Could Mendelev have Dreamt in
OWL?
Robert Stevens
BioHealth Informatics Group
School of Computer Science
University of Man...
Introduction
The challenge
• Periodicity in physicochemical properties
• Modelling inorganic chemistry
• Defining a metal
...
What the Ancients Knew
• Iron, lead, copper, silver, gold, tin,
mercury, carbon, sulphur;
• From 1660 to 1860 found sixty ...
What did the victorians Know?
• Electronic Structure of atom not known
• Atomic weight (mass)
• Basic physicochemical prop...
Moles
• 602,000,000,000,000,000,000,000.
• 6.02 times 10^23
• SI base unit for amount of substance
• A Mole contains Avoga...
Dmitry Mendeleev
…credited as being the creator of the first version
of the periodic table of elements.
- Wikipedia 2008
The Periodic Table
• Arrange elements in order of increasing
atomic weight
• Notice periodicity in physicochemical
propert...
Periodic Table
Al
? ZnGe
In
Predicting Gallium
Ga
The Task
• How much of the grouping within the
periodic table can we infer using OWL and
automated reasoning?
• Use only k...
The Modern Way
• Mendeleev’s periodic table based on chemistry matches
the electronic structure of the atom
• 1860’s vs 19...
Thomas leaves the room
Thing
AmountOfSubstance PhysicalObject
Atom Ion Molecule
MoleOfIon MoleOfCompoundChemical MoleOfElementalChemicalMoleOfMol...
Thomas enters the room
Assumptions
• Standard conditions
• Substances have only one boiling point
etc.
• No units
• Functional data type properti...
Ontology Statistics
• 721 classes
• 28 defined classes
• 18 data type properties
• 12 object type properties
• 3294 subcla...
Class: SodiumAtom
SubClassOf: Atom
that hasPart exactly 11 Proton
and hasPart exactly 11 Electron
and hasPart only (Proton...
Mole of Atom
Class: MoleOfAtom
madeOfAtom exactly 602000000000000000000000 Atom
Mole of Sodium Atom
Class: MoleOfSodiumAtom
SubClassOf: MoleOfAtom
that madeOfAtom onlysome SodiumAtom
and hasColour some ...
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 s...
Defining a Metal
• Formation of metal bonds; nuclei in sea of
electrons;
• Freely moving electrons gives conductivity
etc....
Electrical Conductivity
Mole of Metal atom
Class: MoleOfMetalAtom
equivalentTo: MoleOfAtom
that hasElectricalConductivity some double[>= 5.405]
• ...
Mole of Metal Atom
• I need metal ion and mole of metal ion
(plus non-metal equivalents)
• Therefore, need metal atom
Defining Metal Atom
Class: MetalAtom
EquivalentTo: Atom
that formsMoleOfAtom onlysome MoleOfMetalAtom
• Somewhat dodgey
• ...
Metalloids
• Some properties of metals and some of
non-metals
• Not equivalent to semi-conductor (carbon
semi-conducts)
• ...
Non-Metals
• Don’t conduct (except carbon in its
graphite isoform)
• NOT (MetalAtom or MetalloidAtom)
Once we have Metals
• Metal Atoms
• Metal Ions
• Moles of Metal Ion, non-metal ion
• Cation = positively charged ion (meta...
Mole of Sodium Chloride
Class: MoleOfSodiumChloride
SubClassOf: MoleOfCompoundChemical
that madeOfMoleOfIon exactly 1 Mole...
Defining a Salt
• “A salt”, not salt
• Some metal ion and some anion: NaCl, KCl, CaCO3
Class: MoleOfSalt
EquivalentTo: Mol...
Defining Alkali Metal Salts
• Form halid in ratio 1:1
• Form oxide in ratio 2:1
Class: MoleOfAlkaliMetalChloride
Equivalen...
Salt Density (g/cm3
)
Caesium chloride 3.99
Copper (I) chloride 4.140
Gold (I) chloride 8.25
Lithium chloride 2.07
Potassi...
Defining Alkaline Earth Salts
• Same technique
• Works less well
• Ratio, density, colour get all of the alkaline
earths, ...
Alkaline Earth Oxides
Class: MoleOfAlkaliEarthOxide
EquivalentTo: MoleOfCompoundChemical
that madeOfMoleOfIon exactly 1 Mo...
…This works better
Class: AlkalineEarthAtom
EquivalentTo: Atom
That formsIon onlysome (Ion that
hasCharge exactly 1 Positi...
Defining Halides
• Same methods work
Class: HalogenAtom
EquivalentTo: Atom
that formsIon some
(Ion that hasCharge exactly ...
Defining Noble Gases
• They don’t really do anything
• Don’t form ions (except under extreme
conditions)
• Might look at i...
Transition Elements
• Variable oxidation state
• Dense
• Coloured compounds
• Not quite exclusive conditions (lead has
mul...
Counting Oxidation State
• Give me atoms that have more than one
oxidation state
CopperAtom formsIon (CopperIon that hasCh...
What do I need?
• Describe trends nicely
• Describe relationships between values for
data types (reactivity, volume, mass,...
What’s Next?
• Cannot describe giant structure of salts in
OWL
• So, describe their features
• Molecules
• Molecular struc...
Carbon dioxide (CO2)
C
OO
Cyclohexane
Image from http://www.chemvc.com/~tim/organic%20alkanes.html
Conclusions
• It is possible to make a lot of inferences
that could help with formulating a periodic
table
• Definite limi...
Acknowledgements
• Simon Jupp
• Dmitry Tsarkov
• Alan rector
• Uli Sattler
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Could Mendelev have Dreamt in OWL?

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Talk at CSIR, pretoria, 2009

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  • Dmitry Mendeleev
    Slide showing Dmitry Mendeleev.
    Text says: “…credited as being the creator of the first version of the periodic table of elements. - Wikipedia 2008”
  • Predicting Gallium
    Slide to show the four boxes of Al (north), Ge (East), Zn (West), In (South).
    Slide animation on click to replace ? with Ga.
  • Top level: Thing
    2nd level: AmountOfSubstance and PhysicalObject
    3rd Level - PhysicalObject divides into: FundamentalSubAtomicParticle, Atom, Ion, Molecule
    3rd Level - AmountOfSubstance divides into: MoleOfIon, MoleOfCompoundChemical, MoleOfElementalChemical, MoleOfMolecule
    4th Level MoleOfElementalChemical has MoleOfAtom child.
    each child is connected to a parent by an upwards pointing arrow.
  • Salt Data
    Text says:
    SaltDensity (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
  • Could Mendelev have Dreamt in OWL?

    1. 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. 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. 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. 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. 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. 6. Dmitry Mendeleev …credited as being the creator of the first version of the periodic table of elements. - Wikipedia 2008
    7. 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. 8. Periodic Table
    9. 9. Al ? ZnGe In Predicting Gallium Ga
    10. 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. 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. 12. Thomas leaves the room
    13. 13. Thing AmountOfSubstance PhysicalObject Atom Ion Molecule MoleOfIon MoleOfCompoundChemical MoleOfElementalChemicalMoleOfMolecule MoleOfAtom FundamentalSubAtomicParticle
    14. 14. Thomas enters the room
    15. 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. 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. 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. 18. Mole of Atom Class: MoleOfAtom madeOfAtom exactly 602000000000000000000000 Atom
    19. 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. 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. 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. 22. Electrical Conductivity
    23. 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. 24. Mole of Metal Atom • I need metal ion and mole of metal ion (plus non-metal equivalents) • Therefore, need metal atom
    25. 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. 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. 27. Non-Metals • Don’t conduct (except carbon in its graphite isoform) • NOT (MetalAtom or MetalloidAtom)
    28. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 40. What do I need? • Describe trends nicely • Describe relationships between values for data types (reactivity, volume, mass, radius, etc) • Reactions • Counting
    41. 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. 42. Carbon dioxide (CO2) C OO
    43. 43. Cyclohexane Image from http://www.chemvc.com/~tim/organic%20alkanes.html
    44. 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. 45. Acknowledgements • Simon Jupp • Dmitry Tsarkov • Alan rector • Uli Sattler

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