biopax2cabiom is a script to transform BioPAX RDF data from a triplestore to a CADBIOM model.

usage: biopax2cabiom [-h] [-vv [VERBOSE]] {tests,model} ...

Named Arguments

-vv, --verbose Default: “info”



Translate BioPAX test cases to cadbiom models and compares
them with the cadbiom model reference (if it exists).
biopax2cabiom tests [-h]


Build CADBIOM model based on BioPAX data obtained from a triplestore.

biopax2cabiom model [-h]
                    (--getGraphUris | --listOfGraphUri LISTOFGRAPHURI [LISTOFGRAPHURI ...])
                    [--provenanceUri [PROVENANCEURI]]
                    [--triplestore [TRIPLESTORE]]
                    [--limit_sparql_results [LIMIT_SPARQL_RESULTS]]
                    [--pickleBackup] [--pickleDir [PICKLEDIR]]
                    [--cadbiomFile [CADBIOMFILE]] [--convertFullGraph]
                    [--numericCompartmentsNames] [--no_scc_fix]
                    [--blacklist [BLACKLIST]]

Named Arguments


Get the list of RDF and BioPAX graphs stored on the triplestore.

Default: False

 List of RDF graphs to be queried on the triplestore.
 URI of the queried subgraphs.

URL of the triplestore.

Default: “


Limit the number of results for each SPARQL query.This allows to fine-tune the requests depending on the server being queried.

Default: 4000


Allows to save/reuse the results of SPARQL queries.The goal is to save querying time during tests with same inputs.

Default: False


Output file path to save the script variables.

Default: “/tmp/backupPickle/backup.p”


Filepath of the created Cadbiom model.Two models are created: A default model and a model without strongly connected components that block the solver of CADBIOM.

Default: “output/model.bcx”


Converts all entities to Cadbiom nodes, even entities not involved in reactions.

Default: False


If set, names of compartments will be based on numeric values instead of their real names.

Default: False


If set, strongly connected components will NOT be fixed in a second model file.

Default: False

--blacklist If set, entities of the given file will beexcluded from conditions of transitions (ex: cofactors or entities of energy metabolism)