Project Prospect and the Semantic Web

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Project Prospectand the Semantic Web

• Colin Batchelor
• Royal Society of Chemistry, Cambridge, UK
• batchelorc_at_rsc.org

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Project Prospectand the Semantic Web

• Who we are
• What weve done
• Motivation
• Means
• The InChI and the Semantic Web
• Ontology development for chemistry
• RXNO and MOP

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Who we are
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Royal Society of ChemistryAdvancing the Chemical
Sciences

• Learned and professional society
• Scientific publisher
• 25 journals, 8 databases and a growing book
  program
• 8000 articles yearly
• Covering a broad spectrum of chemical sciences
  from systems biology (Molecular BioSystems) to
  physical and theoretical chemistry (PCCP)

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What weve done
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The motivation
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The motivation

• Scientific papers are formulaic and consistently
  structured (but not necessarily IMRD see later)
• There may be infinitely many possible chemical
  compounds
• BUT
• Nomenclature is productive and susceptible to
  machine parsing

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The means
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The meanshow publishing really works
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Data capture
Editing and proof-reading
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Enhanced HTML
Database
Text mining (Oscar)
Manual QA
Enhanced RSS
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Regular polysemy

• where words stand for multiple things in a
  consistent way.
• Examples
• Brand names
• Grinding
• Figureground
• Exactclasspart polysemy in chemistry
• Peter Corbett, Colin Batchelor and Ann Copestake
  (2008), Pyridines, pyridine and pyridine rings,
  Proc. BERBMTM08 at LREC 2008, Marrakech, Morocco.

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Regular polysemy

• Brand names
• Learning to buy a Renault and talk to BMW
• Grinding
• The squirrel scampered down the path and kept
  stopping and looking at the officers to check
  they were behind
• vs.
• the trick was to serve squirrel fresh and
  not to leave it hanging like other game

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Regular polysemy

• Figureground
• Audrey Hepburn painted the door (figure)
• Audrey Hepburn walked through the door (ground)
• The Incredible Hulk walked through the door
  (ambiguous)

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Imidazole
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An imidazole
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The imidazole side-chain/group/ring/etc.
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Can ChEBI handle this?

• Imidazoles (!) (CHEBI24780)
• Imidazole (CHEBI16069)
• Imidazole ring not yet
• Imidazolyl group not yet (but methyl, benzyl,
  etc.)
• and there are no disambiguation cues

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Disambiguation

• One Sense per Discourse (Gale et al. 1992)
• this doesnt hold at all
• One Sense per Collocation (Yarowsky 1993)
• matches our intuitions

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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

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Why is this hard?
Coordination resolution
Part of speech ambiguity tosylates noun or verb?
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Why is this hard?

• How many numbered compounds actually are named in
  a given paper?
• iloprost (1)
• tributyl-1-hexynylstannane (2)
• the desired 2-heptyne (3)
• methylPd(II) iodide 4 or 4'
• alkynylstannane 5
• the hypervalent stannate 6
• (alkynyl)(methyl)Pd(II) complex 7
• the desired methylalkyne 8
• compounds 914

• the stannyl precursors 15 and 16
• methylated compounds 17 and 18
• stannyl precursor 19
• iloprost methyl ester 20
• iloprost methyl ester is the real name, but you
  need to know that iloprost is a monocarboxylic
  acid!

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Why is this hard?

• For compound names
• 60 Oscar (Corbett and Murray-Rust 2006,
  Batchelor and Corbett 2007)
• 20 PubChem
• 20 ChemDraw
• For compound numbers
• 70 author ChemDraw
• 30 editors

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What are we marking up?

• Chemical compounds (InChI, ChEBI)
• Chemical classes and parts (ChEBI)
• Nanoparticles (in ChEBI from end of October)
• Chemical terms from the IUPAC Gold Book
• Name reactions (RXNO)
• Gene products function, process, location (GO)
• Nucleotide and polypeptide sequence terms (SO)
• Cell types (CL)

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InChI and the Semantic Web
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What InChI is for

• Can represent complete molecules (may be ions or
  radicals) of less than 1024 heavy (non-H) atoms.
• (however)
• Cannot yet represent metal atom geometry.
• Cannot yet represent polymers.
• Cannot yet represent diradicals etc.

