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ChemSpider – The Vision and Challenges Associated with Building a Free Online Community Resource for Chemists
The document summarizes the vision and challenges of ChemSpider, a free online database for chemists. Key points: - ChemSpider aims to connect chemistry online by allowing structure and substructure searching across databases and literature. - It was built as a "hobby project" on limited resources but has grown significantly. - Ensuring data quality is challenging due to errors inherited from other databases that propagate. - Crowdsourcing curation and developing identification standards like InChI can help address data quality issues. - Future work includes expanding search capabilities, curating more data sources, and developing collaborative curation.
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ChemSpider – The Vision and Challenges Associated with Building a Free Online Community Resource for Chemists
- 1. ChemSpider – TheVision and Challenges Associated with Building a Free Online Community Resource for Chemists Antony Williams AZ, February 2011
- 2. What’s the Statusof Chemistry online? Encyclopedic articles (Wikipedia) Chemical vendor databases Metabolic pathway databases Virtual Screening databases Property databases Screening assay results Patents with chemical structures ADME/Tox data Scientific publications Compound aggregators Blogs/Wikis and Open Notebook Science
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- 4. Org Prep Daily (Blog)
- 5. Molbank (Open AccessJournal)
- 6. Lots of “PublicCompound” Databases PubChem Drugbank ChEBI/ChEMBL KEGG LipidMAPs ChemIDPlus eMolecules ZINC Lots of chemical vendors ChemSpider
- 7. Where Would Youlook? What Do You Trust?
- 8. Linked Data onthe Web
- 9. What is acompound? “ARTAs”
- 10. Vision: Connect Chemistryon the Web The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar) Chemistry articles are indexed and searchable by a free online service The web is linked together through the “language of chemistry” Publicly funded research data is linked
- 11. We Have Deliveredthe Vision “ Build a Structure Centric Community to Serve Chemists” Integrate chemical structure data on the web Create a “structure-based hub” to information, data and algorithmic predictions Let chemists contribute their own data Allow the community to curate/correct data
- 12. How Was ChemSpiderBuilt? ChemSpider was a “hobby project” Housed in a basement and running off three servers – one bought, two built Sensitive to weather and power stability Went live at ACS Spring 2007 in Chicago
- 13. How Did WeBuild It? We deal in Molfiles or SDF files We do rudimentary filtering – valence checking, charge imbalance – prior to deposition We have our own “business logic” to standardize Link out to external sites where possible using IDs
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- 15. We Want toAnswer Questions Questions a chemist might ask… What is the melting point of n-heptanol? What is the chemical structure of Xanax? Chemically, what is phenolphthalein? What are the stereocenters of cholesterol? Where can I find publications about xylene? What are the different trade names for Ketoconazole? What is the NMR spectrum of Aspirin? What are the safety handling issues for Thymol Blue?
- 16. Search for aChemical…by name
- 17. Link off astructure in ChemSpider Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “ Everything”
- 18. Available Information… Linkedto vendors, safety data, toxicity, metabolism
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- 20. Clickthrough to Patent(SureChem)
- 21. Crowdsourced “Annotations” RegisteredUsers can add Descriptions/Syntheses/Commentaries Links to PubMed articles Links to articles via DOIs Add spectral data Add Crystallographic Information Files Add photos Add MP3 files Add Videos
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- 25. Search for achemical…by structure Substructure search coming…
- 26. Inherited Errors Inheritederrors from every database… all public compound databases, including ours, have errors “ Incorrect” structures – assertions, timelines etc “ Incorrect” names associated with structures ENORMOUS CHALLENGE
- 27. What is theStructure of Vitamin K?
- 28. MeSH A lipidcofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants , VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K
- 29. What is theStructure of Vitamin K1?
- 30. What is theStructure of Vitamin K1?
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- 33. “ 2-methyl-3-(3,7,11,15-tetramethyl hexadec-2-enyl)naphthalene-1,4-dione”Variants of systematic names on PubChem 2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E)-3,7,11,15-tetramethyl 2-methyl-3-(3,7,11,15-tetramethyl 2-methyl-3-[(E)-3,7,11,15-tetramethyl
- 34. Question Everything online:www.dhmo.org
- 35. It’s all onWikipedia…
- 36. Chemistry on TheInternet Is Messy
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- 40. What ELSE is Methane???
