Mendeleev could have used an OWL ontology to help organize the periodic table by defining classes of elements and compounds based on their chemical properties. The ontology classified over 700 chemical classes with over 40,000 axioms. It was able to group many elements correctly based on properties like conductivity, ion formation, and reaction ratios. However, it had limitations in describing complex structures of salts and predicting unknown elements. While useful, fully modeling inorganic chemistry exceeds OWL's capabilities.

1. Could Mendelev have Dreamt in
OWL?
Robert Stevens
BioHealth Informatics Group
School of Computer Science
University of Manchester
Robert.Stevens@manchester.ac.uk

2. Introduction
The challenge
• Periodicity in physicochemical properties
• Modelling inorganic chemistry
• Defining a metal
• Defining a salt
• Alkali metals, alkaline earths
• Halogens
• Transition elements
• Noble gases
• What cannot be done

3. What the Ancients Knew
• Iron, lead, copper, silver, gold, tin,
mercury, carbon, sulphur;
• From 1660 to 1860 found sixty more
elements
• Needed to organise them

4. What did the victorians Know?
• Electronic Structure of atom not known
• Atomic weight (mass)
• Basic physicochemical properties
• Proportions in which elements combined
in salts: Moles
• Ions: Charged particles

5. Moles
• 602,000,000,000,000,000,000,000.
• 6.02 times 10^23
• SI base unit for amount of substance
• A Mole contains Avogadro’s number of
entities (atoms, ions, molecules, etc.)
• The mass in grams of a Mole of an atom
equals the mass in AMU
• 12g Carbon and Carbon has mass 12
amu

6. Dmitry Mendeleev
…credited as being the creator of the first version
of the periodic table of elements.
- Wikipedia 2008

7. The Periodic Table
• Arrange elements in order of increasing
atomic weight
• Notice periodicity in physicochemical
properties
• Arrange similar elements to be vertically
juxtaposed
• Predictive gaps
• Infer properties of element in gaps from
surrounding elements

8. Periodic Table

9. Al
? ZnGe
In
Predicting Gallium
Ga

10. The Task
• How much of the grouping within the
periodic table can we infer using OWL and
automated reasoning?
• Use only kinds of physicochemical
properties known in 1860 or modern
equivalents (atomic mass not atomic
weight)

11. The Modern Way
• Mendeleev’s periodic table based on chemistry matches
the electronic structure of the atom
• 1860’s vs 1920s
• Alkali metal = valence shell is s with one electron
• Alkaline earth metals = valence shell is s with two
electrons
• Halogens = valence shell is P with five electrons
• Transition metals = valence shell is d with one -- 10
electrons
• Noble gases = valence shell is p with six electrons
• Explains all chemistry (with a couple of wrinkles for
hydrogen and helium)

12. Thomas leaves the room

13. Thing
AmountOfSubstance PhysicalObject
Atom Ion Molecule
MoleOfIon MoleOfCompoundChemical MoleOfElementalChemicalMoleOfMolecule
MoleOfAtom
FundamentalSubAtomicParticle

14. Thomas enters the room

15. Assumptions
• Standard conditions
• Substances have only one boiling point
etc.
• No units
• Functional data type properties
• Data ripped from NIST, Wikipedia, the
Web, my school data book
• Data a little flakey

16. Ontology Statistics
• 721 classes
• 28 defined classes
• 18 data type properties
• 12 object type properties
• 3294 subclass axiom
• 40,316 disjoint axiom
• DL expressivity: ALCHQ(D)
• 25 mins to classify with 64 bit FaCT++ on 2 x
2.66 Ghz Dual-Core Intel Xeon, 16 GB ram
• With “anywhere blocking” takes 10 seconds

