The OWL Data Converter is a console application that reads an Ontology file in the OWL RDF/XML format and converts the data to a tab-delimited text file.
OWL files are described at https://www.w3.org/TR/owl-parsing/ and can be edited / managed using Protégé, available at https://protege.stanford.edu/products.php#desktop-protege
Download a .zip file with the executable from: https://github.com/PNNL-Comp-Mass-Spec/OWL-Data-Converter/releases
The latest version of the application is available for six months on the AppVeyor CI server
OWLDataConverter.exe
InputFilePath [/O:OutputFilePath] [/PK:Suffix] [/NoP] [/NoG] [/Def] [/Com]
The input file is the OWL file to convert (in RDF/XML format)
Optionally use /O to specify the output path If not provided the output file will have extension .txt or .txt.new
Use /PK to specify the string to append to the ontology term identifier when creating the primary key for the Term_PK column. By default uses /PK:MS1
By default the output file includes parent terms; remove them with /NoP
By default the output file includes grandparent terms; remove them with /NoG
- Using /NoP auto-enables /NoG
By default the output file will not include the term definitions; include them with /Def
By default the output file will not include the term comments; include them with /Com
OWLDataConverter.exe bto.owl /PK:BTO1
Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA) in 2016
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics\
Source code: https://github.com/PNNL-Comp-Mass-Spec/OWL-Data-Converter
Licensed under the Apache License, Version 2.0; you may not use this program except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0