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unable to convert owl format to obo #1001
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Hey @lmanchon
Has nothing to do with OBO. Just ignore it #829 OBO structure:
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You also asked elswhere where to get OBO files from? Many OBO Foundry ontologies provide OBO format outputs, but to be honest, most use For downstream processing I recommend using ROBOT table generation processes: https://oboacademy.github.io/obook/tutorial/sparql-report-robot/ |
so nothing obvious for the owl --> obo conversion. |
To be honest, I think this would be a great ROBOT feature. I struggle with this so much as well. I have been debugging dozens of OBO format violations. |
it's a problem with all these file formats. |
The OBO community requires all projects to publish an OWL file in RDF/XML format as their primary release product. All other products are optional. If you use OBO community projects, building your tools to use OWL in RDF/OWL format makes good sense, so why doesn't everybody do that?
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-Hi,
last version of robot failed to convert this owl file:
https://raw.githubusercontent.com/stemcellontologyresource/OSCI/master/src/ontology/osci.owl
is there a specific parameter i need to add ? Thank you.
java -jar ./robot.jar convert --input osci.owl --format obo --output osci.obo
ERROR Input ontology contains 3 triple(s) that could not be parsed:
OBO STRUCTURE ERROR Ontology does not conform to OBO structure rules:
multiple def tags not allowed. in frame:Frame(CLO:0000001 id( CLO:0000001)comment( A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. )name( cell line cell)property_value( IAO:0000111 cell line cell xsd:string)def( A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture)def( A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
)property_value( IAO:0000412 http://purl.obolibrary.org/obo/clo.owl)property_value( IAO:0000117 Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters xsd:string)property_value( IAO:0000412 http://purl.obolibrary.org/obo/obi.owl)relationship( RO:0001000 CL:0000001)is_a( OBI:0001866{{is_inferred=true} }))
For details see: http://robot.obolibrary.org/errors#obo-structure-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
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