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- 46. Public Domain ChemistryDatabases Our databases are a mess… Non-curated databases are proliferating errors We source and deposit data between databases Original sources of errors hard to determine Curation is time-consuming, challenging and exacting An examination of quality in databases – inter/intra lab comparison of processes for 150 drugs
- 47. Drug Name GenericName ChEBI ChemSpider CAS Com. Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia Spiriva Tiotropium Bromide No Hits No Hits 4/0 Depakote Valproate 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
- 48. Symbicort: Budesonide +Formoterol
- 49. Symbicort: Budesonide +Formoterol ChemIDPlus Wikipedia
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- 51. Symbicort: Budesonide +Formoterol PubChem 8 structures called Budesonide. 1 “correct” 6 structures called Formoterol. 1 “correct” Search on “Symbicort” gives 1 structure.
- 52. Taxol: Paclitaxel 44 structures
- 53. Taxol: Paclitaxel Bioassay Data
- 54. Taxol: Paclitaxel Bioassay Data Most Bioassay data associated with structure with one ambiguous stereocenter
- 55. Consider searching eachof 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.
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- 60. The Final SearchStrategy
- 61. All Those Names,One Structure
- 62. Searching Chemistry onthe Internet How complete a result set will we get if we search for “chemicals” by name? Is there a better way to link chemistry databases? Linking by “names” is dangerous Chemists want structure and SUBstructure searching
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- 65. InChIStrings Hash toInChIKeys
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- 70. Vancomycin Search MolecularSKELETON Search Full Molecule
- 71. Full Molecule Search: 4 Hits
- 72. Full Skeleton Search: 104 Hits
- 73. Vancomycin Who willcurate? How would you clean such a large dataset?
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- 81. Name Searching is“Easier”
- 82. Name Searching is“Easier”
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- 85. Content is Kingand Quality Costs Curated Chemistry “content” is expensive to create Patent searching Structures and properties Drug databases Literature databases Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information 104 years of content >50 million substances Proprietary platform
- 86. The EXPERTS mustget it right?!
- 87. Wikipedia, C&E News,PubChem C&E News (from ACS)
- 88. Feedback from SteveRitter “ Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.” “ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”
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- 93. Semantic Mark-up forChemistry Semantic mark-up for chemistry is here RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies Nature publishing group compound linking
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- 98. And linked toSTITCH…
- 99. Success Depends onDictionaries
- 100. Online Curation Onlinedatabases generally do NOT allow curation or annotation If you find errors they stay there! ChemSpider allows immediate curation
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- 106. Crowdsourcing Works >130people have deposited data and participated in data curation Different level curators check each other Wikipedia is the modern primary example
- 107. ChemSpider and PublishingThe curation efforts on ChemSpider led to a set of validated dictionaries Integrate best-in-class entity extraction with validated name dictionaries Already text-mined the RSC archive and presently linking!
- 108. Crowdsourcing Synthesis ChemSpiderSyntheticPages
- 109. Crowdsourcing Synthesis ChemSpiderSyntheticPages
- 110. ChemSpider Everywhere: Whatdo computers want? Web services
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- 112. ChemSpider Everywhere Linkedfrom Wikipedia and many Public Databases Linked from Open Notebook Science sites Linked from Blogs using Structure/Spectra EMBED Integrated into structure drawing packages Integrated to software offerings from Thermo, Waters, Agilent, Bruker
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- 115. ChemSpider Everywhere CrowdsourcedCuration of Spectra
- 116. ChemSpider Everywhere :ChemMobi
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- 121. There will alwaysbe gaps... What ChemSpider does not deal with, yet... Materials Minerals Polymers Biological macromolecules
- 122. Collaborative Data CurationHow can we COLLECTIVELY clean online data? Developing ways to share curation actions back to original data sources A mindset of bigger is better is problematic. How many “real chemicals” are in the public databases?
- 123. Future Work Continuecuration work Extend search capabilities Expand existing databases Text-mine RSC archive and link chemistry Project: pre-competitive data sharing and linking for Life Sciences Integrate to metabolic pathways tools
- 124. The Future ofChemistry on the Web? Public compound databases federate & build a linked environment of validated data! Data validation needs are not ignored Publishers layer on information to make publications discoverable Public-Private databases can be linked Open Data proliferate The “ Semantic Web ” in action
- 125. It’s a longroad ahead…
- 126. Thank you Email:[email protected] Twitter: ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams