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S. E.
Stein, S. R. Heller, D. V. Tchekhovskoi
Physical & Chemical Properties Division
NIST |
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Chemical structure is the true ‘identifier’ |
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But, structures are not unique or convenient for
computers |
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Convert structure (connection table) to unique
string of characters by algorithms |
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The Iupac CHemical Identifier (IChI) |
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Originators |
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Capable of full representation |
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Eliminate ‘conventions’ |
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Maximum application |
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‘Clients’ |
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Robust |
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Selectable specificity |
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Software |
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Implement through external structure processing
software |
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Chemicals |
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Rapid reaction (tautomerization) |
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Ambiguous/uncertain structure |
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Chemists |
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Differing conventions |
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Based on discipline, education and convenience |
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Chemistry |
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‘Normalize’ Input Structure |
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Implement chemical rules |
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Math |
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‘Canonicalize’ (label the atoms) |
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Equivalent atoms get the same label |
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Convention |
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‘Serialize’ the Labeled Structure |
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Output as a Series of Bytes |
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Ignore ‘Electron Density’ |
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Double/Triple/Coordination bonds |
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Odd-electrons/Charges |
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Stereochemistry |
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Free rotation around single bonds |
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No stereo < 8-membered rings (default) |
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Divide structure information into ‘layers’ |
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Not required for compound identification |
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Represent ‘excited states’ |
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Simplify representations |
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Delocalization, aromaticity, zwitterions,
coordination … |
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Formula |
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Connectivity |
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Stereochemistry |
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Isotopic ‘Corrections’ |
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Disconnect metals and H-atoms |
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Reconnect metals |
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Reconnect H-atoms |
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Non-mobile (non-tautomers) |
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Mobile (distinguish tautomers) |
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sp2 – double bond |
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sp3 – tetrahedral |
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{others added later} |
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Byproduct of IChI Creation |
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Assist chemists for structure confirmation |
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Byproduct |
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Label stereogenic atoms |
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Identify equivalent atoms |
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Warnings/Errors |
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Unusual valences |
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Unrecognized input |
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‘Reversibility’ |
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Coordinates |
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Bond/Charge Location |
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Each term on a PDF page |
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Looks like printed page |
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Links to other definitions |
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For display only |
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Not easily convertible |
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Graphics, symbols, equations |
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Text not ‘parsed’ |
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No ‘metadata’ |
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Text |
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Perceive and tag data types and relationships |
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Simple Structures |
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To connection tables/CML/SVG |
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Equations |
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To MathML |
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Figures & Complex Schemes |
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Redraw in SVG |
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Use by Other MLs |
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Schema |
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Integrate dictionary via STMML |
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Internal Maintenance |
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Develop ‘authoring’ procedures |
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Provide uniform chemical terminology for XML
documents |
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Traceablity of terminology |
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Root for the ‘tagging’ of chemistry |
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Model for future IUPAC recommendations |
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‘Template’ for numeric property validation in
chemistry |
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Ensure proper units and representation |
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Traceability
to IUPAC definition |
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Basic Standards for Numeric Data ‘Tagging’ |
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Periodic Table and Relative Molar Masses |
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‘Official’ digital source |
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Connect to relevant IUPAC information |
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Root of chemical information ‘tree’ |
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Spectroscopy, electrochemistry, thermochemistry,
catalysis, … |
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Nov 12-14 Meeting at NIST |
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IChI |
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Final Beta Nov. 2002 |
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Dissemination |
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Version 2 |
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XML Data Dictionary |
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Finish Gold Book Conversion |
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Maintenance Path |
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Begin Green Book |
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Notes