Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
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Antony Williams discusses the challenges of hosting public domain chemicals data online, emphasizing the need for capable tools, data exchange standards, and the importance of data quality. He highlights the limitations of current chemical identifiers like CAS numbers and the benefits of using InChI as a solution for small molecules. The document also addresses the inadequacies of existing databases and the necessity for collaborative efforts to establish community standards and improve data representation in chemistry.
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Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
- 1. Hosting public domain chemicals data online for the community – the challenges of handling materials Antony Williams NIST Diffusion/CALPHAD Data Informatics and Tools Workshop May 14th , 2015 ORCID ID:0000-0002-2668-4821
- 2. Disclaimer… • Previously at the Royal Society of Chemistry • Now I am here…
- 3. Many challenges are the same • What I will discuss in terms of publisher, public domain databases, curated chemistry challenges etc. are the same… • Need capable tools to handle the data • Need standards for data exchange • Meshing data without review is dangerous! • Quality costs – time, effort and money • Algorithms can help clean data
- 4. Where is chemistry online? • Encyclopedic articles (Wikipedia) • Chemical vendor databases • Metabolic pathway databases • Property databases • Patents with chemical structures • Drug Discovery data • Scientific publications • Compound aggregators • Blogs/Wikis and Open Notebook Science
- 5. Chemistry on the Internet… • Most searching for chemistry on the internet… • Name searching Google/Bing/Yahoo • Name searching Wikipedia • Name searching Wolfram Alpha • Name, name, name, name…searching
- 6. The issue of identifiers
- 9. Some names for Aspirin..
- 10. The CAS Number • MUCH integration is done using CAS Numbers • MANY searches are CAS Numbers and Names
- 11. CAS Numbers are GREAT!
- 12. The CAS Number Index grows…
- 13. Scifinder
- 15. CAS Numbers are “Trademarked”? • From http://www.cas.org/legal/infopolicy
- 16. CAS and Wikipedia • http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation
- 19. 7900 CAS Chemicals Online…
- 20. How many CAS Numbers?
- 21. How many CAS Numbers? • >34 million chemicals from >500 sources
- 22. But CAS is hard to “Resolve”
- 23. Why CAS Numbers are not great • There is no free service…like DOIs • The resolver is a “Google Search” • Maybe we need another “identifier”? • And thanks to IUPAC/NIST….
- 25. Multiple Layers
- 26. InChI • SINGLE code base managed by IUPAC – integrated into drawing packages and used by MANY databases. No variability as with SMILES
- 28. InChI • SINGLE code base managed by IUPAC – integrated into drawing packages and used by MANY databases. No variability as with SMILES • InChI Strings can be reversed to structures – same problem as with SMILES – no layout • Adopted by the community (databases, blogs, Wikipedia) – good for searching the internet
- 29. InChIStrings Hash to InChIKeys
- 30. InChIs for small molecules… • InChIs are good for “small molecules” • Read here: http://www.jcheminf.com/series/InChI
- 31. A Vision in December 2006
- 32. Lots of data coming online…
- 33. ChemSpider
- 34. ChemSpider
- 35. ChemSpider
- 39. Google Books
- 40. Vendors and data sources
- 41. Structure search the web
- 42. Exact Search
- 43. Skeleton Search
- 44. 6 years ago this week…
- 45. ChemSpider strengths • Serves over 40,000 unique users per day • Advanced searching of >34 million chemicals
- 48. Data Quality/Standardization • MANY structures meant to be something online are MISREPRESENTED. • Commonly you will have better success finding information by name searches than structure – with many caveats of course… • Validating chemical structure representations is laborious work – and it’s shocking to review data…
- 49. What is the Structure of Vitamin K1?
- 50. Data Quality Issues Williams and Ekins, DDT, 16: 747-750 (2011) Science Translational Medicine 2011
- 51. Data quality is a known issue
- 52. Data quality is a known issue
- 53. Patent data in public databases
- 54. Patent data in public databases
- 55. Depiction vs Accurate Representation
- 56. Depiction vs Accurate Representation
- 57. There are Unused Standards!
- 58. There are Unused Standards!
- 59. There are Unused Standards!
- 60. Nitro groups
- 61. Salt and Ionic Bonds
- 62. Ammonium salts
- 63. Can we MAKE Quality Data? • Systems for everyone to validate and standardize their data would be useful • Would improve structure data in publications, databases etc. and make searching across resources better • Collaboration to establish community rules would be good!
- 65. CVSP Rules Sets
- 66. CVSP Filtering of DrugBank
- 67. CVSP Filtering of DrugBank
- 68. CVSP is Open to Anyone!
- 69. ChemSpider limitations • Supports “small molecules” only – no InChI, no possibility to register a compound • SO MUCH of chemistry is “materials” • Severe limitation in chemistry coverage: • Monomers but no polymers • Inorganic and organometallic handling • Ambiguous structures – “Markush” • Nanomaterials • Minerals • Bound to beads, surfaces etc
- 70. ORGANICS vs. Materials • Comment – you don’t know all of the challenges until you start to work in the area! • We, and cheminformatics companies, have solved MANY, but not all of the issues regarding organic chemistry management • The majority of our approaches do not map to materials • No standard ways to represent compounds • No InChI for materials
- 71. Questions to consider… • Organics are hard enough! • What are your best dictionaries of materials? • We have chemical ontologies. Status for materials? • Is open annotation of your databases possible? • What standards do you have for materials data exchange?
- 73. Known Challenges • Many materials are non-stoichiometric • How to represent composite materials (e.g. supported catalysts)? • Methods to distinguish novelty in materials (equivalent to diversity in organic structures)? • Lots of challenges ahead..a curated “community dictionary” would be of value…
- 74. Mapped DICTIONARIES… • Structure IDs • Systematic name(s) • Trivial Name(s) • SMILES • InChI Strings • InChIKeys • Database IDs • Registry Number
- 77. Pragmatism wins
- 79. Wouldn’t it be nice if…
- 80. Thank you Email: tony27587@gmail.com ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams