Verbose and debug output¶
Biopax2Cadbiom comes with a build feature that can outputs a lot of debug information when enabled.
Logs are stored in
/tmp/biopax2cadbiom.log on GNU/Linux. By default the logging level outputs only
warnings and errors, but the verbosity can be increased with a similar command:
$ biopax2cadbiom -vv debug ...
Warnings and permanent nodes¶
During the conversion, some warnings with the following format can be generated:
WARNING: Reflexive transition: <ENTITY> -> <ENTITY> - This transition will not be taken into account. Please review your model or use a PermanentNode instead.
This means that a transition reflects an autogeneration of an entity in the translated network. This is not usually supposed to happen and when the Cadbiom model is loaded, these transitions will not be interpreted.
During the development, these warnings help to solve and identify the unsupported cases of the BioPAX standard. However, in a release version, these are often inconsistencies in the BioPAX file. In the following you will find a number of real cases accompanied by explanations.
Inconsistencies in ModificationFeatures¶
STAT1-3 (dimer)that contains two dimeric complexes:
STAT3(ids: Complex_4db5f804f0956c670c3408800208ecd7, Complex_177aaa44ccf4e366dd236d4775e2f28c). However, each complexes already have a ModificationFeatures characterizing their activation. Therefore when decompiling classes, and applying their own modifications to their child entities, we obtain two auto-generating reactions for respectively
STAT3__dimer___1a. The problem is that dimers should not have posttranslational modifications here.
Useless reaction 1¶
Delta_1_1a -> Delta_1_1aand
sDelta_1_1a -> sDelta_1_1atransitions are useless in the final model. Note that Chibe does not distinguish
Delta_1_1aand displays the name of the gene instead (
Useless reaction 2¶
Useless reaction 3¶
Useless reaction 4¶
Useless reaction 5¶
There may be errors related to the translation of some interactions defined in the BioPAX formalism.
Type of reaction is deliberately unsupported because it is too imprecise: <BIOPAX_URI>
According to the BioPAX standard ,
MolecularInteractionsare produced by high throughput systems that does not satisfy the level of detail (i.e. enough experimental evidence) required to model them with
ComplexAssemblyclass. These interactions will not be translated.
UNEXCEPTED REACTION: <BIOPAX_URI>
During the development of Biopax2Cadbiom, we have never encountered this type of interaction in the databases used. These interactions will not be translated.
|||BioPAX – Biological Pathways Exchange Language - Level 3, Release Version 1 Documentation, 2010. Available: http://www.biopax.org/release/biopax-level3.owl|