1. Chemical Naming Daniel Bonniot, PhD October 2008

2. Naming history Structure to Name since 2007 Name to Structure since 2008 (Marvin/JChem 5.1) Document to Structure: in progress

3. Structure to IUPAC Name Usage Plugin in MarvinView and MarvinSketch Label updated in real-time in MarvinSketch Batch: Save As: IUPAC Name in MarvinView Batch: command line (molconvert, cxcalc) Instant JChem 2

4. Structure to IUPAC Name Evaluation Test on random molecules from PubChem Semi-automatic testing with manual inspection Names generated for 99.9% of the structures Correct name for 99.6%

5. Structure to IUPAC Name Future work Complex fused rings Specialized nomenclatures (e.g. sugars) depending on demand Extend traditional nomenclature

6. Name to Structure Usage Paste a name in MarvinView and MarvinSketch Automatic format recognition Open IUPAC Name file in MarvinView or MarvinSketch (.name extension) Import name file into InstantJChem database Batch from command line (molconvert)

7. Name to Structure Evaluation ChemAxon name import on ChemAxon generated names: Name imported in 87.3% of the cases Correct structures: 95.6% ChemAxon name import on LexiChem generated names: Name imported in 81.4% of the cases Correct structures: 89% (+4% where only stereochemistry is wrong)

8. Document to Structure Find chemical names in a text document (PDF, HTML,...) Convert those names into chemical structures As required: extract them, annotate the document,... Demo web service website adds annotations to any public webpage: http://www.chemicalize.org

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