Chemical diagrams and the IAO

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Presented at the ICBO 2011 conference in Buffalo, we tackle the controversial 'is about' relationship in the information artifact ontology (IAO) in the context of chemical diagrams.

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  • \\Submariners loveperiscopes." is a declarative sentence with a transitive verb regardless of whetherit is a fact that submariners love periscopes. The same is true for expressions ofdiagrammatic languages.
  • Is about is not enough in the sense that in these cases, there is no aboutness, so, these kinds of chemical diagrams can’t be included as chemical entities within the framework of the IAO. In the rst two cases the CD might or might not be about molecules thatexist. In the third case chemists expect, and in the fourth case they are certainthat, the aboutness criterion of the IAO is violated. Nevertheless, these CDs areused by chemists to communicate and exchange information in the same ways asCDs that are known to correspond to something in reality. Thus, the way CDsare used does not justify treating only a subset of them as information entities.It also indicates that Denition 4 is not along the right lines.
  • One obvious problem with this approach is that it leads to a massive level ofparallel maintenance, since most types of ICE can appear twice in the ontology.A more fundamental objection is that this approach violates the fundamentaldesign principles of BFO: categorization according to ontological nature, whichdoes not change. For example, it is impossible for a tree (an independent contin-uant) to become a temporal region, or for a smile (a dependent continuant) tobecome a soccer game (an occurrent). However, according to the approach in [3]a CD might be a non-referring ICE now, but become a referring ICE tomorrow,because somewhere in some lab somebody accidentally synthesized the corre-sponding molecule. Thus, in contrast to the other ontological categories in BFO,it would be possible for non-referring ICEs to change their ontological nature.Even worse, the ontological nature of CDs would be aected by events that hadno causal connection to the CD and did not change its structure in any way.Since the ontological nature of an entity is not aected by Cambridge changes,that is to say changes only in its description, we conclude that `non-referringICE' and `referring ICE' are not true ontological categories.
  • Is about is also not enough in the sense that it doesn’t allow categorisation of types of chemical entities that are all about the same thing
  • The elements of the vocabulary of the diagrammatic language do need to cor-respond to something existing, otherwise the diagrams will not be scienticallyrelevant. However, not all combinations of the vocabulary that are permissibleby the grammar will correspond to something in reality. It would seem strangeindeed, on giving an ontological account of natural language, to divide all sen-tences into those that are about facts and those that are not.
  • The second diagram is a structural diagram of agiven instance of a caffeine molecule x, since it is possible to map the spheresof the diagram to the atoms that are part of x and the links of the diagram tothe chemical bonds of x such that the connections in the diagrams correspondsto the chemical reality in the molecule. Conversely, if the diagram contains alink that does not correspond to a bond in a given molecule x or if it containsa sphere that is mapped to a type of atoms that do not occur as part of x, thenthe diagram does not represent x.
  • The terms ‘structural diagram’ and ‘diagrammatic language’ do not currently exist in IAO, we would have to submit them (following this approach).
  • Chemical diagrams and the IAO

    1. 1. What’s in an ‘is about’ link?Chemical diagrams and the IAO<br />Janna Hastings 1,2<br />Colin Batchelor3<br />FabianNeuhaus4<br />Christoph Steinbeck 1<br />1 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK<br />2 Swiss Centre for Affective Sciences, University of Geneva, Switzerland<br />3 Royal Society of Chemistry, Cambridge, UK<br />4 National Institute of Standards and Technology, Gaithersburg, MD, USA<br />5 University of Maryland Baltimore County, MD, USA<br />
    2. 2. Communication<br />Submariners love periscopes<br />Periscopes are loved by submariners<br />It is the case that submariners love periscopes<br />Submariners lovepinkperiscopes Love submariners periscopes<br />Saturday, July 30, 2011<br />2<br />
    3. 3. Communication in chemistry<br />Saturday, July 30, 2011<br />3<br />Chemical graphs and diagrams are used to describe chemical entities<br />
    4. 4. The Information Artifact Ontology<br />Saturday, July 30, 2011<br />4<br />
    5. 5. Chemical diagrams are information entities<br />Saturday, July 30, 2011<br />5<br />
    6. 6. Some chemical diagramsare not about anything<br />Plannedmolecules (pre-synthesis)<br />Hypothesisedmolecules (active research programs)<br /> Chemically infeasible molecules <br />Impossibleconstructions (violating the laws underlying the diagrammatic formalism) <br />Saturday, July 30, 2011<br />6<br />
    7. 7. One suggested solution(following Smith, Ceusters, JBMS 2010)<br />Saturday, July 30, 2011<br />7<br />But what happens when a planned molecule is synthesised?<br />
    8. 8. ‘Is about’ doesn’t help us distinguish between different information entities that are about the same thing<br />Saturday, July 30, 2011<br />8<br />
    9. 9. Non-referring chemical diagramsare still information content entities: they are well-specified expressions in a diagrammatic language<br />Saturday, July 30, 2011<br />9<br />
    10. 10. Saturday, July 30, 2011<br />10<br />Diagrammatic language<br />Syntax<br />Vocabulary<br />Composition<br />rules<br />Symbols<br />Icons<br />E.g. Carbon can have at most 4 bonds…<br />E.g. <br />INTERPRETATION<br />Oxygen atom<br />
    11. 11. A diagram conforms toa diagrammatic languagewhich is interpreted to map it to what it is about<br />Saturday, July 30, 2011<br />11<br />3D ball-and-stick<br />diagrammatic<br />language<br />
    12. 12. If a chemical diagram is about something, then that thing is a molecular entity<br />Saturday, July 30, 2011<br />12<br />
    13. 13. Saturday, July 30, 2011<br />13<br />
    14. 14. 2D diagrams are coarser than 3D diagrams because 3D diagramsprovide more information<br />Saturday, July 30, 2011<br />14<br />
    15. 15. Saturday, July 30, 2011<br />15<br />ATP<br />is about<br />is about<br />coarser than<br />Non-conformant to the DL (and thus impossible)<br />conforms to<br />conforms to<br />2D chemical DL<br />3D chemical DL<br />conforms to<br />
    16. 16. Acknowledgements<br />Funding<br />BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological resources" fund <br />Saturday, July 30, 2011<br />16<br />
    17. 17. SHAPES 1.0<br />The Shape of Things Workshop on shape, form and structure<br />CONTEXT 2011, Karlsruhe, Germany<br />September 26-27, 2011<br />Abstracts: 15 August <br />http://cindy.informatik.uni-bremen.de/cosy/events/shapes/<br />17<br />

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