Chemical named entity recognition and literature mark-up

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.

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&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>

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

Is possibly chemically part of:
Lead(2+) part_of lead diacetate
(most lead(2+) isn’t)
Electron part_of muonium (!)

Is part of a mixture
Kanamycin A part_of kanamycin

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 (?!)

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?

Chemical named entity recognition and literature mark-up

by Duncan Hull on Mar 11, 2008

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