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Enhancing Chemical Named Entity Recognition and Ontology Development

This project explores chemical entity recognition and RDF markup in literature. It aims to identify compounds, gene products, and sequence terms. Emphasis is on representing chemical objects accurately in an ontology. Challenges include disambiguation and defining part-whole relationships. Open questions focus on integrating ontologies with disambiguation and distinguishing molecules from samples.

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Enhancing Chemical Named Entity Recognition and Ontology Development

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  1. Chemical named entity recognition and literature mark-up Colin Batchelor Informatics Department Royal Society of Chemistry batchelorc@rsc.org

  2. 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.

  3. 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

  4. 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

  5. RDF in an RSS reader

  6. 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”.

  7. 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"/> </rdf:li> <rdf:li> <content:item rdf:about=“http://purl.org/obo/owl/SO#SO:0000028”/> </rdf:li> </rdf:Bag> </content:items> </item>

  8. Basics for a chemical ontology • Unambiguous representation of objects of chemical discourse • Proper parthood relations

  9. 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

  10. Imidazole

  11. An imidazole

  12. The imidazole side-chain/group/ring

  13. 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

  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

  15. 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”

  16. 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

  17. 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 (!)

  18. Basics for a chemical ontology:2. Parthood relations • Is part of a mixture Kanamycin A part_of kanamycin

  19. 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 (?!)

  20. Basics for a chemical ontology:2. Parthood relations Solution 2 (for discussion): Distinguish molecular-level relationships from sample-level relationships • Carbonyl compoundmolecule has_part carbonyl substituent • Muonium atom has_part electron • Kanamycin has_component kanamycin A • Lead diacetate has_component lead(2+) (?!)

  21. 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?

  22. Acknowledgements University of Cambridge: Peter Corbett OBO Foundry: Chris Mungall (Berkeley), Barry Smith (Buffalo) www.projectprospect.org

  23. 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?

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