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Open Structures:
Current Issues & Future Plans
Open semantic chemical structures:
Ideas on the use of JSON-LD for
representation of chemical entities
Stuart J. Chalk, Department of Chemistry
University of North Florida
schalk@unf.edu
CINF Paper 6 – August 20, 2017
Outline
 Inspiration
 Chemical File Formats
 YACFF
 JavaScript for Linked Data (JSON-LD)
 Building on JSON-LD
 Reasoning Chemical Concepts
 Conclusion
 International Chemical Identifier (InChI)
http://www.inchi-trust.org/
 Chemical JSON from Open Chemistry
https://github.com/OpenChemistry/
 Common Standard for eXchange (CSX)
https://doi.org/10.1021/acs.jpca.6b10489
 Hastings J, Magka D, Batchelor C, et al. Structure-
based classification and ontology in chemistry.
Journal of Cheminformatics. 2012;4:8.
https://doi.org/10.1186/1758-2946-4-8.
Inspiration
 Over 100 different file formats
http://openbabel.org/docs/2.3.0/FileFormats/Overview.html
 Represent many different types of information
 Atoms, bonds (special bone types), positions, valence,
charge, isotope, radical, lone pairs, aromaticity,
stereochemistry, groups, mixtures, reactions, markush,
line notations, computational properties
 Binary, plain text, XML – some open, most not
Chemical File Formats
Chemical File Formats
MJ171500
5 4 0 0 0 0 0 0 0 0999 V2000
-0.3102 0.4946 -0.0220 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7301 -0.0740 -0.7743 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.5159 0.1117 0.8127 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.4187 0.5156 -0.1089 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.5247 1.0372 -0.0454 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
 No!
 A chemical file framework
 Built using JavaScript for Linked Data (JSON-LD)
 Open
 Extensible
 Designed for semantic chemical applications
 JSON schema can be applied
Yet Another Chemical File Format
 Technical Recommendation Jan 2014
https://www.w3.org/TR/json-ld/
 JSON representation of Resource Description
Framework (RDF) https://www.w3.org/RDF/
 Representation of ‘things’ using ‘triples’
<subject> <predicate> <object>
JavaScript Object Notation
for Linked Data (JSON-LD)
JavaScript Object
Notation for Linked Data
(JSON-LD)
 @context – aliases
 @id – unique id’s
 @type – data type
 @base – define the type
of ‘thing’ that this file is
about
JavaScript Object Notation
for Linked Data (JSON-LD)
<http://schema.org/Person/stuchalk>
<http://purl.org/dc/terms/identifier>
"0000-0002-0703-7776"^^<http://www.w3.org/2001/XMLSchema#string> .
<http://schema.org/Person/stuchalk>
<http://schema.org/name>
"Stuart Chalk"^^<http://www.w3.org/2001/XMLSchema#string> .
<http://schema.org/Person/stuchalk>
<http://schema.org/worksfor>
"University of North Florida"^^<http://www.w3.org/2001/XMLSchema#string> .
<http://schema.org/Person/stuchalk>
<http://xmlns.com/foaf/0.1/mbox>
"schalk@unf.edu"^^<http://www.w3.org/2001/XMLSchema#string> .
