Review of existing technology and recent advances in the semantic representation of chemical 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/

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?