Examples

Test cases

Reactome - Homarus_americanus.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/homarus

ImageOfHomarusTestCase

Reactome - Crithidia_fasciculata.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/crithidia

ImageOfCrithidiaTestCase

Reactome - Vigna_radiata_var._radiata.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/vigna

ImageOfVignaTestCase

ImageOfVignaTestCase

Reactome - Triticum_aestivum.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/triticum

ImageOfTriticumTestCase

Reactome - Cavia_porcellus.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/cavia

ImageOfCaviaTestCase

Virtual Cases - virtualCase1.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/1

ImageOfVirtualCase1

Virtual Cases - virtualCase2.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/2

ImageOfVirtualCase2

Reactome - Escherichia_coli.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/escherichia

ImageOfEscherichia

Reactome - Cricetulus_griseus.owl

Command: python -m biopax2cadbiom --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/cricetulus

ImageOfEscherichia

Reactome - Mycobacterium_tuberculosis.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://reactome.org/mycobacterium

Virtual Cases - virtualCase3.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/3

ImageOfVirtualCase3

Virtual Cases - virtualCase4.owl

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/4

ImageOfVirtualCase4

Virtual Cases - virtualCase5.owl

Command: python -m biopax2cadbiom model --convertFullGraph --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/5

ImageOfVirtualCase5

Virtual Cases - virtualCase6.owl

Challenge: A class A with 2 members A1 and A2 that are not reused elsewhere. A is a component of the complex AB that regulates the reaction C -> D. Without –convertFullGraph, A1 and A2 must not be present in the model.

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/6

ImageOfVirtualCase6

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/6 --convertFullGraph

ImageOfVirtualCase6full

Virtual Cases - virtualCase6b.owl

Challenge: Same as virtualCase6 but A is a simple protein instead a class.

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/6b

ImageOfVirtualCase6b

Virtual Cases - virtualCase7.owl

Challenge: A class A with 3 members A1, A2 and A3; A1 and A3 are reused elsewhere. A1 is a control of the reaction B -> C. A3 participates to the reaction A3 -> D and A participates to the reaction A -> E. Without –convertFullGraph, A2 must not be present in the model. Thus A must subsist to represent A1, and a reaction from “A entities” to E must be present to translate the genericity of class A.

PS: From now, in test cases multiple members of classes were not reused in the model.

Command: python -m biopax2cadbiom model --listOfGraphUri http://biopax.org/lvl3 http://virtualcases.org/7

ImageOfVirtualCase7