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Scientific Applications of XML

Scientific Applications of XML. Arvind Hulgeri, Shantanu Godbole aru@cse.iitb.ernet.in shantanu@it.iitb.ernet.in. MathML. Math Markup Language. MathML Objectives. Encode mathematical material for teaching and scientific communication

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Scientific Applications of XML

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  1. Scientific Applications of XML Arvind Hulgeri, Shantanu Godbole aru@cse.iitb.ernet.inshantanu@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 Content: <apply> <plus/> <ci>a</ci> <ci>b</ci> </apply> Presentation: <mrow> <mi>a</mi> <mo>+</mo> <mi>b</mi> </mrow>

  6. Example: (a + b)2 Presentation: <msup> <mfenced> <mrow> <mi>a</mi> <mo>+</mo> <mi>b</mi> </mrow> </mfenced> <mn>2</mn> </msup> Content: <apply> <power/> <apply> <plus/> <ci>a</ci> <ci>b</ci> </apply> <cn>2</cn> </apply>

  7. t   dx x 0 Annotations <mrow> <msubsup> <mo>&int;</mo> <mn>0</mn> <mi>t</mi> </msubsup> <mfrac> <mrow> <mo>&dd;</mo> <mi>x</mi> </mrow> <mi>x</mi> </mfrac> </mrow> Presentation

  8. t   dx x 0 Annotations <apply> <int/> <bvar><ci>x</ci></bvar> <lowlimit><cn>0</cn></lowlimit> <uplimit><ci>t</ci></uplimit> <apply> <divide/> <cn>1</cn> <ci>x</ci> </apply> </apply> Content

  9. Annotations <semantics> Content encoding <annotation-xml encoding="MathML-Presentation"> Presentation encoding </annotation-xml> </semantics>

  10. Why Two Markups? • Same notation may represent several mathematical ideas • xi = x power i • = ith element of vector x • Same mathematical idea often has several notations nCm

  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. <molecule>, <reaction>, <crystal>) used to indicate chemical 'objects'. • E.g. a <molecule> will contain a <list> of <atom>s, which in turn have three <float>s specifying Cartesian coordinates for each atom

  16. Partial XML file - “ethanol” • <cml title="ethanol" id="cml_ethanol" > • <molecule title="ethanol" id="mol_ethanol" • xmlns="x-schema:cml_schema_ie_02.xml" convention="mol" > • <formula>C2 H6 O </formula> • <string title="CAS" >64-17-5 </string> • <float title="molecular weight" >46.07 </float> • <list title="atoms" > • <atom id="ethanol_a_1" convention="mol" > • <integer builtin="atomId" >1 </integer> • <float builtin="x3" units="A" >1.0303 </float> • <float builtin="y3" units="A" >0.8847 </float> • <float builtin="z3" units="A" >0.9763 </float> • <string builtin="elementType" >C </string> • </atom> …

  17. Some XSL processing • <xsl:template match="molecule"> <!-- Pull out @id="" etc --> • <table> • <tr><td>Molecule ID:</td> • <td>Formula:</td> • <td>CAS:</td> </tr> • <tr><td><xsl:value-of select="@id"/></td> • <td><xsl:value-of select="formula"/></td> • <td><xsl:value-of select="*[@title = 'CAS']"/></td></tr> • <tr><td>Alternate Names:</td> • <td colspan="6"> <xsl:for-each select="list[@title = 'alternate names']/string[@title='name']"> • <xsl:value-of select="text()"/>, </xsl:for-each> </td> </tr> • </table> • </xsl:template>

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

  19. 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/

  20. 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/

  21. 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/

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

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

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