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