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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 1995. Websites are increasingly interfaces to dynamic applications Database driven backends. 2 Tier design. MCM Server. Update. - PowerPoint PPT Presentation
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MCM Website
The underlying technology
Dr Stephen PascoeBritish Atmospheric Data Centre
Evolving use of the Web
Use of the web has changed a lot since 1995. Websites are increasingly interfaces to dynamic
applications Database driven backends.
2 Tier design
Web Server
Web Browser
MCM Server
Developer
MySQL Database
Update
Query
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)CCCalculateCanonical No. 7438297
Name SMILES Canon
PROPANOL C(O)CC 7438297
… … …
DatabaseLookup
Accord can do thisBUT not on the web server
Finding Reactions
Raction id Species Type
1 NBUTANE Reactant
1 OH Reactant
1 CCCO[O.] Product
2 … …
Reaction id Expression Rate
1 NBUTANE + OH = CCCO[O.] …
2 … …
Relational approach
Accord DB
Full Text Search
MySQL
Indexed words
Developer interaction
Accord data
Name
Species
Accord data
Name
Species
Reaction category
Rate expression
Reaction expression
Reactions
Reaction category
Rate expression
Reaction expression
Reactions
Structural information
Canonical number
SMILES
Name
Species
Structural information
Canonical number
SMILES
Name
SpeciesLocal Tables
Reaction category
Rate expression
Reaction expression
Reactions
Reaction category
Rate expression
Reaction expression
Reactions
MySQL Tables
AccessAccord ODBCParametersParameters
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 thisBUT not on the web server
Developer interaction
Accord data
Name
Species
Accord data
Name
Species
Reaction category
Rate expression
Reaction expression
Reactions
Reaction category
Rate expression
Reaction expression
Reactions
Structural information
Canonical number
SMILES
Name
Species
Structural information
Canonical number
SMILES
Name
SpeciesLocal Tables
Reaction category
Rate expression
Reaction expression
Reactions
Reaction category
Rate expression
Reaction expression
Reactions
MySQL Tables
AccessAccord ODBCParametersParameters
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.