 Use layers for data
 Create framework using @context
 Identify the type of ‘chemical thing’ described
 Include ‘table of contents’ for discovery
 Define ‘required’ layers using JSON schema
JSON-LD for Chemical Structure
JSON-LD for
Chemical
Structure
JSON-LD for Chemical Structure
JSON-LD for
Chemical
Structure
JSON-LD for Chemical Structure
JSON-LD for
Chemical
Structure
JSON-LD for
Chemical
Structure
JSON-LD for Chemical Structure
JSON-LD for Chemical Structure
JSON-LD for Chemical Structure
JSON-LD for Chemical Structure
JSON-LD for Chemical Structure
 The JSON-LD file is RDF
 Convert of the files to RDF triples…
 …store in a graph database
 Use Semantic Web languages to do more with
data, e.g. use the Web Ontology Language
https://www.w3.org/OWL/
Building on the JSON-LD
https://en.wikipedia.org/w
iki/Chlorofluoromethane
https://en.wikipedia.org/wiki/
Bromochlorofluoromethane
Protégé
Describing Chemical Concepts
Inferring
Chemical
Concepts
Inferring
Chemical
Concepts
Extending the
Framework
 A semantic framework for storing chemical entity data
has great potential to improve interoperability
 Can be extended as far as chemists can imagine
 Can be used to infer the presence of chemical concepts
 May require the use of more sophisticated semantic
languages – e.g. Shapes Constraint Language (SHACL)
https://www.w3.org/TR/shacl/
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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Open semantic chemical structures

  • 1. Open Structures: Current Issues & Future Plans Open semantic chemical structures: Ideas on the use of JSON-LD for representation of chemical entities Stuart J. Chalk, Department of Chemistry University of North Florida schalk@unf.edu CINF Paper 6 – August 20, 2017
  • 2. Outline  Inspiration  Chemical File Formats  YACFF  JavaScript for Linked Data (JSON-LD)  Building on JSON-LD  Reasoning Chemical Concepts  Conclusion
  • 3.  International Chemical Identifier (InChI) http://www.inchi-trust.org/  Chemical JSON from Open Chemistry https://github.com/OpenChemistry/  Common Standard for eXchange (CSX) https://doi.org/10.1021/acs.jpca.6b10489  Hastings J, Magka D, Batchelor C, et al. Structure- based classification and ontology in chemistry. Journal of Cheminformatics. 2012;4:8. https://doi.org/10.1186/1758-2946-4-8. Inspiration
  • 4.  Over 100 different file formats http://openbabel.org/docs/2.3.0/FileFormats/Overview.html  Represent many different types of information  Atoms, bonds (special bone types), positions, valence, charge, isotope, radical, lone pairs, aromaticity, stereochemistry, groups, mixtures, reactions, markush, line notations, computational properties  Binary, plain text, XML – some open, most not Chemical File Formats
  • 5. Chemical File Formats MJ171500 5 4 0 0 0 0 0 0 0 0999 V2000 -0.3102 0.4946 -0.0220 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7301 -0.0740 -0.7743 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.5159 0.1117 0.8127 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.4187 0.5156 -0.1089 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.5247 1.0372 -0.0454 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 1 5 1 0 0 0 0 M END
  • 6.  No!  A chemical file framework  Built using JavaScript for Linked Data (JSON-LD)  Open  Extensible  Designed for semantic chemical applications  JSON schema can be applied Yet Another Chemical File Format
  • 7.  Technical Recommendation Jan 2014 https://www.w3.org/TR/json-ld/  JSON representation of Resource Description Framework (RDF) https://www.w3.org/RDF/  Representation of ‘things’ using ‘triples’ <subject> <predicate> <object> JavaScript Object Notation for Linked Data (JSON-LD)
  • 8. JavaScript Object Notation for Linked Data (JSON-LD)  @context – aliases  @id – unique id’s  @type – data type  @base – define the type of ‘thing’ that this file is about
  • 9. JavaScript Object Notation for Linked Data (JSON-LD) <http://schema.org/Person/stuchalk> <http://purl.org/dc/terms/identifier> "0000-0002-0703-7776"^^<http://www.w3.org/2001/XMLSchema#string> . <http://schema.org/Person/stuchalk> <http://schema.org/name> "Stuart Chalk"^^<http://www.w3.org/2001/XMLSchema#string> . <http://schema.org/Person/stuchalk> <http://schema.org/worksfor> "University of North Florida"^^<http://www.w3.org/2001/XMLSchema#string> . <http://schema.org/Person/stuchalk> <http://xmlns.com/foaf/0.1/mbox> "schalk@unf.edu"^^<http://www.w3.org/2001/XMLSchema#string> .
  • 10.  Use layers for data  Create framework using @context  Identify the type of ‘chemical thing’ described  Include ‘table of contents’ for discovery  Define ‘required’ layers using JSON schema JSON-LD for Chemical Structure
  • 12. JSON-LD for Chemical Structure
  • 14. JSON-LD for Chemical Structure
  • 17. JSON-LD for Chemical Structure
  • 18. JSON-LD for Chemical Structure
  • 19. JSON-LD for Chemical Structure
  • 20. JSON-LD for Chemical Structure
  • 21. JSON-LD for Chemical Structure
  • 22.  The JSON-LD file is RDF  Convert of the files to RDF triples…  …store in a graph database  Use Semantic Web languages to do more with data, e.g. use the Web Ontology Language https://www.w3.org/OWL/ Building on the JSON-LD
  • 28.  A semantic framework for storing chemical entity data has great potential to improve interoperability  Can be extended as far as chemists can imagine  Can be used to infer the presence of chemical concepts  May require the use of more sophisticated semantic languages – e.g. Shapes Constraint Language (SHACL) https://www.w3.org/TR/shacl/ Conclusions
  • 29.  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?