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What’s in an ‘is about’ link? Chemical diagrams and the IAO. Janna Hastings 1,2 Colin Batchelor 3 Fabian Neuhaus 4 Christoph Steinbeck 1. 1 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK 2 Swiss Centre for Affective Sciences, University of Geneva, Switzerland

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what s in an is about link chemical diagrams and the iao

What’s in an ‘is about’ link?Chemical diagrams and the IAO

Janna Hastings 1,2

Colin Batchelor3

FabianNeuhaus4

Christoph Steinbeck 1

1 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK

2 Swiss Centre for Affective Sciences, University of Geneva, Switzerland

3 Royal Society of Chemistry, Cambridge, UK

4 National Institute of Standards and Technology, Gaithersburg, MD, USA

5 University of Maryland Baltimore County, MD, USA

communication
Communication

Submariners love periscopes

Periscopes are loved by submariners

It is the case that submariners love periscopes

Submariners lovepinkperiscopes Love submariners periscopes

communication in chemistry
Communication in chemistry

Chemical graphs and diagrams are used to describe chemical entities

some chemical diagrams are not about anything
Some chemical diagramsare not about anything

Plannedmolecules (pre-synthesis)

Hypothesisedmolecules (active research programs)

Chemically infeasible molecules

Impossibleconstructions (violating the laws underlying the diagrammatic formalism)

one suggested solution following smith ceusters jbms 2010
One suggested solution(following Smith, Ceusters, JBMS 2010)

But what happens when a planned molecule is synthesised?

slide8
‘Is about’ doesn’t help us distinguish between different information entities that are about the same thing
slide9
Non-referring chemical diagramsare still information content entities: they are well-specified expressions in a diagrammatic language
slide10

Diagrammatic language

Syntax

Vocabulary

Composition

rules

Symbols

Icons

E.g. Carbon can have at most 4 bonds…

E.g.

INTERPRETATION

Oxygen atom

a diagram conforms to a diagrammatic language which is interpreted to map it to what it is about
A diagram conforms toa diagrammatic languagewhich is interpreted to map it to what it is about

3D ball-and-stick

diagrammatic

language

slide15

ATP

is about

is about

coarser than

Non-conformant to the DL (and thus impossible)

conforms to

conforms to

2D chemical DL

3D chemical DL

conforms to

acknowledgements
Acknowledgements

Funding

BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological resources" fund

http cindy informatik uni bremen de cosy events shapes

SHAPES 1.0

The Shape of Things Workshop on shape, form and structure

CONTEXT 2011, Karlsruhe, Germany

September 26-27, 2011

Abstracts: 15 August

http://cindy.informatik.uni-bremen.de/cosy/events/shapes/