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The importance of the InChI identifier as a foundation technology for eScience platforms
The document emphasizes the significance of the InChI identifier as a foundational technology for chemistry data platforms like ChemSpider, enabling access to a vast and growing database of chemical information. It discusses the challenges and limitations of using InChI for complex molecules, as well as efforts to extract and standardize data from publications. The overarching theme highlights the need for ongoing data validation, standardization, and the potential for evolving InChI applications in the future.
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The importance of the InChI identifier as a foundation technology for eScience platforms
- 1. The Importance ofthe InChI Identifier as a Foundation Technology for eScience Platforms at RSC Antony Williams Bio-IT, Boston, April 27th 2014
- 2. Without the InChI… •ChemSpider is unlikely to have been built • It would not have grown into one of the domains primary online chemistry resources • The Royal Society of Chemistry would not have it as an online database, would not have a large cheminformatics team and would not be involved in a number of large scale funded projects around chemistry data
- 3. • ~30 millionchemicals and growing • Data sourced from >500 different sources • Crowd sourced curation and annotation • Ongoing deposition of data from our journals and our collaborators • Structure centric hub for web-searching • …and a really big dictionary!!!
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- 9. So what isYohimbine?
- 10. Of course itis out there… Drugbox: 3001/5080 with InChIs Chembox:5436/7690 with InChIs
- 11. Tell me more… •Where can I find the molfile for Yohimbine? • Papers/Patents about Yohimbine? • What are the side effects of Yohimbine? • Where can I order Yohimbine? • What are the physicochemical properties? • Metabolic pathways? • Different synonyms of Yohimbine? • Synthesis of Yohimbine? • Side effects of Yohimbine? • Etc….
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- 14. Downsides of OverallApproach • Meshing data together based on InChIs worked for simple molecules • 2D layout errors inherited or limited by algorithm • Complex molecules that are meant to be the same thing were NOT deduplicated. Compounds differing by one stereocenter, named the same, meant to be the same, are not the same
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- 16. So where canwe travel???
- 17. So where canwe travel???
- 19. InChI String Searchvia Google Give me InChIKeys…
- 20. And where canwe travel???
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- 23. How do webuild it? • We deal in Molfiles or SDF files – with coordinates • Deposit anything that has an InChI – we support what InChI can handle, good and bad • Standardization based on “InChI standardization” • InChIs aggregate (certain) tautomers • We link out to external sites using their IDs
- 24. Downsides of InChI •InChI was a moving target (multi versions) but overall worked as planned. • Good for small molecules – but no polymers, issues with inorganics, organometallics, imperfect stereochemistry. ChemSpider is “small molecules” • InChI used as the “deduplicator” – FIRST version of a compound into the database becomes THE structure to deduplicate against…
- 25. Side Effects ofInChI Usage
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- 27. Side Effects ofInChI Usage
- 28. Standardization Issues Depiction basedon molfile
- 29. Standardize Use the SRSas a guidance document for standardization Adjust as necessary to our needs
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- 31. Salt and IonicBonds
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- 35. Checking include InChI •Many SDF files contain InChIs and SMILES – comparing the structure contained within the file with the associated InChI is useful – turned up a number of errors in checking online databases
- 36. So, I’m writingan article…
- 37. With these…I willlose data
- 38. But linking withInChI …
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- 40. Data in Publications •This is not new, you know the story… • So much data of value is contained within a publication and delivered in a PDF form • PDF files, and unclear licensing/copyright, limit access to data so I can rework, reuse, repurpose, text mine etc. • “I specialize in XXXX. I want a database of YYYY extracted from publications and made available, for free, with the capabilities I need, and the publishers should just do it”
- 41. “Data enable” publications? •We would LOVE to bring data out of our archive • What could we do? • Find chemical names and generate structures • Find chemical images and generate structures • Find reactions – and make a database! • Find data (MP, BP, LogP) and host. Build models! • Find figures and database them • Find spectra (and link to structures) • Validate the data algorithmically
- 42. RSC Archive –since 1841
- 43. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4- thiadiazol-5-yl)ureaprepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser . The reaction mixture was heated at reflux with stirring , for a period of about one-half hour . After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2- trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
- 44. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4- thiadiazol-5-yl)ureaprepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser . The reaction mixture was heated at reflux with stirring , for a period of about one-half hour . After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2- trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
- 45. But names =structures • Systematic names can be generated FROM chemical structures algorithmically
- 46. But names =structures • …and structures from systematic names
- 47. But what oftrivial names? • What about trivial names, trade names, CAS numbers, multilingual names etc.?
- 48. Searching that lipidin patents
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- 54. But Context GivesReactions The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4- thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser . The reaction mixture was heated at reflux with stirring , for a period of about one-half hour . After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2- trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
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- 56. ChemSpider as aFoundation • >30 million chemicals (and growing) • ChemSpider is free to access for everyone – and the API means people program against it • What projects can we benefit?
- 57. Support grant-based services •Multiple European consortium-based grants • PharmaSea (FP7 funded) • Open PHACTS (IMI funded) • UK National Chemical Database Service (http://cds.rsc.org) – developing data repository for lab data, integrate Electronic Lab Notebooks • Open Drug Discovery projects
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- 60. • 3-year InnovativeMedicines Initiative project • Integrating chemistry and biology data using semantic web technologies • Open code, open data, open standards • Academics, Pharmas, Publishers… • To put medicines in the pipeline…
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- 62. All Databases WeGenerate… • All databases and systems we build now include generated InChIs • InChIs are facilitating discoverability via searching on Google (see Chris’ talk) but also for querying and linking
- 63. But we arestill VERY LIMITED • RSC deals with way more than organics, inorganics, organometallics – we are building a data repository to include materials, polymers, ambiguous materials etc. • There are many plans for InChI moving forward – Markush, polymers, organometallics etc
- 64. The great promiseshould be obvious • InChIs are here to stay • They will evolve, they will encompass, we will adopt and adapt • Public and private databases will federate & build a linked environment of validated data! • Data validation and standardization is needed • Open Data will continue to proliferate • InChIs are in the “Semantic Web” already
- 65. If InChI neverexisted … • ChemSpider would never have been built • Database linking would suffer dramatically • The web would not be “structure searchable” • Cheminformatics tools would likely not be linking to public domain databases in the same way
- 66. Thank you Email: [email protected] ORCID:0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams