Scientific Applications of XML

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Scientific Applications of XML

• Arvind Hulgeri, Shantanu Godbole
• aru_at_cse.iitb.ernet.in shantanu_at_it.iitb.ernet.in

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MathML

• Math
• Markup
• Language

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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

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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

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Example a b
Content ltapplygt ltplus/gt ltcigtalt/cigt
ltcigtblt/cigt lt/applygt
Presentation ltmrowgt ltmigtalt/migt ltmogtlt/mogt ltmigt
blt/migt lt/mrowgt
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Example (a b)2
Presentation ltmsupgt ltmfencedgt
ltmrowgt
ltmigtalt/migt
ltmogtlt/mogt
ltmigtblt/migt lt/mrowgt
lt/mfencedgt ltmngt2lt/mngt lt/msupgt
Content ltapplygt
ltpower/gt ltapplygt
ltplus/gt
ltcigtalt/cigt ltcigtblt/cigt
lt/applygt
ltcngt2lt/cngt lt/applygt
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Annotations
ltapplygt ltint/gt ltbvargtltcigtxlt/cigtlt/bvargt
ltlowlimitgtltcngt0lt/cngtlt/lowlimitgt
ltuplimitgtltcigttlt/cigtlt/uplimitgt ltapplygt
ltdivide/gt ltcngt1lt/cngt
ltcigtxlt/cigt lt/applygt lt/applygt
Content
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Annotations
ltmrowgt ltmsubsupgt ltmogtintlt/mogt
ltmngt0lt/mngt ltmigttlt/migt
lt/msubsupgt ltmfracgt ltmrowgt
ltmogtddlt/mogt ltmigtxlt/migt
lt/mrowgt ltmigtxlt/migt
lt/mfracgt lt/mrowgt
Presentation
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Annotations
ltsemanticsgt Content encoding ltannotation-xml
encoding"MathML-Presentation"gt Presentation
encoding lt/annotation-xmlgt lt/semanticsgt
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Why Two Markups?

• Same notation may represent several mathematical
  ideas (e.G. Xi)
• Same mathematical idea often has several
  notations (factorial)

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CML

• Chemical
• Markup
• Language

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CML Objectives

• 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

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CML

• chemical elements (e.g. ltmoleculegt, ltreactiongt,
  ltcrystalgt) used to indicate chemical 'objects'.
  For example, a ltmoleculegt will contain a ltlistgt
  of ltatomgts, which in turn have three ltfloatgts
  specifying Cartesian coordinates for each atom

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CML Supports Chemical Components

• Spectra and other instrumental output
• Crystallography
• Organic and inorganic molecules
• Physicochemical quantities (including units)
• MO calculations
• Macromolecules Sequence protein, ligand and
  sequence
• Molecular Hyperglossaries text and molecules
• Unidirectional hyperlinks and Multidirectional
  hyperlinks

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CML has core elements for

• molecule . A connected set of atoms.
• atom . An atom (usually within a molecule
• bond . A link between 2 (or more) atom s within a
  molecule
• atomArray and bondArray . Containers for atom s
  and bond s.
• electron . Provides details of electrons in atom
  s, bond s and molecule s

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CML Objectives

• Absence of mechanisms in HTML for directly
  handling chemical information e.g. molecular
  structures
• 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

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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
• The lack of a clear separation of content from
  the formatting or presentation in the HTML
  document
• Need for a single, human readable format
  combining both textual and non textual
  information within a single document

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CML Objectives
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CML Objectives

• Absence