Machines first, humans second: On the importance of algorithmic interpretation of open chemistry data

Journal of Cheminformatics

Volumn 7, Issue 1, 2015, Pages

  Clark, Alex M ^a   Williams, Antony J ^b   Ekins, Sean ^c,d  

^a Molecular Materials Informatics   (Canada)

^b ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

^c Collaborations in Chemistry ^*  (United States)

^d Collaborative Drug Discovery ^*  (United States)

Author keywords

Cheminformatics; File formats; Machine learning; Open lab notebooks; Public data

Indexed keywords

EID: 84938930570     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-015-0057-7     Document Type: Article

References (66)

1. Pence HE, Williams AJ. ChemSpider: An Online Chemical Information Resource. J Chem Educ. 2010;87:1123-4.
2. Williams AJ. ChemSpider: Integrating Structure-Based Resources Distributed across the Internet. In: Belford RE, Moore JW, Pence HE, editors. Enhancing Learning with Online Resources, Social Networking, and Digital Libraries. Washington: American Chemical Society; 2010. doi:10.1021/bk-2010-1060.ch002.
3. Williams AJ. Public Compound Databases - How ChemSpider changed the rules making molecules on the web free. In Collaborative Computational Technologies for the Life Sciences, Edited by Ekins S, Hupcey MAZ and Williams AJ.
4. Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS One. 2011;6:e25513.
5. Li Q, Cheng T, Wang Y, Bryant SH. PubChem as a public resource for drug discovery. Drug Discov Today. 2010;15:1052-7.
6. Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: A Free Tool to Discover Chemistry for Biology. J Chem Inf Model. 2012;52:1757-68.
7. Interview with Jean-Claude Bradley. The Impact of Open Notebook Science. 2014 [ http://www.infotoday.com/IT/sep10/poynder.shtml ]
8. Harvey MJ, Mason NJ, Rzepa HS. Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks. J Chem Inf Model. 2014;54:2627-35.
9. Williams AJ, Wilbanks J, Ekins S. Why open drug discovery needs four simple rules for licensing data and models. PLoS Comput Biol. 2012;8:e1002706.
10. Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D. Utopia documents: linking scholarly literature with research data. Bioinformatics. 2010;26:568-74.
11. Chemistry Add-in for Word [ http://research.microsoft.com/en-us/projects/chem4word ] (accessed October 2014)
12. Jessop DM, Adams SE, Willighagen EL, Hawizy L, Murray-Rust P. OSCAR4: a flexible architecture for chemical text-mining. J Cheminf. 2011;3:41.
13. Hawizy L, Jessop DM, Adams N, Murray-Rust P. ChemicalTagger: A tool for semantic text-mining in chemistry. J Cheminf. 2011;3:17.
14. Corbett P, Murray-Rust P. High-Throughput Identification of Chemistry in Life Science Texts. In: Berthold MR, Glen R, Fischer I, editors. Computational Life Sciences II. Heidelberg: Springer Berlin; 2006. p. 107-18.
15. Cohen AM, Hersh WR. A survey of current work in biomedical text mining. Brief Bioinform. 2005;6:57-71.
16. Filippov IV, Nicklaus MC. Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution. J Chem Inf Model. 2009;49:740-3.
17. Ibison P, Jacquot M, Kam F, Neville AG, Simpson RW, Tonnelier C, et al. Chemical literature data extraction: The CLiDE Project. J Chem Inf Comp Sci. 1993;33:338-34.
18. Valko AT, Johnson AP. CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition. J Chem Inf Model. 2009;49:780-7.
19. Williams AJ, Ekins E. A quality alert and call for improved curation of public chemistry databases. Drug Discov Today. 2011;16:747-50.
20. Williams AJ, Ekins S, Tkachenko V. Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation. Drug Discov Today. 2012;17:685-701.
