ChEBI,text mining

and ontological best practice

Colin BatchelorRoyal Society of Chemistry

2008-05-19batchelorc@rsc.org

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What is text mining?

Marti Hearst, Berkeley:“Text Mining is the discovery by computer of new, previously unknown information, by automatically extracting information from different written resources.”

Can ChEBI help?

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Overview

Reasoning

ChEBI as dictionary

Regular polysemy in chemistry

Some possible solutions

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Reasoning

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Reasoning

Reasoning is using the logical structure of an ontology to automatically infer facts about the world which have not been explicitly added by a human being.

Computers have no real-world knowledge beyond what we tell them.

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Logical structure:properties of relations

We only have time to look at transitivity and is_a.

Smith et al., “Relations in Biomedical Ontologies”, Genome Biol., 2005, 6, R46.

Relation Transitive Symmetric Reflexive Anti-symmetric

is_a Yes No Yes Yes

part_of Yes No Yes Yes

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ChEBI’s is_a is not transitive (1)

If a relation R is transitive, then:

If a R b and b R c, then a R c.

glutathione is_a cofactor cofactor is_a biological role

therefore glutathione is_a biological role

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ChEBI’s is_a is not transitive (2)

water is_a amphiprotic solvent amphiprotic solvent is_a protophilic solvent (*) protophilic solvent is_a Bronsted base (*) Bronsted base is_a base base is_a biological role

therefore water is_a basetherefore water is_a biological role

* how come “protophilic solvent” and “Bronsted base” only have one child each?

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ChEBI’s is_a is not transitive (3)

N-hydroxy-L-aspartic acid is_a hydroxamic acids

hydroxamic acids is_a organic functional classes

therefore N-hydroxy-L-aspartic acid is_a organic functional classes

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is_a has many meanings!

1. An amount of a compound has a biological role: tris is_a buffer.*

2. An amount of a compound has an application: sodium dodecyl sulfate is_a detergent.*

3. A less-abstract type is an example of a more abstract type: propane is_a alkanes.

4. ?!: metals is_a atoms.*

* Not a property of a lone atom or molecule!

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Computers need facts about the world, not about ChEBI curation

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ChEBI as dictionary

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Evaluating name–structure conversion with ChEBI

ChEBI release 37 (26 September 2007) contains 12688 annotated entities, of which 8486 have InChI strings.

We use OSCAR3 (oscar3-chem.sourceforge.net) for name–structure conversion.

We convert chebi.obo to an XML file, each paragraph containing either a ChEBI name or an IUPAC name.

The layered structure of the InChI lets us give partial credit for incomplete matches.

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Results: IUPAC names

Total 8447

Identified as chemical 8255 (97.73%)

With InChI (upper bound) 1810 (21.43%)

Matching InChI, disregarding fixed hydrogen layer 1734 (20.53%)

Matching InChI, disregarding stereo 1176

Matching InChI, exact (lower bound) 1174 (13.90%)

Not all of name matched 1024

Name identified as two or more separate names 974 (11.53%)

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Results: ChEBI names

Total 8146

Identified as chemical 7173 (88.06%)

With InChI (upper bound) 1036 (12.72%)

Matching InChI, disregarding fixed hydrogen layer 953 (11.70%)

Matching InChI, disregarding stereo 637

Matching InChI, exact (lower bound) 628 (7.71%)

Not all of name matched 764

Name identified as two or more separate names 373 (4.58%)

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Regular polysemy

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Regular polysemy

… where words stand for multiple things in a consistent way.

Examples: Brand names Grinding Figure–ground Exact–class–part 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

Figure–ground 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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Methyl, the radical (exact)

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Methyl, the group (part)

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Can ChEBI handle methyl?

methyl group (CHEBI:32875) YESmethyl radical (CHEBI:29309) YES

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Imidazole (exact)

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An imidazole (class)

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imidazole side-chain/group/ring (part)

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Can ChEBI handle imidazole?

imidazoles (CHEBI:24780) YESimidazole (CHEBI:16069) YES

imidazole ring not yetimidazolyl group not yet

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Mapping exact, class and part to entries in ChEBI

Tests:1. Has InChI: exact2. Name is plural: class3. Ends in –yl, “group” or “residue”: part

Test 2 doesn’t work for applications or roles.Test 3 is brittle.

I would much rather use the logical structure of the ontology.

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Some possible solutions

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Some possible solutions (1)

ChEBI must represent facts about the world rather than about itself.

Examples: If unclassified compounds have a structure, they

should be in the molecular structure tree rather than the unclassifieds tree.

“organic functional classes” is a tool for assigning nomenclature. No chemical compound is an “organic functional class”.

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Some possible solutions (2)

ChEBI must distinguish between what is always true and what is only sometimes true.

Example: Replace some is_a relationships with

has_biological_role and has_application.

We need ChEBI to represent parts of molecules that aren’t substituents. They should all be descendants of molecular part (a new term), as should amino acid residues and nucleoside residues.

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Questions?