Navigating the Complex Web of Chemistry Using ChemSpider
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ChemSpider is a structure-centric hub for chemists, aggregating over 22 million compounds from more than 200 data sources, allowing for extensive searching and linking of chemical information across the internet. It promotes crowdsourced curation and aims to improve the quality and accessibility of chemical data while highlighting the importance of authoritative sources for chemical structures. As an evolving platform, ChemSpider embraces web technologies to enhance the sharing and validation of chemical information, ultimately aiming to create a collaborative network for the chemistry community.
![Name Recognition Azo aldehyde 2 was synthesized according to a reported method [17]. To a stirred solution of azo aldehyde 2 (1.08 g, 3.76 mmol ) in dry CH2Cl2 (30.00 mL) were successively added. (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and an excess of anhydrous MgSO4 (2.00 g, 16.67 mmol) .](https://image.slidesharecdn.com/cfakepathnavigatingthecomplexwebofchemistryusingchemspider-091009211700-phpapp02/85/Navigating-the-Complex-Web-of-Chemistry-Using-ChemSpider-77-320.jpg)
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Navigating the Complex Web of Chemistry Using ChemSpider
- 1. Navigating the Complex Web of Chemistry Using ChemSpider
- 2. Imagine a time when …. 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 can be shared and discussed in the Open, maybe as ONS?
- 3. It’s Coming…Linked Data Cloud
- 5. Org Prep Daily (Blog)
- 6. Molbank (Open Access Journal)
- 8. For Chemical Compounds Vendor sites – Aldrich, Alfa Aesar, TCI and 100s of others Government databases – PubChem, DSSTox, FDA databases, ChemIDPlus,… Biological Databases – Protein Database, Stitch, KEGG, ChEBI,… Analytical databases – Red Hen Spectra, NMRShiftDB,…
- 9. For Chemical Compounds Vendor sites – Aldrich, Alfa Aesar, TCI and 100s of others Government databases – PubChem, DSSTox, FDA databases, ChemIDPlus,… Biological Databases – Protein Database, Stitch, KEGG, ChEBI,… Analytical databases – Red Hen Spectra, NMRShiftDB,…
- 10. What is ChemSpider? ChemSpider is: Building a Structure Centric Community for Chemists 22.2 million compounds, >200 data sources A deposition and curation platform A publishing platform for the community Grows daily – more depositions, more links, more data sources
- 11. How Was ChemSpider Built? 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
- 18. Linked across the internet
- 19. Kyoto Encyclopedia of Genes and Genomes
- 20. Link off a structure in ChemSpider Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “ Everything”
- 21. Links to Patents based on structure
- 22. Clickthrough to Patent (SureChem)
- 24. Answering Questions for Chemists Questions a chemist might ask… What is the melting point of n-butanol? 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?
- 25. Complex Data and Information
- 26. ChemSpider is a structure-centric hub ChemSpider aggregates and links out across the internet Data aggregate based on “structures and links” What defines a chemical compound?
- 27. What is a compound?
- 28. Question Everything online: www.dhmo.org
- 29. PubChem
- 31. Vancomycin Who will curate? PubChem is not resourced to clean these errors How would you clean such a large dataset?
- 32. Vancomycin on ChemSpider 1 compound – 3 days
- 33. The EXPERTS must get it right?!
- 34. Wikipedia, C&E News, PubChem C&E News (from ACS)
- 35. Feedback from Steve Ritter “ As for where we source our structures, our primary source is the researcher and peer-reviewed papers , because many compounds are novel. ..we always double check them against one or more primary sources, typically Merck Index and SciFinder. 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.”
- 36. Feedback from Steve Ritter “ As a rule, we at C&EN don’t use Wikipedia as a primary source for structures or chemical information, and I recommend that policy to anyone .” “ 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 .”
- 38. Comments on the Blog Kirill Degtyarenko says: September 15th, 2009 at 1:57 pm It looks like both ChEBI and Wikipedia structures are wrong as far as aglycon is concerned. According to http://www3.interscience.wiley.com/journal/20330/abstract “… for the first time to confirm beyond all doubt the structure suggested by Tschesche and Wulff for digitonin by means of modern NMR techniques, and to assign all proton and carbon resonances.” Structure 1 shows methyl group at C-20 going UP, i.e. 20β (while by default spirostan is 20α).
- 39. CAS as an authority
- 40. The Blogging Community Participate
- 41. Will it ever end? The community says the structure of digitonin has “up” 20-Methyl. If so, then multiple substances related to digitonin have OPPOSITE stereo at 20-Methyl The spirostane skeleton is considered to have a “down” Methyl group so all spirostane-related structures would be wrong The ACD/Dictionary has 24 structures with close skeleton and all have the “down” Methyl group.
