Usage

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

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

Named Arguments

-vv, --verbose Default: “info”

Sub-commands:

tests

Run unit tests. Translate BioPAX test cases to Cadbiom models and
compare them to the reference models.
biopax2cabiom tests [-h]

model

Build a Cadbiom model based on the BioPAX data obtained from a triplestore.

biopax2cabiom model [-h]
                    (--get_graph_uris | --graph_uris GRAPH_URIS [GRAPH_URIS ...])
                    [--provenance_uri [PROVENANCE_URI]]
                    [--triplestore [TRIPLESTORE]] [--limit [LIMIT]]
                    [--backup_queries] [--backup_file [BACKUP_FILE]]
                    [--cadbiom_model [CADBIOM_MODEL]] [--full_graph]
                    [--numeric_compartments] [--no_scc_fix]
                    [--blacklist_file [BLACKLIST_FILE]] [--show_metrics]

Triplestore options

--get_graph_uris
 

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

Default: False

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

Address (URL) of the triplestore endpoint.

Default: “http://127.0.0.1:8890/sparql/

--limit

Limit the size of data chuncks retrieved by a SPARQL query. This makes it possible to fine-tune the requests according to the configuration of the server queried.

Default: 4000

Backup options

--backup_queries
 

Allow to save and reload the results of SPARQL queries without re-interrogating the server. The goal is to save time and bandwidth on requests as long as the server data does not change.

Default: False

--backup_file

Backup file to save and reload the results of SPARQL queries.

Default: “backup.p”

Cadbiom model options

--cadbiom_model
 

Filepath of the created Cadbiom model.Two models are created by default: A default model, and a model without Strongly Connected Components. See –no_scc_fix.

Default: “output/model.bcx”

--full_graph

Convert all entities to Cadbiom nodes, even the members of classes that aren’ involved in reactions.

Default: False

--numeric_compartments
 

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

Default: False

--no_scc_fix

If set, strongly connected components will NOT be fixed in asecond model.

Default: False

--blacklist_file
 File which provides uris of entities that will be removed from the model (use it to eliminate cofactors or entities from energy metabolism for example).
--show_metrics

Provide a summary about the data ready to be used to design a model.

Default: False

remove_scc

Remove Strongly Connected Components from a Cadbiom model.

biopax2cabiom remove_scc [-h] cadbiom_model

Positional Arguments

cadbiom_model Cadbiom model (.bcx file) from which strongly connected componentswill be deleted to give a new model.