PANTHER Pathway - no Controls explicitely included (e.g., in pathwayComponet), but some reactions are in fact catalysed

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Data source: PANTHER Pathways 3.2.1, 05-Jun-2013
Date downloaded: 22 August 2013
Version, if available: 3.2.1
File name downloaded:
File location: ftp://ftp.pantherdb.org/pathway/3.2.1/BioPAX.tar.gz

Data source issue: For all PANTHER pathways, pathway.pathwayComponent does not 
contain any Controls, only reactions, whereas some reactions are controlled by 
(Catalyses). Also, pathwayOrder, pathway steps, are not used (where the 
relationship between controls and a reaction could be stored as well). The 
problem is that, if given a pathway one traverses into all its properties, then 
no Controls can be seen among pathway's child biopax elements (to find those - 
relationships between controls and reactions - one has to either start from all 
controls instead, or - lookup controlledOf inverse biopax property of each 
member reaction, which, although is fortunately possible with Paxtools, is not 
part of the BioPAX specification).
Currently, using Cytoscape CyPath2 app, if you find and get by URI a Panther's 
pathway from PC2, the network will contain only reactions and their 
participants, and no catalyses.

Is the data source aware of the issue?
Yes. We're waiting for comments and final decision.

We can fix this in the PantherCleanerImpl for the next release, or the data 
provider will fix,  or we'd temporarily fix/hack in the "/get" (by URI) web 
service logic (for current release)...

Original issue reported on code.google.com by rod...@gmail.com on 3 Dec 2013 at 9:24

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Fixed in the "/get" (by URI) web service logic (in CPathServiceImpl.fetch)

Original comment by rod...@gmail.com on 9 Dec 2013 at 3:37

• Changed state: Fixed

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Now fixed in the PantherCleaner. And, previous fix (cod) probably can be 
removed from the CPathServiceImpl.fetch method, for it's not required anymore. 
See issue #189

Original comment by rod...@gmail.com on 16 Oct 2014 at 8:32