting chemical data Development and extension of a Chemical Markup Language (CML) and techniques to allow the display of molecules, spectra and reactions within a web browser

14. CML Objectives A present day online chemical paper might consist of HTML text, static bit-map images, diagrams and molecular structures from an external legacy data file (e.g. MOL, PDB) The external data files become isolated from the text and from each other Need for a single, human readable format combining both textual and non textual information within a single document

15. CML – Chemical components Chemical Components (e.g.,, ) used to indicate chemical 'objects'. E.g. a will contain a of s, which in turn have three s specifying Cartesian coordinates for each atom

16. Partial XML file - “ethanol” <molecule title="ethanol" id="mol_ethanol" xmlns="x-schema:cml_schema_ie_02.xml" convention="mol" > C2 H6 O 64-17-5 46.07 1 1.0303 0.8847 0.9763 C …

17. Some XSL processing Molecule ID: Formula: CAS: Alternate Names:,

23. Web Resources MathML http://www.w3c.org/math CML http://www.xml-cml.org

24. Other Scientific Applications Wireless Markup Language (WML) http://www.oasis-open.org/cover/wap- wml.html Bioinformatics Sequence Markup Language (BSML) http://www.visualgenomics.com/bsml/index. html The BIOpolymer Markup Language (BIOML) http://www.proteometrics.com/BIOML/

25. Other Scientific Applications(contd…) Vector Markup Language (VML) http://www.w3.org/TR/NOTE-VML Precision Graphics Markup Language (PGML) http://www.oasis- open.org/cover/pgmlDTD19980410.html XML Digital Signature (Signed XML) http://www.oasis- open.org/cover/xmlSig.html smartX ['SmartCard'] Markup Language (SML) http://www.smartxml.com/

26. Other Scientific Applications(contd…) Web Interface Definition Language (WIDL) http://www.w3.org/TR/NOTE-VML Weather Observation Markup Format (OMF) http://www.oasis- open.org/cover/omfDesc19980610.html X-ACT - XML Active Content Technologies Council http://www.x-act.org/

27. Some More Links… http://www.xml.com http://www.w3c.org/ http://www.oasis- open.org/cover/xml.html

28. Last but not the least!!! http://www.cse.iitb.ernet.in /~dbms/Data/Conferences /XMLWorkshop/ http://www.google.com/