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Chemical named entity recognition and literature mark-up
 

Chemical named entity recognition and literature mark-up

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Presentation by Colin Batchelor, Royal Society of Chemistry publishing, in Manchester, March 2008

Presentation by Colin Batchelor, Royal Society of Chemistry publishing, in Manchester, March 2008

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    Chemical named entity recognition and literature mark-up Chemical named entity recognition and literature mark-up Presentation Transcript

    • Chemical named entity recognition and literature mark-up Colin Batchelor Informatics Department Royal Society of Chemistry [email_address]
    • Overview
      • Project Prospect: what we find and how we find it.
      • RDF: How should we be disseminating it?
      • Next steps: Basics for a chemical ontology.
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    • Project Prospect: What do we find?
      • Chemical compounds
      • Chemical terms from the IUPAC Gold Book
      • Gene products: function, process, location
      • Nucleotide and polypeptide sequence terms
      • Cell types
    • Project Prospect: How do we find it?
      • 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
    •  
    • RDF in an RSS reader
    • RDF: how we do it now
      • Content module from RSS 1.0
      • http://web.resource.org/rss/1.0/modules/content
      • In what sense does an article “contain” pyridine or base pairs?
      • We would much rather have proper rdf predicates – e.g. “is_about”, “mentions”.
    • RDF: what it looks like now
      • <item rdf:about=http://xlink.rsc.org/?DOI=b716356h&amp;RSS=1>
      • <title> [… title] </title>
      • <link>http://xlink.rsc.org/?DOI=b716356h&RSS=1</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/c1-13-16-11-21(26-4)20(25-3)10-15(16)8-18-17-12-22(27-5)19(24-2)9-14(17)6-7-23(13)18/h6-12H,1-5H3/q+1&quot;/>
      • </rdf:li>
      • <rdf:li>
      • <content:item rdf:about=“http://purl.org/obo/owl/SO#SO:0000028”/>
      • </rdf:li>
      • </rdf:Bag>
      • </content:items>
      • </item>
    • Basics for a chemical ontology
      • Unambiguous representation of objects of chemical discourse
      • Proper parthood relations
    • Basics for a chemical ontology: 1. Objects of chemical discourse
      • Must be able to represent and clearly distinguish
      • Compounds
      • Classes of compound
      • Parts of molecules
      • Mixtures
      • Would be nice to have:
      • Disambiguation cues for the first three
    • Imidazole
    • An imidazole
    • The imidazole side-chain/group/ring
    • Can ChEBI handle this?
      • Imidazoles (!) (CHEBI:24780)
      • Imidazole (CHEBI:16069)
      • Imidazole ring not yet
      • Imidazolyl group not yet (but methyl, benzyl, etc. )
      • … and there are no disambiguation cues
    • Disambiguation
      • One Sense per Discourse (Gale et al. 1992)
      • … this doesn’t hold at all
      • One Sense per Collocation (Yarowsky 1993)
      • … matches our intuitions
    • Disambiguation: What a one sense per collocation feature set might look like
      • 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”
    • Basics for a chemical ontology: 2. Parthood relations
      • Parthood in ChEBI means at least three things:
      • is necessarily chemically part of
      • carbonyl group part_of carbonyl compounds
    • Basics for a chemical ontology: 2. Parthood relations
      • Is possibly chemically part of:
      • Lead(2+) part_of lead diacetate
      • (most lead(2+) isn’t)
      • Electron part_of muonium (!)
    • Basics for a chemical ontology: 2. Parthood relations
      • Is part of a mixture
      • Kanamycin A part_of kanamycin
    • Basics for a chemical ontology: 2. Parthood relations
      • Solution 1: define relationships according to pattern: all instances of X have a relationship with some Y. (Smith et al. , “Relations in biomedical ontologies”, 2005)
      • carbonyl compound has_part carbonyl group
      • Lead diacetate has_part lead(2+) (?!)
      • Muonium has_part electron
      • Kanamycin has_part kanamycin A (?!)
    • Basics for a chemical ontology: 2. Parthood relations
      • Solution 2 (for discussion): Distinguish molecular-level relationships from sample-level relationships
      • Carbonyl compound molecule has_part carbonyl substituent
      • Muonium atom has_part electron
      • Kanamycin has_component kanamycin A
      • Lead diacetate has_component lead(2+) (?!)
    • Open questions
      • How do we represent the relationship between named entities and documents?
      • How do we integrate ontologies and word-sense disambiguation?
      • What is the best way of distinguishing molecules and samples?
    • Acknowledgements
      • University of Cambridge: Peter Corbett
      • OBO Foundry: Chris Mungall (Berkeley), Barry Smith (Buffalo)
      • www.projectprospect.org
    • Open questions
      • How do we represent the relationship between named entities and documents?
      • How do we integrate ontologies and word-sense disambiguation?
      • What is the best way of distinguishing molecules and samples?