Information modeling is at the heart of informatics.
The molecular information model is cool.
Discuss problems/solutions.

One usually needs to represent real things in a computer program using digital representations.

• Abstract things are easiest, e.g., numbers.
• Even simple numbers are non-trivial (odd ones too ;-)
  Remember PL/1, with a dozen ways to represent an number?
• IBM made a fortune using numbers to represent money.

Fundamental chemical informatics: 1 of 8

What chemical entities are useful to represent?

• Molecules (valence, LCAO, ab initio/quantum models)
• Reactions (same as molecular models, also dynamics)
• Substances (not necessarily molecular models)
• Mixtures (may or may not be molecular)
• Molecular patterns (theoretical, statistical, legal)
• other ... crystals, large molecules, polymers, alloys, catalysts

Fundamental chemical informatics: 2 of 8

• Storage/retrieval Basic input and output. Efficiency
• Identity Are two entities same or different?
• Reactions (same as molecular models, also dynamics)
• Substances (not necessarily molecular models)
• Mixtures (may or may not be molecular)
• Molecular patterns (theoretical, statistical, legal)
• other ... crystals, large molecules, polymers, alloys, catalysts

E.g., SMILES are semantically well-defined representations of a specific valence models for molecules and reactions. Names are more useful for representing things without a useful valence model, e.g., "Turpentine" or "Unknown 123".

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4. Fundamental chemical informatics: Part THREE

How can we represent chemical entities in a computer?

• Name (IUPAC, index name, common name, etc.)
• Number (e.g., CAS Registry Number
• Picture (e.g., WIMP)
• Properties (e.g., ECN)
• Connection table (e.g., SDF, MOL, MOL2, etc.)
• Linear notation (WLN, SMILES, ROSDAL)

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0. How can one do anything useful with a computer?
1. What chemical entities are useful to represent?
2. What operations on chemical entities are useful?
3. How can we represent chemical entities in a computer?
4. How can we associate properties with chemical entities?

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5. Fundamental chemical informatics: Part FOUR

How can we represent a chemical entities in a computer?

• Name (IUPAC, index name, common name, etc.)
• Number (e.g., CAS Registry Number
• Picture (e.g., WIMP)
• Connection table (e.g., SDF, MOL, MOL2, etc.)
• Linear notation (WLN, SMILES, ROSDAL)

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