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


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Authors

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

Description

-ontospecies_aboxes_april2023_allspecies.ttl: data dump in Turtle format that contains information about OntoSpecies ABoxes as of April 2023. It encompasses information on approximately 35,000 species and it provides a wide range of data related to these species. Turtle is a serialization format for RDF data, commonly used to represent semantic information. -ontospecies_aboxes_april2023_500species.ttl: data dump of the OntoSpecies ABoxes subset used for SHACL validation in Turtle format. SHACL is a specification for describing and validating the shapes (structure and constraints) that RDF data should adhere to. -ontospecies_v2-shapesfile.ttl: file that contains SHACL shapes that specify the expected structure and constraints for the data in ontospecies_aboxes_april2023_500species.ttl. -shacl_validation_log.txt: log file of SHACL validation. -OntoSpecies_v2-revised.owl: This file represents a revised version of the OntoSpecies TBox (ontology schema or terminology) after incorporating feedback and comments from reviewers. -use-cases-notebooks.zip: The notebooks in this zip file contain code to reproduce the results of use cases related to the OntoSpecies data and ontology. They can provide guidance on how to work with the OntoSpecies data, perform analyses, and use the ontology for various purposes.

Version

Software / Usage instructions

-ontospecies_aboxes_april2023_500species.ttl and ontospecies_v2-shapesfile.ttl: These files can be used as input to any SHACL validation tool (like pySHACL) to validate the RDF data in ontospecies_aboxes_april2023_500species.ttl against the SHACL shapes defined in ontospecies_v2-shapesfile.ttl. -use-cases-notebooks.zip: file can be run as Jupyther notebooks.

Keywords

OntoSpecies, The World Avatar, web ontology

Publisher

Sponsorship
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.
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Version History

Now showing 1 - 2 of 2
VersionDateSummary
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
* Selected version