17. Class: SodiumAtom
SubClassOf: Atom
that hasPart exactly 11 Proton
and hasPart exactly 11 Electron
and hasPart only (Proton or Neutron or Electron)
and formsIon some SodiumIon
and formsIon only SodiumIon
and hasAtomicRadius value 77.2f
and hasAtomicVolume value 23.7f
and hasAtomicWeight value 22.98977f
and hasElectronAffinity value 52.868f
and hasElectronNegativity value 0.93f
and hasFirstIonisation value 495.8f
and hasSecondIonisation value 4562.4f
and hasThirdIonisation value 6912.2f
DisjointWith: <all other atoms>

18. Mole of Atom
Class: MoleOfAtom
madeOfAtom exactly 602000000000000000000000 Atom

19. Mole of Sodium Atom
Class: MoleOfSodiumAtom
SubClassOf: MoleOfAtom
that madeOfAtom onlysome SodiumAtom
and hasColour some SilverColour
and hasCrystalStructure some BodyCentredCubicStructure
and hasState some SolidState
and hasMeltingPoint value 371.01
and hasMeltingPoint value 371.01
and hasBoilingPoint value 1154.6
and hasDensity value 0.971
and hasElectricalConductivity value 209.6
and hasHeatOfAtomisation value 109.0
and hasHeatOfFusion value 2.598
and hasSpecificHeat value 1.23
and hasThermalConductivity value 142.0
and hasVapourisation value 96.960

20. Salts
• A salt is an ionic compounds of at least
one metal ion and at least one non-metal
ion
• That is, some cation and some anion
• Distinction between metal and non-metal
fundamental to basic inorganic chemistry

21. Defining a Metal
• Formation of metal bonds; nuclei in sea of
electrons;
• Freely moving electrons gives conductivity
etc.
• So, defining indirectly...
• Really an extensional definition: The
metals are those I say are metals
• Almost everything a metal at high enough
pressure

22. Electrical Conductivity

23. Mole of Metal atom
Class: MoleOfMetalAtom
equivalentTo: MoleOfAtom
that hasElectricalConductivity some double[>= 5.405]
• Infers all moles of metal
• Conductivity proxy for “sea of electrons”

24. Mole of Metal Atom
• I need metal ion and mole of metal ion
(plus non-metal equivalents)
• Therefore, need metal atom

25. Defining Metal Atom
Class: MetalAtom
EquivalentTo: Atom
that formsMoleOfAtom onlysome MoleOfMetalAtom
• Somewhat dodgey
• Assumption that all atoms are parts of moles—collectives of those atoms
• Optionality or “may”...
• Assumption of purity etc.

26. Metalloids
• Some properties of metals and some of
non-metals
• Not equivalent to semi-conductor (carbon
semi-conducts)
• Tend to be amphoteric
• Another extensional definition

27. Non-Metals
• Don’t conduct (except carbon in its
graphite isoform)
• NOT (MetalAtom or MetalloidAtom)

28. Once we have Metals
• Metal Atoms
• Metal Ions
• Moles of Metal Ion, non-metal ion
• Cation = positively charged ion (metal ion)
• Anion = negatively charged ion
• Metal/non-metal cation/anion basis of
much of the element’s chemistry

29. Mole of Sodium Chloride
Class: MoleOfSodiumChloride
SubClassOf: MoleOfCompoundChemical
that madeOfMoleOfIon exactly 1 MoleOfChlorideIon
and madeOfMoleOfIon exactly 1 MoleOfSodiumIon
and madeOfMoleOfIon only (MoleOfChlorideIon or MoleOfSodiumIon)
and hasMolarMass value 58.442
and hasDensity value 2.16
and hasColour some WhiteColour
and hasState some SolidState
and hasBoilingPoint value 1465.0
and hasMeltingPoint value 801.0
and hasSolubilityInWater value 35.9

30. Defining a Salt
• “A salt”, not salt
• Some metal ion and some anion: NaCl, KCl, CaCO3
Class: MoleOfSalt
EquivalentTo: MoleOfChemicalCompound
that madeOfMoleOfIon some MoleOfMetalIon
and madeOfMoleOfIon some MoleOfAnion
and madeOfMoleOfIon only (MoleOfMetalIon or MoleOfAnion)
• Also, crystal structure, etc.