21. Clark AM: The real reason for junk chemical data [ http://cheminf20.org/2011/05/17/the-real-reason-for-junk-chemical-data ] (accessed October 2014).
22. Fant A, Muratov E, Fourches D, Sharpe D, Williams AJ, Tropsha A: On the Accuracy of Chemical Structures Found on the Internet. ACS San Diego, March 2012: [ http://www.slideshare.net/AntonyWilliams/on-the-accuracy-of-chemical-structures-found-on-the-internet ] (accessed October 2014)
23. Williams AJ, Ekins S, Tkachenko V: Mining public domain data as a basis for drug repurposing. ACS Philadelphia, August 2012 [ http://www.slideshare.net/AntonyWilliams/mining-public-domain-data-as-a-basis-for-drug-repurposing ] (accessed October 2014)
24. Golotvin SS, Vodopianov E, Lefebvre BA, Williams AJ, Spitzer TD. Automated structure verification based on 1H NMR prediction. Magn Reson Chem. 2006;44:524.
25. Golotvin SS, Vodopianov E, Pol R, Lefebvre BA, Williams AJ, Rutkowske RD, et al. Automated structure verification based on a combination of 1D 1H NMR and 2D 1H-13C HSQC spectra. Magn Reson Chem. 2007;45:803-13.
26. checkCIF: [ http://journals.iucr.org/services/cif/checkcif.html ] (accessed October 2014).
27. PubChem, ChemSpider and ChEBI are regularly cited internet resources, which can be accessed via the URLs [ http://pubchem.ncbi.nlm.nih.gov ], [ http://chemspider.com ] and [ http://www.ebi.ac.uk/chebi ] respectively (accessed October 2014).
28. Antony J. Williams, private communication: [ http://www.chemspider.com/feedbackcurated.aspx ]
29. Slide 56: [ http://www.slideshare.net/AntonyWilliams/crowdsourcing-chemistry-for-the-community-5-years-of-experiences ] (accessed October 2014)
30. The mobile app is available without charge for both iOS- and Android-based mobile devices. AppStore and Google Play links can be found on the main ChemSpider page: [ http://chemspider.com ] (accessed October 2014)
31. ChemSpider JSON API. [ http://www.chemspider.com/JSON.ashx ] (accessed October 2014).
32. ChemSpider Synthetic Pages. [ http://cssp.chemspider.com ] (accessed October 2014)
33. Brecher J. Graphical representation of stereochemical configuration (IUPAC Recommendations 2006). Pure Appl Chem. 2006;78:1897-970.
34. Brecher J. Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008). Pure Appl Chem. 2008;80:277-410.
35. Coles SJ, Frey JG, Bird CL, Whitby RJ, Day AE. First steps towards semantic descriptions of electronic laboratory notebook records. J Cheminf. 2013;5:52.
36. Day AE, Coles SJ, Bird CL, Frey JG, Whitby RJ, Tkachenko VE, et al. ChemTrove: Enabling a generic ELN to support Chemistry through the use of transferable plug-ins and online data sources. J Chem Inf Model, ASAP Article, doi:10.1021/ci5005948.
37. Clark AM, Labute P, Santavy M. 2D Structure Depiction. J Chem Inf Model. 2006;46:1107-23.
38. Clark AM. Detection and Assignment of Common Scaffolds in Project Databases of Lead Molecules. J Med Chem. 2009;52:469-83.
39. Clark AM. 2D Depiction of Fragment Hierarchies. J Chem Inf Model. 2010;50:37-46.
40. Clark AM. Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting. J Chem Inf Model. 2011;52:3149-57.
41. Bachrach SM. InChI: a user's perspective. J Cheminf. 2012;4:344.
42. SketchEl SourceForge Page [ http://sketchel.sourceforge.net ] (accessed October 2014)
43. SketchEl molecule format definition: [ http://molmatinf.com/fmtsketcher.html ] (accessed October 2014)
44. Green Lab Notebook app: [ http://molmatinf.com/products.html#gln ] (accessed October 2014).
45. SAR Table app: [ http://molmatinf.com/products.html#sartable ] (accessed October 2014).
