Semantic properties and units

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Stuart Chalk

Review of existing technology and recent advances in the semantic representation of chemical properties and units.

 Semantic Chemical Property Data
 IUPAC Green Book for Properties & Units for Chemistry
 Concepts in Metrology – the VIM
 QUDT – Semantic Metrology of the VIM
 The IUPAC Gold Book – Now and Future
 Conclusions
Overview

 Semantic –> Resource Description Framework (RDF)
 Store data as Subject-Predicate-Object triples
i.e. benzene containsAtomtype carbon (object)
benzene hasMolarMass 78.11 (literal)
molarMass hasUnit g/mol
Semantic Chemical Property Data

 A generic data model to store scientific data
 Can be implemented in any file/database format
 For semantic applications
 format in JSON-LD (https://www.w3.org/TR/json-ld/)
 use the Scientific Data Model Ontology (SDMO)
 Model + ontology creates hybrid relational/graph DB
SciData Data Model

The IUPAC
Green Book
3rd Edition
RSC, 2007
Published by
IUPAC Division I
Physical Chemistry

BIPM
International Vocabulary of Metrology (VIM)

BIPM International Vocabulary of Metrology (VIM)
http://www.bipm.org/en/publications/guides/vim.html

 Quantities
 Quantity kinds
 System of quantities
 Dimensions
 Dimension vectors
 Units
 Unit system
Metrology Concepts
If machines are going to capture and
process chemical property data
machine actionable representation of
these concepts is needed.
This can be encoded by semantic
annotation of property values and
units.

 Quantities, Units, Dimensions and DataTypes (QUDT)
 Defines common units and quantities
 Can be used to define any unit or quantity
 Include semantic representation of the VIM concepts
QUDT Ontology
https://qudt.org/

QUDT Metrology Terms
 Unit, SIUnit, DerivedUnit, ImperialUnit, CoherentUnit
isDerivedCoherentUnitOfSystem, applicableUnit,
applicableSIUnit, applicableImperalUnit
 Quantity, QuantityKind, hasQuantityKind
 SystemOfQuantities, belongsToSystemOfQuantities
 QuantityDimensionVector, hasQuantityDimensionVector
 Plus - hasEquivalentUnit, hasCorrespondingUnit …
 … and hasBaseSIUnit ?

$ Counts of entities – 12 books  Radian – L/L  Steradian – L2/L2  Mole fraction – mol/mol  Parts per million – mg/kg or µg/g  Percent - %(w/w) or %(v/v) Dimensionless Quantities$

 How do we show these are different to a computer?
 Create a representation of the dimensionvector that is
unique for each dimensionless quantity
 For radian (L/L)
L'0'M'1'T'0'I'0'H'0'N'0'J'0'D'0'_L'0'M'1'T'0'I'0'H'0'N
'0'J'0'D'0’_D1 OR M'1'_M'1’_D1
 For steradian (L2/L2)
L'0'M’2'T'0'I'0'H'0'N'0'J'0'D'0'_L'0'M’2'T'0'I'0'H'0'N
'0'J'0'D'0’_D1 OR M’2’_M’2’_D1
Dimensionless Quantities

Units of Measure Interoperability Service

 ‘The Compendium of Chemical Terminology’
 Contains over 7000 definitions of chemistry concepts
 Some terms are out of date
 Currently under renovation to make terms machine
accessible
The IUPAC GoldBook

 Add terms defined in all current IUPAC PAC
recommendations
 Add synonyms, acronyms, legacy terms
 Improve linking between terms
 Create an ontology for Chemistry
Future of the GoldBook

 Semantic chemical data is important in the move
toward knowledge discovery
 Semantic unit representation requires clear
representation of quantity kinds and
dimensionvectors for interoperability
 All chemical properties need to be represented
semantically
Conclusions

 schalk@unf.edu
 Phone: 904-620-1938
 Skype: stuartchalk
 LinkedIn: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
Questions?