31. Defining Alkali Metal Salts
• Form halid in ratio 1:1
• Form oxide in ratio 2:1
Class: MoleOfAlkaliMetalChloride
EquivalentTo: MoleOfCompoundChemical
that madeOfMoleOfIon exactly 1 MoleOfMetalIon
and madeOfMoleOfIon exactly 1 MoleOfChlorideIon
and madeOfMoleOfIon only (MoleOfMetalAtom or MoleOfChlorideIon)
• Want to say “and in no other ratio”
• Really like to use other chemical properties if necessary

32. Salt Density (g/cm3
)
Caesium chloride 3.99
Copper (I) chloride 4.140
Gold (I) chloride 8.25
Lithium chloride 2.07
Potassium chloride 1.987
Rubidium chloride 2.8
Silver (I) chloride 5.56
Sodium chloride 2.16
Thallium (I) chloride 7.004
Alkali Metal Chloride Data

33. Defining Alkaline Earth Salts
• Same technique
• Works less well
• Ratio, density, colour get all of the alkaline
earths, but include too much
• Need trends and reactions

34. Alkaline Earth Oxides
Class: MoleOfAlkaliEarthOxide
EquivalentTo: MoleOfCompoundChemical
that madeOfMoleOfIon exactly 1 MoleOfMetalIon
and madeOfMoleOfIon exactly 1 MoleOfOxygen2Ion
and madeOfMoleOfIon only (MoleOfMetalIon or MoleOfOxygen2Ion)
and hasDensity some double[<= 6.0]
and hasColour some WhiteColour
• Again light, but barium and strontium confound; use colour
• Leaves only Zinc(II) oxide
• Very soluble; alkaline earths moderately soluble or react with water

35. …This works better
Class: AlkalineEarthAtom
EquivalentTo: Atom
That formsIon onlysome (Ion that
hasCharge exactly 1 PositiveCharge)
• Not really based on 1860’s chemistry and
is not ontologically good

36. Defining Halides
• Same methods work
Class: HalogenAtom
EquivalentTo: Atom
that formsIon some
(Ion that hasCharge exactly 1 PositiveCharge
and hasCharge only PositiveCharge
and hasCharge min 1 PositiveCharge)
• Gets all and only halogens
• Works for group 1 and group 2
• Maybe others too

37. Defining Noble Gases
• They don’t really do anything
• Don’t form ions (except under extreme
conditions)
• Might look at ionisation energy
• This is where the open world assumption
doesn’t help

38. Transition Elements
• Variable oxidation state
• Dense
• Coloured compounds
• Not quite exclusive conditions (lead has
multiple oxidation states)
• Trends confound simple definitions
• More sophisticated relationships?

39. Counting Oxidation State
• Give me atoms that have more than one
oxidation state
CopperAtom formsIon (CopperIon that hasCharge exactly 1 PositiveCharge)
CopperAtom formsIon (Copper2Ion that hasCharge exactly 2 PositiveCharge)
• Can’t just ask the simple question
• Have to ask for all combinations: 1 or 2; 1
or 3; 1 or 4;...; 2 or 3;...3 or 4; ...

40. What do I need?
• Describe trends nicely
• Describe relationships between values for
data types (reactivity, volume, mass,
radius, etc)
• Reactions
• Counting

41. What’s Next?
• Cannot describe giant structure of salts in
OWL
• So, describe their features
• Molecules
• Molecular structure hard to describe
• Describe features or describe the
molecule
• Description graphs offer a way out

42. Carbon dioxide (CO2)
C
OO

43. Cyclohexane
Image from http://www.chemvc.com/~tim/organic%20alkanes.html

44. Conclusions
• It is possible to make a lot of inferences
that could help with formulating a periodic
table
• Definite limitations
• Prediction not on the cards...
• Scalability a issue
• Modelling compromises
• Should I do this in OWL?

45. Acknowledgements
• Simon Jupp
• Dmitry Tsarkov
• Alan rector
• Uli Sattler