[Gramene] SorghumCyc Feedback: upgrading Sorghumcyc 12.5 into 14

[Sidibe bocs Stephanie]

Dear curators,

As explained below, we have problems  upgrading from your SorghumCyc 
database obtained with the PathwayTools version 12.5 into our 
PathwayTools version 14.0.
The ptools-support don't support the old pathway tools versions and 
suggested to contact you  to obtained an upgraded version of your  work.
Do you have the same problem? Could you please update SorghumCyc for 
Pathway Tools version 14.0 ?

Thank you very much for your help, best regards,

Le 24/06/2010 21:43, Markus Krummenacker a écrit :
> Sidibe bocs Stephanie writes:
>   >  Dear all,
>   >
>   >  We downloaded BioCyc / Pathway Tools Bundle Version 14.0.
>   >  For a first try, we want to browse and compare of already computed plant
>   >  data from our Web server connected to our database server.
>   >  So we also downloaded riceCyc, AraCyc, PoplarCyc, PlantCyc
>   >  http://www.plantcyc.org:1555/ARA/server.html?
>   >  http://www.gramene.org/pathway/
>   >
>   >  Apparently there is a problem of version compatibility and the update
>   >  process does not work (see details below).
>   >  Should we work with the 12.5 Biocyc version ? if yes, where can we
>   >  download it ?
>
> Hi,
>
> Due to limited resources, we generally can't support such an old
> Pathway Tools version, and it is no longer made available for download.
>
> But it is true that the upgrade of various plant-related PGDBs from
> 12.5 to 14.0 caused several problems.  If I understand the situation,
> PlantCyc and AraCyc have been successfully upgraded by now.  I don't
> know when those new versions are made available for download.
>
> I suggest that you contact the staff at PlantCyc directly, and ask
> them how you could obtain the upgraded versions that work with Pathway
> Tools 14.0 .  This will save you a lot of problems.
>
>    

--------------------------------------------------------------------------------------------------
I have problems with three biocyc databases : aracyc, plantcyc and 
sorghumcyc.
When I use pathwaytools in Web mode with this commande line
$ ./pathway-tools -www

This dialogue window open :
The following PGDB(s) were built with, or last upgraded to Pathway Tools 
version 12.5, and may be incompatible with the current Pathway Tools 
version 14.0. Do you wish to upgrade now ?
If you choose to upgrade now, you will need to specify a new version 
number for each PGDB.
If you choose not to upgrade, Pathway Tools will exit.
Arabidopsis thaliana col (ARA)
PlantCyc (PLANT)
Sorghum biolor BTx623 (SORGHUM)

I click on Upgrade Now, the window for changing the version number for 
each PGDB opens and when I click on OK , this window close and I have 
this error message :

244931920 bytes have been tenured, next gc will be global.
See the documentation for variable EXCL:*GLOBAL-GC-BEHAVIOR* for more 
information.
Error: Invalid frame name RNA(N) in KB ARABASE:
  Frame name "RNA(N)" contains the illegal character "("
Error: KB ARABASE contains one or more frames whose names
(unique identifiers) are syntactically invalid
(contain illegal characters or exceed the allowed length).
  [condition type: INVALID-FRAME-NAME]

Restart actions (select using :continue):
0: Abort entirely from this (lisp) process.

[changing package from "COMMON-LISP-USER" to "ECOCYC"]
[Current process: Initial Lisp Listener]

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