1. Chemoinformatics and eScience
P. Murray-Rust
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Topics
Need to bring bioinformatics thinking and practice into chemoinformatics, so… * Development of Open, Modular, Systems * Collaborative working * Interoperable data and new methods of data capture * Adoption of Web and other standards * Re-use of data and components * Ontologies * Demos (May need to cover Jeremy Frey?)
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eScience
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eScience
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Data
Chemistry is micropublished and most data is lost or corrupted at/before publication * IP problems (publishers, aggregators) Current approaches: * work w. early adopter publishers (Nature, RSC, IUCr) * publicise concern in eScience and (SPARC) * develop and promote modern authoring tools * encourage data in institutional repositories (
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Code and algorithms
Almost all chemoinformatics code is closed. * Algorithms are not visible or re-usable * innovation is reduced. * systems cannot be freely redistributed * “free to academics” is of dubious value * data resource (parameterisation) is usually opaque So, emulate bioinformatics : * toolkits (“The blue Obelisk”: CDK, JUMBO, Jmol, JChempaint, Openbabel * workflows (myGrid, Taverna, Kepler, Hades…) * web services (
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“Standards”
Virtually no standards in chemistry, some proprietary approaches: * Molecules: MOLFile, SMILES * Reactions: RXN Must extend to Web approaches: * XML, RDF, RSS, XSLT, OWL, BPEL * Chemistry: CML, ThermoML * Properties: ? (IUPAC etc. transformed to RDF)
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8. Ontologies and Metadata
Chemical ontology is implicit; few explicit formalisations * However many subdomains are well understood and formalised on paper (e.g. IUPAC) Standard approaches to metadata: * simple metadata: Dublin core * structured metadata: MPEG21-DIDL * require formalisation of chemical semantics, e.g. through RDF/OWL * Example: materialsGrid is a computational materials project (Frankfurt, Cambridge, Daresbury, IBM, Accelrys, funded by DTI/eScience, 2005Q4) which will create formal metadata and dictionaries.
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9. Chemoinformatics Open Grid
UK eScience Phase3 (EPSRC). 2-3 projects to be funded ca. 3M GBP each. * UCC has gathered a consortium with: Manchester (lead for myGrid, Taverna); Southampton (ontologies), Cologne (CDK), and 3 commercial partners. * Intensive Collaboration with IU and NIH/NCI. * Primary goal is to develop Grid-based approaches for application to data from PubChem * shortlist to be announced
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