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What InChI is not for

• Classes of molecule
• Parts of molecule
• (these have been done in ChemBlast)

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InChI in RDF

• (We dont like this.)
• We use the RSS content module. (As if articles
  contained molecules.)
• And we use infoinchi URIs.
• Look

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Some RDF

• ltcontentitemsgt
• ltrdfBaggt
• ltrdfligt
• ltcontentitem rdfabout"infoinchi/InChI1/C15
  H22O9/c1-8(16)19-6-15(7-20-9(2)17)12(21-10(3)18)11
  -13(24-15)23-14(4,5)22-11/h11-13H,6-7H2,1-5H3/t11?
  ,12-,13/m1/s1"/gt
• lt/rdfligt
• ltrdfligt
• ltcontentitem rdfabout"infoinchi/InChI1/C21
  H34O9/c1-6-9-14(22)25-12-21(13-26-15(23)10-7-2)18(
  27-16(24)11-8-3)17-19(30-21)29-20(4,5)28-17/h17-19
  H,6-13H2,1-5H3/t17?,18-,19/m1/s1"/gt
• lt/rdfligt
• lt/rdfBaggt
• lt/contentitemsgt
• ltcontentitemsgt
• ltcontentitemgt ltowlClass rdfID"GO_0016298"gt
  ltrdfslabelgtlipase activitylt/rdfslabelgt
• lt/owlClassgtlt/contentitemgt
• lt/contentitemsgt

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RXNO

• David Barden
• Colin Batchelor
• Celia Gitterman

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RXNOthe name reaction ontology (1)

• Every chemist knows about famous chemists like
  Wittig, Cannizzaro, Diels, Alder, benzoin
• Theyre pretty unambiguous and well-suited to
  logical definitions
• But what organizing principle do we use?

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RXNOthe name reaction ontology (2)

• Sort reactions by what they do to the skeleton
  of the molecule.
• Skeleton-changing reactions
• Joinings, cleavings, rearrangements, ring
  formation, ring expansion
• Skeleton-preserving reactions
• Additions, eliminations, substitutions,
  protections, deprotections

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RXNOthe name reaction ontology (3)

• Quality? Subjectivity?
• Get our curators to assign reactions to
  categories without conferring, check percentage
  agreement, discuss disagreements, improve
  guidelines, iterate to convergence.

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RXNOthe name reaction ontology (4)
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What do people say?
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The spectroscopists tale

• The enriched html version came as something of a
  revelation and the current emphasis on links to,
  and through biomolecular terminology was very
  much a plus for us, since my colleagues and I are
  a mix of physical and biological chemists who are
  dabbling in inter-disciplinary waters. Given the
  steadily increasing burden of keeping up with the
  current literature and accessing earlier
  publications - a fortiori when conventional
  disciplinary boundaries are being crossed - the
  ability to 'grow a tree' from current articles
  (including one's own) is going to make 'targeted
  sleuthing' a great deal easier.
• John Simons, Oxford

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The high-throughput screeners tale

• An interesting opportunity particularly for
  managers, students and beginners that are not
  that deeply immersed in the detail and the
  terminology. It further opens access to those who
  want to explore areas they are not specialists
  in. Great idea!
• Eberhard Krausz, MPI-CBG Dresden

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Lastly

• My only criticism would be the need for a time
  warning I spent 4 hours digging about which
  generated at least six new research ideas printed
  half a ream of paper and I missed my bus home. At
  least it was a new excuse my wife had not heard,
  so another first.
• An analytical chemist, The North.

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Acknowledgements

• Royal Society of Chemistry
• Richard Kidd, Jeff White, David Barden, Celia
  Gitterman, Hilary Burch, the Informatics team
• University of Cambridge
• Peter Corbett, Simone Teufel, Ann Copestake,
  Peter Murray-Rust
• OBO
• Karen Eilbeck, Midori Harris, Jen Deegan, Jane
  Lomax, Chris Mungall, Barry Smith, the ChEBI team

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