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Research data supporting "A chemical species ontology for data integration and knowledge discovery"

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Pascazio, Laura 
Naseri, Ali 
Mosbach, Sebastian 
Akroyd, Jethro 


  • inchi-list.csv: The file contains a list of InChI (International Chemical Identifier) given as input to the software agent (PubChemAgent) used to populate the knowledge graph.
  • OntoSpecies.owl: OntoSpecies TBox (see preprint for detailed explanation) containing the full class and relational definitions.


Software / Usage instructions

- inchi-list.csv: The agent described in the manuscript takes an inchi string as input. The software agent source code is publicly available on GitHub (see link provided) under the MIT licence. This agent can be installed locally using the installation script provided or building and running the docker image. The agent can be used as a simple command line tool or as a web agent. The agent can be run from the command line via the `pubchemagent` command which accepts the following option: pubchemagent --inchi='inchistring' or as web agent sending a http request of the type: http://localhost:3838/pubchemagent/query/species?inchi='inchi_string' More information on how to install the software can be found in the README file in the github folder. - OntoSpecies.owl: The TBox is not directly used by the software but helps the structure of the ontology and to construct special SPARQL queries. It can be visualised with any ontology visualisation tool, such as WebVOWL.


OntoSpecies, The World Avatar, web ontology


This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore under its Campus for Research Excellence and Technological Enterprise (CREATE) programme. Part of this work was supported by Towards Turing 2.0 under the EPSRC Grant EP/W037211/1 and The Alan Turing Institute. S. D. Rihm acknowledges financial support from Fitzwilliam College, Cambridge, and the Cambridge Trust. M. Kraft gratefully acknowledges the support of the Alexander von Humboldt Foundation. For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising.

Version History

Now showing 1 - 2 of 2
2023-09-25 13:16:36
Additional and updated files from the original version following peer review of the associated paper
2023-07-06 08:45:48
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