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ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry Resources (and lessons from President Bush). Antony Williams 5th Meeting on U.S. Government Chemical Databases and Open Chemistry August 2011. I want to know about “Vincristine”.
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ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry Resources (and lessons from President Bush) Antony Williams5th Meeting on U.S. Government Chemical Databases and Open Chemistry August 2011
ChemSpider • The Free Chemical Database • A central hub for chemists to source information • >26 million unique chemical records • Aggregated from >400 data sources • Chemicals, spectra, CIF files, movies, images, podcasts, links to patents, publications, predictions • A central hub for chemists to deposit & curate data
Essential aspects of ChemSpider • ChemSpider is a BIG database..and growing • Our focus has increasingly become QUALITY over quantity • Data curation and validation is our strength – crowdsourcing is contributing, more is required • Validated data has enabled linking of the internet
“All That Glisters is Not Gold”What is the structure of Discodermolide?
Data Curation…long torturous task • Data curation – JUST structure-name validation is a long, torturous, iterative task. • How about validating “data” – PhysChem data such as logP data, boiling points, melting points (J.C.Bradley’s talk), spectra
Hand on my heart • No offence meant by what follows! We ALL have quality issues!
PHYSPROP Database The freely downloadable database under the EPI Suite prediction software Very Basic filters suggest data quality issues
The Stereochemistry challenge.12500 chemicals with “missed” stereo
Data Curation…long torturous task • Data curation – JUST structure-name validation is a long, torturous, iterative task. • How about validating “data” – PhysChem data such as logP data, boiling points, melting points (J.C.Bradley’s talk), spectra • The crowd in crowdsourcing is …generally small • Which of the large databases are doing careful curation. How can we share the workload? Hmm..
Consider searching each of these chemical databases by chemical name (systematic name, trade name or synonym). Please mark each online resource according to how much you generally trust the results.
ChemSpider can “do it” for us • ChemSpider has built a curation interface used by the community and ourselves for curating. • All curation activities are available for review, online immediately, iteratively checked. • Curators have different abilities based on their profile: There are only a few “Master Curators”. • Can we “share” the curation workload?
Identifier Dictionaries • Reciprocal curation processes…share curation with each other. • If a database has a compound already then use InChiKeys to match “suggested” validation against the compound. • A series of “added” and “removed” synonyms against InChIKeys for matching. • Who will participate???
User Understanding of Data • Users searching “Yohimbine” expect to find it…not labeled versions of it, not ambiguous stereochemistries, not partial stereochemistries. • Data “aggregation” into a meaningful form is a major challenge. e.g. Assays for radiolabeled compounds linked to actual drugs. • Data curation efforts such as ChEMBL are essential!
