MCM Website The underlying technology Dr Stephen Pascoe British Atmospheric Data Centre

Evolving use of the Web Use of the web has changed a lot since Websites are increasingly interfaces to dynamic applications Database driven backends.

2 Tier design Web Server Web Browser MCM Server Developer MySQL Database Update Query Response URL HTML

Requirements 1. Find reactions of a species quickly. 2. Search for species by SMILES string. 3. Extract sub-mechanisms. 4. Depict (draw) structures. 5. Attach context (metadata) to reactions. 6. Interact easily with current developers tools (Accord) Indexing Coordinates Database design

Indexing What can we index? MCM name: Unique  NOT Systematic SMILES string: Systematic  NOT Unique We need a Unique Systematic Identifier. Unique linear representation: USMILES, IChI Canonical number. Accord, ICAMS.

Searching Web form Search: C(O)CC Calculate Canonical No NameSMILESCanon PROPANOLC(O)CC ……… Database Lookup Accord can do this BUT not on the web server

Finding Reactions Raction idSpeciesType 1NBUTANEReactant 1OHReactant 1CCCO[O.]Product 2…… Reaction idExpressionRate 1NBUTANE + OH = CCCO[O.]… 2…… Relational approach Accord DB Full Text Search MySQL Indexed words

Developer interaction

Depicting The hard part is generating the 2D coordinates. We need a connection table. MDL Mol file Accord Chemistry MDL Molfile MySQL Database MCM Server PNG image Export Insert Render Connection Table Accord can do this BUT not on the web server

Developer interaction Export Mol Calc canon.

Context Every reaction belongs to a category. Categories are web template URL. General categories can be refined into more specific ones. Rate parameters also have a context URL. By explicitly parameterising SAR rates we could provide full context for rates.

Future Context for rate coefficients Know the source of a rate. Evaluate uncertainty We would need to redo all SAR calculations. New developments in Cheminformatics CML: Could replace Mol files IChI: The new SMILES? OpenSource development tools CDK: Depiction & uninque id. Generation. Integrated species editor.

The End Thanks.