The OBO Data Converter reads an Ontology file in the OBO format and converts the data to a tab-delimited text file.

OBO files are described at https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html and are typically edited / managed using OBO-Edit: https://wiki.geneontology.org/index.php/OBO-Edit

Downloads

Download a .zip file with the executable from: https://github.com/PNNL-Comp-Mass-Spec/OBO-Data-Converter/releases

Syntax

OBODataConverter.exe
 InputFilePath [/O:OutputFilePath] [/PK:Suffix] 
 [/NoP] [/NoG] 
 [/Def] [/StripQuotes] 
 [/Com] [/NoObsolete] 
 [/Postgres]

The input file is the OBO file to convert

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

When using /Def, use /StripQuotes to look for definitions of the form "Description of term" [Ontology:Source] and only include the text between the double quotes as the definition

• Using /StripQuotes auto-enables /Def

By default the output file will not include the term comments

• Include them with /Com

Use /NoObsolete to exclude obsolete terms

Syntax Example

rem Syntax when importing into Postgres
OBODataConverter.exe psi-ms_4.1.80.obo psi-ms_4.1.80_WithDefinition_StripQuotes_IncludeObsolete.txt /Def /StripQuotes /Com /PK:MS1 /Postgres

rem Syntax when importing into SQL Server
OBODataConverter.exe psi-ms_4.1.80.obo psi-ms_4.1.80_WithDefinition_StripQuotes_IncludeObsolete.txt /Def /StripQuotes /Com /PK:MS1

Contacts

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/OBO-Data-Converter

License

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