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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 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

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  1. 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

  2. Communication Submariners love periscopes Periscopes are loved by submariners It is the case that submariners love periscopes Submariners lovepinkperiscopes Love submariners periscopes

  3. Communication in chemistry Chemical graphs and diagrams are used to describe chemical entities

  4. The Information Artifact Ontology

  5. Chemical diagrams are information entities

  6. Some chemical diagramsare not about anything Plannedmolecules (pre-synthesis) Hypothesisedmolecules (active research programs) Chemically infeasible molecules Impossibleconstructions (violating the laws underlying the diagrammatic formalism)

  7. One suggested solution(following Smith, Ceusters, JBMS 2010) But what happens when a planned molecule is synthesised?

  8. ‘Is about’ doesn’t help us distinguish between different information entities that are about the same thing

  9. Non-referring chemical diagramsare still information content entities: they are well-specified expressions in a diagrammatic language

  10. Diagrammatic language Syntax Vocabulary Composition rules Symbols Icons E.g. Carbon can have at most 4 bonds… E.g. INTERPRETATION Oxygen atom

  11. A diagram conforms toa diagrammatic languagewhich is interpreted to map it to what it is about 3D ball-and-stick diagrammatic language

  12. If a chemical diagram is about something, then that thing is a molecular entity

  13. 2D diagrams are coarser than 3D diagrams because 3D diagramsprovide more information

  14. 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

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

  16. 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/

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