46. Mobile Molecular DataSheet app: [ http://molmatinf.com/products.html#mmds ] (accessed October 2014).
47. Karapetyan K, Tkachenko V, Batchelor C, Sharpe D, Williams AJ. The RSC chemical validation and standardization platform, a potential path to quality-conscious databases. ACS Spring Meeting, New Orleans, April 2013 [ http://www.slideshare.net/AntonyWilliams/the-rsc-chemical-validation-and-standardization-platform-a-potential-path-to-qualityconscious-databases ] (accessed October 2014).
48. Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL. Open PHACTS: Semantic interoperability for drug discovery. Drug Discov Today. 2012;17:1188-98.
49. Batchelor C, Brenninkmeijer CYA, Chichester C, Davies M, Digles D, Dunlop I, et al. Scientific Lenses to Support Multiple Views over Linked Chemistry Data. The Semantic Web - ISWC. 2014;8796:98-113.
50. Linstrom PJ, Mallard WG. NIST Chemistry WebBook. Gaithersburg MD: NIST Standard Reference Database Number 69, National Institute of Standards and Technology; 2014. p. 20899 [ http://webbook.nist.gov ].
51. Cotton FA, Wilkinson G, Gaus PL. Basic Inorganic Chemistry. 3rd ed. New York: John Wiley; 1995. ISBN 978-0-471-50532-7.
52. Theys RD, Dudley ME, Hossain MM. Recent chemistry of the 5-cyclopentadienyl dicarbonyl iron anion. Coord Chem Rev. 2009;253:180-234.
53. Hosted by Molecular Materials Informatics, Inc. http://molmatinf.com
54. Clark AM. Rendering Molecular Sketches for Publication Quality Output. Mol Inf. 2013;32:291-301.
55. Dalby A, Nourse JG, Hounshell WD, Gushurst AKI, Grier DL, Leland BA, et al. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J Chem Inf Com Sci. 1992;32:244.
56. Townsend JA, Murray-Rust P. CMLLite: a design philosophy for CML. J Cheminf. 2011;3:39.
57. Rzepa HS, Murray-Rust P, Whitaker BJ. The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World Wide Web Information Exchange". J Chem Inf Comp Sci. 1998;38:976-82.
58. Ekins S, Clark AM, Williams AJ. Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration. Mol Inf. 2012;31:585-97.
59. Ekins S, Clark AM: Secure sharing with mobile cheminformatics apps [ http://figshare.com/articles/Secure-sharing-with-mobile-cheminformatics-apps/95654 ] (accessed October 2014)
60. Ekins S, Clark AM: Using The Open Drug Discovery Teams (ODDT) Mobile App To Bring Molecules & SAR From Behind Journal Paywalls [ http://figshare.com/articles/Using-The-Open-Drug-Discovery-Teams-%28ODDT%29-Mobile-App-To-Bring-Molecules-&-SAR-From-Behind-Journal-Paywalls/93007 ] (accessed October 2014)
61. Ekins S, Clark AM, Wood J: Raising Awareness of the Rare Disease Sanfilippo Syndrome C Using The Open Drug Discovery Teams (ODDT) Mobile App [ http://figshare.com/articles/Raising-Awareness-of-the-Rare-Disease-Sanfilippo-Syndrome-C-Using-The-Open-Drug-Discovery-Teams-ODDT-Mobile-App/156522 (accessed October 2014)
62. Ekins S, Clark AM: The Open Drug Discovery Teams (ODDT) Mobile App For Green Chemistry [ http://figshare.com/articles/The-Open-Drug-Discovery-Teams-%28ODDT%29-Mobile-App-For-Green-Chemistry/92858 ] (accessed October 2014)
63. Ekins S, Perlstein E. Ten Simple Rules of Live Tweeting at Scientific Conferences. PLoS ONE Comp Biol 2014 doi:10.1371/journal.pcbi.1003789.
64. Living Molecules app: [ http://molmatinf.com/products.html#livingmolecles ] (accessed October 2014)
65. Ekins S, Clark AM. Living Molecules App to create Ingredients lists [ http://figshare.com/articles/Living-Molecules-App-to-create-Ingredients-lists/712593 ] (accessed October 2014).
66. Clark AM, Bunin BA, Litterman NK, Schürer SC, Visser U. Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. PeerJ 2014, 524 doi:10.7717/peerj.524.