chemspider – a crowdsourcing environment for hosting and validating chemistry resources
DESCRIPTION
ChemSpider is a structure centric database hosted by the Royal Society of Chemistry and integrating over 25 million chemical compounds to over 400 internet-based resources including many public domain databases, Wikipedia, chemical vendors, patents, publications and other web-based services. The intention is for ChemSpider to become one of the primary online hubs for chemists to source chemistry related data. During the development of the ChemSpider database we have utilized numerous approaches to standardizing, curating and validating the data supplied to us for hosting and integration. This presentation will provide an overview of our initial development of the ChemSpider database and provide an overview of our present processes and procedures for handling incoming data depositions. We will also discuss how crowdsourcing can help to expand, curate and validate the data on the ChemSpider database.TRANSCRIPT
ChemSpider – A Crowdsourcing Environment for Hosting and Validating Chemistry Resources
Antony Williams5th Meeting on U.S. Government Chemical Databases and Open Chemistry
August 2011
I want to know about “Vincristine”
Vincristine: Identifiers and Properties
Vincristine: Vendors and Sources
Vincristine: Patents
Vincristine: Articles
Vincristine: RSC Databases
Searches: The INTERNET
Validated Names for Searching…
And InChIs…
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?
How to distinguish…who’s wrong?
Neither is wrong
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
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
NIST Webbook
EPA’s DailyMed
EPA’s DailyMed
EPA’s DailyMed
PubChem
Linking
Patents
Patents
WYSIWYG compounds
WYSIWYG compounds
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.
Drug Name Generic Name ChEBI ChemSpiderCAS Com.
Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia
SpirivaTiotropium Bromide
No Hits No Hits 4/0
DepakoteValproate semisodium No
Structure
Basen Voglibose No Hits No Hits 2/1 Symbicort 1) Budesonide 8/1 Symbicort 2) Formoterol WRONG No Hits 6/1 Vytorin 1) Ezetimibe No Hits Vytorin 2) Simvastatin 2/1 Taxol Paclitaxel 44/1 Thalidomid Thalidomide No Hits Zocor Simvastatin 2/1 Crestor Rosuvastatin No Hits 2/1
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???
Proof of Concept Data Curation Sharing
Lessons Learned : Big vs Good!
15 compounds called Yohimbine54 Skeletons for Yohimbine
Aggegators suffer dilution…
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!
SciMobileApps.com
SciDBs.com (Coming soon)
Open PHACTS : partnership between European Community and EFPIA
Freely accessible for knowledge discovery and verification. Data on small molecules Pharmacological profiles Pharmacokinetics ADMET data Biological targets and pathways Proprietary and public data sources.
Standardization and Quality
Our initial approaches to standardization were imperfect. We are revisiting to support OpenPHACTS.
Highly dependent on InChI and not enough standardization prior to InChI generation.
InChI is excellent and acknowledged imperfect. Way better than SMILES for linking the internet!
Conclusions
ChemSpider is one of many important chemistry resources on the internet
We have assumed an important role of curating and validating data – specifically name-structure dictionaries are of high importance but data validation is also key
We are a part of the federation of internet databases serving chemistry. MORE collaboration can serve us all better…how?
Acknowledgments
Our development team – headed by THAT man..
Many in this room: InChI, PubChem, DssTOX, FDA, ChEBI/ChEMBL, SureChem, many more
Curators – special gratitude to Barrie Walker!
Software providers – OpenEye, ChemDoodle, ACD/Labs, GGA Software, Open Source (Jmol, JSpecView, OpenBabel)
Thank you
Email: [email protected] Twitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams