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![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) at 0 oC were successively added (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excces of anhydrous MgSO4 (2.00 g,16.67 mmol) . The resulting mixture was stirred for 6 hours at room temperature [18]. The mixture was filtered and washed with dichloromethane . Then the solvent was evaporated under reduced pressure to give azo Schiff base 3 as a red solid which was recrystalized from ethanol 95% (1.28 g, 91 %)](https://image.slidesharecdn.com/checking-curating-and-qualifying-chemistry-1228271700485565-8/75/Checking-Curating-And-Qualifying-Chemistry-34-2048.jpg)
![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) at 0 oC were successively added (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excess of anhydrous MgSO 4 (2.00 g,16.67 mmol) . The resulting mixture was stirred for 6 hours at room temperature [18]. The mixture was filtered and washed with dichloromethane . Then the solvent was evaporated under reduced pressure to give azo Schiff base 3 as a red solid which was recrystalized from ethanol 95% (1.28 g, 91 %)](https://image.slidesharecdn.com/checking-curating-and-qualifying-chemistry-1228271700485565-8/75/Checking-Curating-And-Qualifying-Chemistry-35-2048.jpg)
Checking, Curating And Qualifying Chemistry
The document discusses ChemSpider, a search engine for chemists that provides access to over 21.5 million unique chemical structures from various data sources. It highlights the challenges of data quality during the curation process, including issues with incorrect structures and the need for community involvement in correcting errors. The text also emphasizes the importance of crowdsourced curation to improve data reliability, while mentioning various integrations and collaborative efforts to enhance the overall quality of chemical data online.
Checking, Curating And Qualifying Chemistry
- 1. Checking, Curating andQualifying Chemistry to Build a Structure Centric Community for Chemists Rutgers University 12/2/2008 Antony Williams
- 2. ChemSpider - ASearch Engine 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? ChemSpider can answer all of these questions
- 3. Tell Me AboutGlutathione
- 4. Tell Me AboutGlutathione
- 5. Tell Me AboutGlutathione
- 6. Tell Me AboutGlutathione
- 7. Tell Me AboutGlutathione
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- 9. Links out toKEGG Kyoto Encyclopedia of Genes and Genomes
- 10. How many namesdoes a compound have?
- 11. ChemSpider Data ContentOver 21.5 million unique chemical structures from ca. 150 data sources Online Databases –PubChem, Drugbank, KEGG, Wikipedia Literature – PubMed, J Het Chem, Nature, RSC, Open Access Chemical Vendors – over 40 different vendors and growing Personal Depositions – individual contributions Content database vendors Analytical data collections Patents Web scraping Content is linked back to the original data sources
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- 13. The Quality ofData Online… Aggregating data opens up quality issues Structure-identifier associations are “dirty” Structures are COMMONLY incorrect Manual curation of small databases is enough work – what about millions of structures? Structures are far from perfect. What is a “correct structure”? Full stereochemistry? Historical timeline of structure? Who is the authority?
- 14. Quality is aMajor Issue- Search Butanol OLD EXAMPLE..now fixed
- 15. Wikipedia Chemistry Curationproject Only ca. 5000 organic structures, 7000 total structures Almost a year of work so far for a team of 6 people Many errors removed in the process. Curation process is a daily event for users/depositors Slow and torturous process http://en.wikipedia.org/wiki/Talk:Tacrolimus#IUPAC_Name_and_structure
- 16. Wikipedia Curation Lookingfor self-consistency across a Wikipedia Page Primary key is the article TITLE The chemical shown needs to match the title Cyclic self-consistency – and decisions must get made
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- 19. Sugars – MachineReadable vs Aesthetics Haworth Stereo Fischer
- 20. Wikipedia – CrowdsourcingChemistry
- 21. Thymol Blue onChemSpider Data online includes: UV-vis spectrum Measured experimental properties Link to Wikipedia article Links to chromatography details Multiple identifiers/trade names etc. Links to vendors/suppliers/other databases Safety information http://www.chemspider.com/q/thymol%20blue
- 22. Crowd-sourcing Curation Howto curate data for millions of structures? Robot processes can clean up depositions Search for Chloride and check molecular formula for Cl Check for stereochemistry and remove names with stereo Provide a simple-to-use platform to curate, annotate and tag data Provide curator administration to prevent vandalism (Veropedia)
- 23. Post Comments Anyonecan “Post Comments” associated with a structure. To curate data we require login to track
- 24. Multi-level Curation andApproval
- 25. Crowd-sourcing Chemistry Crowd-sourcedcuration: identify and tag errors, edit names, synonyms, identify records for deprecation ALSO Crowd-sourced deposition: anyone can deposit data (structures, text, images, analytical data)
- 26. Vancomycin Originally 12structures with vancomycin Incomplete stereochemistry Complete but different stereochemistry Different charge states 1 remains after community collaboration with ChEBI
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- 33. “Entity Extraction” Rule-basedrecognition of systematic names: Use a lexeme of name fragments Rules for identifying bounds of a name Look-up dictionary: Drug Names Trivial Names Numbers : Registry IDs, EINECS/ELINCS Massive look-up dictionary of validated identifiers on ChemSpider
- 34. Name Recognition Azoaldehyde 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) at 0 oC were successively added (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excces of anhydrous MgSO4 (2.00 g,16.67 mmol) . The resulting mixture was stirred for 6 hours at room temperature [18]. The mixture was filtered and washed with dichloromethane . Then the solvent was evaporated under reduced pressure to give azo Schiff base 3 as a red solid which was recrystalized from ethanol 95% (1.28 g, 91 %)
- 35. Name Recognition Azoaldehyde 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) at 0 oC were successively added (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excess of anhydrous MgSO 4 (2.00 g,16.67 mmol) . The resulting mixture was stirred for 6 hours at room temperature [18]. The mixture was filtered and washed with dichloromethane . Then the solvent was evaporated under reduced pressure to give azo Schiff base 3 as a red solid which was recrystalized from ethanol 95% (1.28 g, 91 %)
- 36. ChemMantis Chem ical M arkup A nd N omenclature T ransformation I ntegrated S ystem
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- 38. Markup – 3seconds!
- 39. On the flyconversion
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- 41. One Click tomore Info…
- 42. Names and StructuresDichloroacetone Trichloromethylsilane
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- 47. Single Configuration Filedefines entities for markup Algorithms can be built for certain entities but the majority are dictionaries – vendors, Phys Properties, Analytical We can extend our system – should we integrate to PDB somehow?
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- 49. Entity Balloons Structuresare the language of chemistry Show structures to chemists and search/link from there Link to PDB ?
- 50. Other Dictionaries -Species We are considering Bacteria Fungi Enzymes Viruses PDB codes?
- 51. Integrations Out toOther Sources
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- 53. Conclusions The qualityof structure-based data online should always be questioned – that includes ChemSpider Data on ChemSpider are being added and curated on a daily basis but we need more eyeballs helping always ChemSpider has a large validated structure-name dictionary Chemical name extraction and document markup is very enabling