1. A Standard Data Format for
Computational Chemistry: CSX
Stuart J. Chalk1,2, Neil Ostlund1, Mirek Sopek1, Bing Wang1
1) Chemical Semantics Inc., Gainesville FL
2) Department of Chemistry, University of North Florida
schalk@unf.edu
249th ACS Meeting, Denver, CO – March 2015

2.  Semantic Annotation of Data
 Current DOE Project
 Data Transformations
 Common Standard for eXchange (CSX)
 CSX a Standard Data Format
 The CSX Schema
 CSX - Publishing Information
 CSX - Molecular System Information
 CSX - Calculated Result Information
 Future Plans
 Conclusion
Outline

3.  Create a way to ‘teach’ computers what information
means – contextualize the data
 Example
 What is this? 904-620-1938
 A computer just sees it as…
 … a string
 By using an appropriate semantic definition in RDF (the
Resource Description Framework) we can identify to the
computer that the text is a phone number (using the
Friend of a Friend (FOAF) specification), i.e.
Semantic Annotation of Data
RDF Specification http://www.w3.org/RDF/
FOAF Specification http://xmlns.com/foaf/spec/
<foaf:phone rdf:datatype=“#string">904-620-1938</foaf:phone>

4.  RDF can be use to relate information as well as
annotate it
 The following RDF/XML shows how some information is
related (XML is the eXtensible Markup Language)
 Applying this technology to computational chemistry
calculations will allow integration of the calculation and
results with data about chemicals from other sources
Semantic Annotation of Data
<rdf:Description rdf:about=http://example.org/StuartChalk>
<rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Person"/>
<foaf:knows rdf:resource="http://example.org/NeilOstlund"/>
<foaf:phone rdf:datatype=”…#string”>904-620-
1938</foaf:phone>
</rdf:Description>

5.  Chemical Semantics is funded by DOE to create a web
portal to collect, organize and make searchable the
results output from computational chemistry (CC)
calculations
 This will be freely available and will accept output
from all CC software packages
 The intent is to capture calculation results and…
 Software used to calculate the results
 Input parameters used in the calculation
 Methodology by which the calculation was done
 Details of the molecular system studied
DOE SBIR Grant

6.  The approach Chemical Semantics is taking is to
1. Add code to software packages to generate an XML file
alongside the normal output file –OR–
Parse an existing output file (using a free application) and
generate XML file
2. Send the XML file into the web portal
3. Convert the XML file into RDF into turtle format (TTL)
4. Finally, ingest TTL into a triplestore (Virtuoso)
 All the data in Virtuoso can then be search using SPARQL
(SPARQL Protocol and RDF Query Language)
Data Transformations
Virtuoso http://virtuoso.openlinksw.com/
SPARQL http://www.w3.org/TR/sparql11-query/

7.  Why XML?
 Human readable (plain text - UTF-8)
 Platform neutral
 Archivable
 Validatable
 Why not use CML?
 Inability to represent complex structures e.g. residues
 No standard way to add CC results
Intermediate XML File

8.  A CSX file is a text based file written in XML
 It is a structured data container design to hold CC
result data and additional metadata
 Version 0.x was developed by Neil Ostlund
 Version 1.0 is the current stable release developed as
part of Phase 1 of the SBIR grant (limited scope)
 Version 2.0 is currently under development as part of
Phase 2 of the SBIR grant
Common Standard for eXchange (CSX)

9.  It is well know that the formats in which data is
reported in CC output files is:
 Highly variable (software specific)
 Sometimes difficult to interpret
 Standardization would:
 Allow data from different packages to be more easily
compared
 Open up opportunities for software development to
display and reuse data for different applications
 This mirrors movement in the CC community toward a
common driver base for CC software packages
CSX as a Standard Data Format

10.  In order to describe the layout and allowed names of
elements and attributes, and values for both, a schema
document is available for the CSX specification
 This can be used to help new users write valid CSX files
(using XML editing applications such as XML Spy and
oxygenXML) and…
 … validate existing CSX files using any of a number of
XML validators (e.g. Xerces) …
 … and understand the structure of the data especially
for less frequently calculated results
The CSX Schema

11. CSX Schema v1.0

12. CSX Schema v1.0

13. CSX Schema v1.0

14. CSX Schema v1.0

15. CSX – Publication Information

16. CSX – Molecular System Information

17. CSX – Calculated Result Information

18.  Work on CSX 2.0 is ongoing – expand to multiple systems
and sets of calculated results
 Develop CSX focused website with converter
functionality, libraries, and documentation
 Engage CC software users/programmers to get involved
with the project
 Organize a community developer workshop over
summer 2015
 Publish version 2.0 of CSX in Fall 2015
Future Plans

19.  CSX started out as a stepping stone to transfer
information to the CS portal
 Having a data standard for CC is an important
development in of itself
 The CC community can do more with their data
 Leverage XML tools to visualize, process etc…
 Compare results across CC packages
 Validate results
 Reference basis sets (https://bse.pnl.gov/)
Conclusion

20.  schalk@unf.edu
 Phone: 904-620-1938
 Skype: stuartchalk
 LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
 ResearcherID: http://www.researcherid.com/rid/D-8577-2013
Questions?