Project Prospect and the InChI. Colin Batchelor

Transcription

1 Project Prospect and the InChI Colin Batchelor

2 Project Prospect and the InChI: outline What can we do with InChIs that we couldn t do before? Where the InChIs come from Where the InChIs go The human factor 2

3 What we do with InChIs that we couldn t do before InChIs are canonical. InChIs are informative. Low-cost, low-effort route to running a molecular structure database. Supports the extraction of chemical structures from journal articles. 3

4 How does publishing really work? 4

5 Data capture Editing and proof-reading 5

6 Enhanced HTML Database Text mining (Oscar) Manual QA Enhanced RSS 6

7 Where the InChIs come from Compounds with names ~60% Oscar Compounds with numbers ~70% author-supplied ChemDraw ~20% PubChem lookup ~20% ChemDraw ~30% editor-drawn ChemDraw 7

8 Regular polysemy Even a simple chemical name can mean more than one thing Corbett, Batchelor and Copestake, Pyridine, pyridines and pyridine rings, 8 Proceedings of BERBTM-08, next week.

9 Imidazole 9

10 An imidazole 10

11 The imidazole side-chain/ group/ring/etc. 11

12 Can InChI handle this? No. But it was never meant to. So we use ChEBI, an ontology of classes and parts, nanoparticles and other things that InChI was never meant to handle. 12

13 Can ChEBI handle this? Imidazoles (!) (CHEBI:24780) Imidazole (CHEBI:16069) Imidazole ring not yet Imidazolyl group not yet 13

14 Disambiguation One Sense per Discourse (Gale et al. 1992) this doesn t hold at all One Sense per Collocation (Yarowsky 1993) matches our intuitions 14

15 Disambiguation: toy model CLASS: w( 1) = a, an, the, this w(0) plural (bit of a cheat, as not a collocation) PART: w( 1) = bridging, terminal w(+1) = backbone, bridge, chain, core, dyad, fluorophore, fragment, framework (and many more) w(+1)w(+2) = building block, protecting group, side chain 15

16 Where the InChIs go HTML RSS Database 16

17 HTML DisplayHTMLArticleforfree.asp? JournalCode=CC&Year=2009&ManuscriptI D=b823340c&Iss=Advance_Article 17

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20 RSS 2007: First ever routinely-generated RSS feeds containing InChIs 2009: RSS feed bringing together all Prospected articles from across the RSC 20

21 RSS: the gory details <item rdf:about= <title> [ title] </title> <link> <description> [ blah] </description> <content:encoded> [ human-readable stuff</content:encoded> [ dublin core stuff ] <content:items> <rdf:bag> <rdf:li> <content:item rdf:about= info:inchi/inchi=1/c22h22no4/ c (26-4)20(25-3)10-15(16) (27-5)19(24-2)9-14(17)6-7-23(13)18/h6-12h,1-5h3/q+1"/> </rdf:li> <rdf:li> <content:item rdf:about= /> </rdf:li> </rdf:bag> </content:items> </item> 21

22 RSS: the gory details Content module from RSS We would like in future have proper rdf predicates e.g. is_about, mentions. 22

23 Chemical structure search 23

24 Search results 24

25 The human factor: questions from our internal FAQs How do I draw organometallic compounds? Why do organometallic compounds look a mess? Why does my structure look rubbish in the structure drawer? How do I draw a fullerene? 25

26 The human factor Interpreting the InChI! We are developing tools to validate and explain InChIs to technical editors. Documentation wiki Templates for tricky 3D systems Careful enumeration of examples 26

27 Example training slide Dots separate the formulae; semicolons separate the charges. InChI=1/ C8H12.C8H18.C7H15.C6 H12.Mg/ c ;1-7(2,3 )8(4,5)6; ; ;/h1-2,7-8H, 3-6H2;1-6H3;5H, 3-4,6-7H2,1-2H3;6H, 2-5H2,1H3;/q;;-1;;+1/ b2-1-,8-7-;;;; 27

28 Worked examples Alkali metal salts Grignard reagents Delocalized systems Metallocenes cod Phosphine ligands Metal carbonyl complexes Metal carbenes Boranes Dative bonds 28

29 Example delocalized system 29

30 Fun with metal carbonyls 30

31 and more worked examples 31

32 Next steps Tools for explaining and validating InChIs Parallel standard and non-standard InChIs maintained internally. Better handling of compounds with metal atoms. 32

33 What has InChI allowed us to achieve? Workflow set up for chemically-enriched journal articles in a publishing production environment within a year. Industry-leading markup technology Widespread interest Prizes 33

34 "My first forays show [Project Prospect is] brilliant. [It's] great to see the compounds and have machine readable SMILES and InChIs" "Your new system is very impressive, I am sure it will become very useful to a large community It is great and exciting!! Just from the very few minutes I looked into it I realized its great potential and immediately ran to show it to my students!" This is a fantastic resource for the community, and a great use of the GO and SO. Nice work" I have found it very intuitive/ straightforward to use.[i] believe that it will make the manuscript even more appealing to readers." 34

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