- 43. Structures on DailyMed
- 45. Incorrect Structures
- 46. Wow!
- 48. Drugbank
- 49. Taxol on PubChem
- 50. FDA’s DailyMed
- 52. Multiple Layers
- 53. InChIStrings Hash to InChIKeys
- 54. InChIs for Taxol
- 55. Back to Taxol DrugBank: RCINICONZNJXQF-CLDWUXIMDD ChEBI: RCINICONZNJXQF-GXKQXQCDDN Wikipedia: RCINICONZNJXQF-MZXODVADBJ Which one is correct???
- 56. InChIKeys for Taxol DrugBank: RCINICONZNJXQF-CLDWUXIMDD ChEBI: RCINICONZNJXQF-GXKQXQCDDN Wikipedia: RCINICONZNJXQF-MZXODVADBJ ChEBI and Wikipedia are the SAME structure Drugbank is a DIFFERENT structure – ONE stereocenter
- 57. Does one stereocenter matter?
- 58. Does one stereocenter matter? Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
- 59. Does one stereocenter matter? Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
- 60. Building a Structure Centric Community for Chemists
- 61. Assertion and Chemical Entities Who says what Taxol is? What is the “timeline” for a molecule? How do we clean up the Public data? The Quality source is Chemical Abstracts Service…
- 69. Content is King and Quality Costs Chemistry “content” is big money Patent searching Structures and properties Drug databases Literature databases Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information 101 years of content $260 million revenue (2006) >50 million substances >60 million sequences
- 70. Crowd-sourcing Chemistry Curation Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
- 71. Chemistry – A Deposition Platform CAS indexes published literature, patents and chemical vendors CAS indexes ChemSpider – >303,000 records “ Lost Chemistry” – syntheses in theses, lab notebooks? Compounds in private collections? ChemSpider accepts public depositions, linking to websites, hosting of details etc. Accepts structures, text, spectra, images.
- 72. Structure Searching Articles… Searching articles based on chemical structure and substructure is very expensive.. but is changing The web IS ready - when will publishers deliver? Structures can be shown Spectra can be interactive Graphics don’t need to be static Publishers can enhance their articles
- 73. Semantic Mark-up for Chemistry Semantic mark-up for chemistry is here RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies Nature publishing group compound linking ChemSpider Journal of Chemistry
- 74. Nature Chemistry Compound Pages
- 75. Project Prospect
- 76. ChemSpider and Publishing The curation efforts on ChemSpider led to a set of validated dictionaries Integrate best-in-class entity extraction with validated name dictionaries Additional dictionaries gave reactions, groups, families, hardware and software vendors etc
- 77. Name Recognition Azo aldehyde 2 was synthesized according to a reported method [17]. To a stirred solution of azo aldehyde 2 (1.08 g, 3.76 mmol ) in dry CH2Cl2 (30.00 mL) were successively added. (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and an excess of anhydrous MgSO4 (2.00 g, 16.67 mmol) .
- 81. Converting Detected Names… Names are searched against a validated dictionary (this expands as ChemSpider is curated) If not found then they are passed through a Name to Structure algorithm If they cannot convert then ChemSpider is searched for non-validated names
- 82. Manual Curation is Necessary
- 84. Custom Dictionaries Entity Extraction built around modified algorithms from SureChem Optimized for “publications” Dictionaries for chemical entities, groups, reactions, elements, families, species… Dictionaries can be expanded
- 85. Species – linked to Wikipedia
- 86. Semantic Linking of Structures What would you want to link off a structure? Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “ Everything”
- 89. ChemSpider Synthesis ChemSpider Synthesis will be a home for all things “synthetic” An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc. Public peer-review and feedback for synthetic procedures
- 90. Online Journals and Live Data
- 91. ChemSpider Everywhere Linked from Wikipedia Linked from Open Notebook Science sites using EMBED Linked from Blogs using Structure/Spectra EMBED Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets Integrated to software offerings from Thermo, Waters, Agilent, Bruker
- 92. ChemSpider Everywhere : Embed
- 93. ChemSpider Everywhere: Spectral Game
- 94. ChemSpider Everywhere : ChemMobi
- 95. Not in a basement now...
- 96. Conclusions The internet enables chemistry, at a reduced cost Web 2.0 is here and improving quality Question Quality! Crowdsourcing to expand, curate and integrate InChIs are enabling chemistry on the internet
- 97. You are invited.. Deposit your data with us Structures Spectra Synthesis procedures ChemSpider Synthesis is under development What is Digitonin?
- 98. Acknowledgments Valery Tkachenko and Sergey Golotvin RSC infrastructure team The ChemSpider advisory group The Wikipedia Chemistry team JC Bradley, Andy Lang – Spectral Game
- 99. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog