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Computed Knowledge Base for Quantitative Spectroscopy

Knowledge Engineering and Semantic Web 2012. Computed Knowledge Base for Quantitative Spectroscopy. Alexander Fazliev 1 , Alexey Privezentsev 1 , and Dmitry Tsarkov 2 1 Institute of Atmospheric Optics SB RAS, Zuev Square. 1, 634021 Tomsk, Russia

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Computed Knowledge Base for Quantitative Spectroscopy

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  1. Knowledge Engineering and Semantic Web 2012 Computed Knowledge Base for Quantitative Spectroscopy Alexander Fazliev1, Alexey Privezentsev1, and Dmitry Tsarkov2 1 Institute of Atmospheric Optics SB RAS, Zuev Square. 1, 634021 Tomsk, Russia 2 University of Manchester, Oxford Road, Manchester M13 9PL, UK KESW 2012

  2. Computed knowledge base for quantitative spectroscopy Outline • 1. Problem description • 2. Domain area overview • 3. Knowledge base in a nutshell KESW 2012

  3. Computed knowledge base for quantitative spectroscopy Problem Description • 1. W@DIS: an integrated quantitative spectroscopy DB • – 2,500 publications that covers 9 main molecules • 2. Information Source: • Publication + Molecule + Task + Method • 3. The same problem is described in several IS • 4. Checking/ensuring validity is the problem • Solution: use KB to help establish validity of the published spectral data KESW 2012

  4. Computed knowledge base for quantitative spectroscopy Constraints in Validity Problems Formal constraints Data type – quantum numbers – natural numbers, intensity, half-width, frequency, energy levels – positive real numbers, …. Variation interval – 0 <wavenumber< 45000 cm-1, 10-16cm/mol<intensity<10-30cm/mol Selection rules -normal modes - ka+kc=JorJ+1, ….. precise quantum numbers – J<60, 0<s<5, …… Publication constraints Whether a problems’ solution is published or not Non-formal constraints. Experts’ estimations OWL ED-2010

  5. Computed knowledge base for quantitative spectroscopy Non-formal constraints J. Tennyson, P.F. Bernath, L.R. Brown, A. Campargue, M.R. Carleer, A.G. Császár, R.R. Gamache, J.T. Hodges, A. Jenouvrier, O.V. Naumenko, O.L. Polyansky, L.S. Rothman, R.A. Toth, A.C. Vandaele, N. Zobov, L. Daumont, A.Z. Fazliev, T. Furtenbacher, I.F. Gordon, S.N. Mikhailenko, S.V. Shirin, IUPAC Critical Evaluation of the Rotational-Vibrational Spectra of Water Vapor. Part I. Energy Levels and Transition Wavenumbers for H217O and H218O Journal of Quantitative Spectroscopy and Radiative Transfer, July 2009, V.110, no.9-10, P.573-596. J. Tennyson, P.F. Bernath, L.R. Brown, A. Campargue, M.R. Carleer, A.G. Császár, L. Daumont,R.R. Gamache, J.T. Hodges, O.V. Naumenko, O.L. Polyansky, L.S. Rothman, R.A. Toth, A.C. Vandaele, N. Zobov, A.Z. Fazliev, T. Furtenbacher, I.F. Gordon, Shui-Ming Hu,S.N. Mikhailenko, B.A. Voronin, IUPAC Critical Evaluation of the Rotational-Vibrational Spectra of Water Vapor. Part II. Energy Levels and Transition Wavenumbers for HDO, HD17O and HD18O Journal of Quantitative Spectroscopy and Radiative Transfer, 2010, v.111, no.15, p.2160-2184. E. R. Polovtseva, N. A. Lavrentiev, S. S. Voronina, O. V. Naumenko, and A. Z. Fazliev Information System for Molecular Spectroscopy. 5.Ro-vibrational Transitions and Energy Levels of the Hydrogen Sulfide Molecule,Atmospheric and Oceanic Optics, 2012, Vol. 25, No. 2, pp. 157–165. J.Tennyson, Peter F. Bernath, L.R. Brown, A.Campargue, A.G. Császár, L. Daumont, R.R. Gamache, J.T. Hodges, O.V. Naumenko, O.L. Polyansky, L. S. Rothman, A. C. Vandaele, N.F. Zobov, Afaf R. Al Derzi, C. Fábrie, A. Fazliev, T. Furtenbacher, I.E. Gordon, L.Lodi, Irina Mizus, IUPAC Critical Evaluation of the Rotational-Vibrational Spectra of Water Vapor. Part III. Energy Levels and Transition Wavenumbers for H216O, Journal of Quantitative Spectroscopy and Radiative Transfer, 2012, v.112, in press. KESW 2012

  6. Computed knowledge base for quantitative spectroscopy Isolated molecule physical characteristics (T1) Isolated molecule energy levels (T7) Einstein coefficients (T6) Isolated molecules spectral line parameters (T2) Quantum numbers assignment to spectral lines (T5) Spectral line profile parameters (T3) Interacting molecule spectral line parameters (ET) Spectral functions calculation (T4) Model of Molecular Spectroscopy (1-approximation) Direct Problems Inverse Problems Root-mean-squire (standard) deviations KESW 2012

  7. Computed knowledge base for quantitative spectroscopy Quantitative Spectroscopy Domain • 1. Choose a molecule • 2. Choose a task • 3. Choose a problem described in the source • 4. Ontology describes properties of the solutions: • I1: of a single task • I2: of pairs of tasks • e.g., root-mean-square deviation KESW 2012

  8. Computed knowledge base for quantitative spectroscopy KESW 2012

  9. Computed knowledge base for quantitative spectroscopy KESW 2012

  10. Computed knowledge base for quantitative spectroscopy Structure of Individual «information source 2006_BaTeHaTo_c_H2O» V4_T1_102_2006_BaTeHaTo_c_H2O hasMethod DVR3D hasSubstance H2O hasInputData_MD V3_T1_102_T1-InputData_MD isSolutionOf T1 hasOutputData_MD V3_T1_102_T1-OutputData_MD date 2009-03-25 18:18:00 publisher faz comment Quantum numbers - BT2 label 2006_BaTeHaTo_c_H2O hasReferenceR.J.Barber, J. Tennyson, G.J. Harris, R.N. Tolchenov, A High Accuracy Computed Water Line List - BT2. // Mon. Not. R. Astron. Soc., 2006, v. 368, p. 1087-1094 21 statements Subject-predicative structure V4_T1_102_T1-InputData_MD hasAtomicMass10.1111/j.1365-2966.2006.10184.x hasBasicWaveFunction10.1111/j.1365-2966.2006.10184.x hasPotentialEnergyFunction10.1111/j.1365-2966.2006.10184.x V4_T1_102_T1-OutputData_MD hasQuantumNumber_MDV3_T1_102_QuantumNumbers_MD_for_BT2 hasEnergyLevel_MD V3_T1_102_EnergyLevel_MD V4_T1_102_EnergyLevels_MD hasUnit cm-1 hasNumberOfEnergyLevels 221097 hasMinEnergyLevel 0 hasMaxEnergyLevel 29999.840396 V4_T1_102_QuantumNumbers_MD_for_BT2 hasQuantumNumberType BT2 hasNumberOfNonuniqueQuantumNumbers 0 hasNumberOfUnlabeledQuantumNumbers 0 hasNumberOfUniqueQuantumNumbers 221091 hasTotalMaxAngularMomentum 50 hasTotalMinAngularMomentum 0 KESW 2012

  11. Computed knowledge base for quantitative spectroscopy V4_T7_269_NaMaLeTe_D2O_to_V4_T1_284_ShZoPo_D2O_by_EnergyLevels_on_NormalModes_RMSPair hasRMSMember V4_T7_269_NaMaLeTe_D2O hasRMSMember V4_T1_284_ShZoPo_D2O hasPhysicalQuantity EnergyLevels hasRMSBandPair V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_v1_v2_v3_RMSBandPair hasTotalRMSDeviationValue 34.800 hasTotalMaxDifferenceValue 225.9971 hasTotalNumberCorrelationLines 530 V4_T1_284_ShZoPo_D2O …………. hasReferenceS.V. Shirin, N.F. Zobov, O.L. Polyansky, Theoretical line list of D216O up to 16000 cm-1 with an accuracy close to experimental, J. Quant. Spectr. Rad. Trans., 109 (2008) 549 V4_T7_269_NaMaLeTe_D2O_to_V4_T1_284_ShZoPo_D2O_by_EnergyLevels_on_NormalModes_ident_v1_v2_v3_RMSBandPair hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_0_3_3_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_1_1_3_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_1_3_2_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_2_1_2_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_2_3_1_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_3_1_1_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_3_3_0_RMSStateBand hasRMSStateBand V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_4_1_0_RMSStateBand hasNumberOfRMSBands 8 V4_T7_269_NaMaLeTe_D2O ………. hasReferenceO.V.Naumenko, F. Mazzotti, O.M. Leshchishina, J. Tennyson and A. Campargue, Intracavity laser absorption spectroscopy of D2O between 11 400 and 11 900 cm-1. // Journal of Molecular Spectroscopy, 2007, v. 242, no. 1, p. 1-9 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_1_1_3_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_2_3_1_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_1_3_2_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_3_1_1_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_2_1_2_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_4_1_0_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_4_1_0_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_0_3_3_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_0_3_3_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 V4_T7_269_to_V4_T1_284_by_EnergyLevels_on_NormalModes_3_3_0_RMSStateBand hasQuantumNumberBand QuantumNumbers_on_NormalModes_3_3_0_Band hasBandMaxDifferenceValue 121.42 hasBandNumberCorrelationLines 45 hasBandRMSDeviationValue 23.717 Individual «Information source V4_T7_269_NaMaLeTe_D2O_to_V4_T1_284_ShZoPo_D2O_by_EnergyLevels_on_NormalModes_RMSPair» (131 + 5Nbands)statements KESW 2012

  12. Computed knowledge base for quantitative spectroscopy Statistics Table 1. The number of individuals in the ontology for water and carbon dioxide molecules. N/M, N – number of individuals, M – number of statements KESW 2012

  13. Computed knowledge base for quantitative spectroscopy User Toolkit KESW 2012

  14. Computed knowledge base for quantitative spectroscopy A list of classes corresponding to plausible user queries • Vibrational bands found in direct tasks. • Data sources containing a single vibrational band; • All data sources including the root-mean-square deviation for selected vibrational bands ; • Data sources containing transitions in a selected range of wavenumbers; • Data sources that satisfy a set of properties related to formal constraints; • Data sources with no transitions rejected by experts; • Data sources containing the same transitions as in the data source; • Data sources containing only unique transitions; • Canonical information sources; • Pairs of correlated information sources containing only measured data; • Pairs of correlated information sources containing only a selected vibrational band. KESW 2012

  15. Computed knowledge base for quantitative spectroscopy Vibrational bands found in direct tasks VibrationalBand and inverse hasQuantumNumbersOfBand some (inverse hasVibrationalBand_MD some (inverse hasTransitionQuantumNumbers_MD some (inverse hasOutputData_MD some (InformationSource and (isSolutionOf value T2 or isSolutionOf value T3))))). Data sources containing transitions in a selected range of wavenumbers (T2-IS or T3-IS or T5-IS or T6-IS) that hasOutputData_MD some (hasWavenumbers_MD some (Wavenumbers_MD and ((hasMinWavenumber some float[>=0.0,<10.0]) or (hasMaxWavenumber some float[>=0.0,<10.0] )))) KESW 2012

  16. Computed knowledge base for quantitative spectroscopy Summary – Tackling the problem of validity of the published quantitative spectroscopy data – Using the ontology of information sources – 3 layers in the ontology: Base, Application and User – Available at: http://wadis.saga.iao.ru KESW 2012

  17. Computed knowledge base for quantitative spectroscopy Questions? KESW 2012

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