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Semantic properties and units

1. Semantic Properties and Units for Chemistry Stuart Chalk Department of Chemistry University of North Florida schalk@unf.edu

2.  Semantic Chemical Property Data  IUPAC Green Book for Properties & Units for Chemistry  Concepts in Metrology – the VIM  QUDT – Semantic Metrology of the VIM  The IUPAC Gold Book – Now and Future  Conclusions Overview

3.  Semantic –> Resource Description Framework (RDF)  Store data as Subject-Predicate-Object triples i.e. benzene containsAtomtype carbon (object) benzene hasMolarMass 78.11 (literal) molarMass hasUnit g/mol Semantic Chemical Property Data

4.  A generic data model to store scientific data  Can be implemented in any file/database format  For semantic applications  format in JSON-LD (https://www.w3.org/TR/json-ld/)  use the Scientific Data Model Ontology (SDMO)  Model + ontology creates hybrid relational/graph DB SciData Data Model

5. SciData Data Model

6. SciData Data Model

7. The IUPAC Green Book 3rd Edition RSC, 2007 Published by IUPAC Division I Physical Chemistry

8. The IUPAC Green Book

9. The IUPAC Green Book

10. BIPM International Vocabulary of Metrology (VIM)

11. BIPM International Vocabulary of Metrology (VIM) http://www.bipm.org/en/publications/guides/vim.html

12.  Quantities  Quantity kinds  System of quantities  Dimensions  Dimension vectors  Units  Unit system Metrology Concepts If machines are going to capture and process chemical property data machine actionable representation of these concepts is needed. This can be encoded by semantic annotation of property values and units.

13.  Quantities, Units, Dimensions and DataTypes (QUDT)  Defines common units and quantities  Can be used to define any unit or quantity  Include semantic representation of the VIM concepts QUDT Ontology https://qudt.org/

14.

15. QUDT Metrology Terms  Unit, SIUnit, DerivedUnit, ImperialUnit, CoherentUnit isDerivedCoherentUnitOfSystem, applicableUnit, applicableSIUnit, applicableImperalUnit  Quantity, QuantityKind, hasQuantityKind  SystemOfQuantities, belongsToSystemOfQuantities  QuantityDimensionVector, hasQuantityDimensionVector  Plus - hasEquivalentUnit, hasCorrespondingUnit …  … and hasBaseSIUnit ?

16. Dimensionless Quantities

17.  Counts of entities – 12 books  Radian – L/L  Steradian – L2/L2  Mole fraction – mol/mol  Parts per million – mg/kg or µg/g  Percent - %(w/w) or %(v/v) Dimensionless Quantities

18.  How do we show these are different to a computer?  Create a representation of the dimensionvector that is unique for each dimensionless quantity  For radian (L/L) L'0'M'1'T'0'I'0'H'0'N'0'J'0'D'0'_L'0'M'1'T'0'I'0'H'0'N '0'J'0'D'0’_D1 OR M'1'_M'1’_D1  For steradian (L2/L2) L'0'M’2'T'0'I'0'H'0'N'0'J'0'D'0'_L'0'M’2'T'0'I'0'H'0'N '0'J'0'D'0’_D1 OR M’2’_M’2’_D1 Dimensionless Quantities

19. Units of Measure Interoperability Service

20.  ‘The Compendium of Chemical Terminology’  Contains over 7000 definitions of chemistry concepts  Some terms are out of date  Currently under renovation to make terms machine accessible The IUPAC GoldBook

21. The IUPAC GoldBook

22. The IUPAC GoldBook

23.  Add terms defined in all current IUPAC PAC recommendations  Add synonyms, acronyms, legacy terms  Improve linking between terms  Create an ontology for Chemistry Future of the GoldBook

24.  Semantic chemical data is important in the move toward knowledge discovery  Semantic unit representation requires clear representation of quantity kinds and dimensionvectors for interoperability  All chemical properties need to be represented semantically Conclusions

25.  schalk@unf.edu  Phone: 904-620-1938  Skype: stuartchalk  LinkedIn: https://www.linkedin.com/in/stuchalk  ORCID: http://orcid.org/0000-0002-0703-7776 Questions?

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