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Topology of pathway differences between pathway-tools and .owl file

asked 2020-02-18 12:43:36 -0500

JW Carlson gravatar image

Hello, I am using paxtools to parse level 2 and/or 3 .owl files exported from MetaCyc and I've noticed differences between the pathway topology between my parsed output and the view from pathway-tools.

This is one example. I've looked a MetaCyc in version 23.5 for PWY-5733 germacrene biosynthesis. My parsing for the left and right components (getLEFT and getRIGHT in the level 2 parser) and the next reaction step (getNEXT_STEP in level 2-speak) is:

RXN-11527 ReactionStandardName pathwayStep530476
Left component: (2E,6E)-farnesyl diphosphate
Right component: diphosphate
Right component: (+)-germacrene A

RXN-8939 ReactionStandardNamer pathwayStep530477
Left component: (2E,6E)-farnesyl diphosphate
Right component: (+)-germacrene D
Right component: diphosphate
Next step pathwayStep530478
Next step pathwayStep530479
Next step pathwayStep530480

RXN-8562 ReactionStandardName pathwayStep530478
Left component: (2E,6E)-farnesyl diphosphate
Right component: diphosphate
Right component: (-)-germacrene D
Next step pathwayStep530480

RXN-8561 ReactionStandardName pathwayStep530479
Left component: (2E,6E)-farnesyl diphosphate
Right component: germacrene C
Right component: diphosphate
Next step pathwayStep530480

RXN-8553 ReactionStandardName pathwayStep530480
Left component: (2E,6E)-farnesyl diphosphate
Right component: (E,E)-germacrene B
Right component: diphosphate

The information regarding the left and right components of each reaction agrees with the view in pathway-tools. However the next step information links the reactions in a way not otherwise present. My reading of the .owl files confirm that these reactions are linked. Is there a problem in creating the .owl files? Or is my parsing incorrect?

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answered 2020-03-05 14:25:48 -0500

Suzanne Paley gravatar image

Hi, it looks like the problem is not with our biopax output but with how that particular pathway is represented within our database. Although it's done in a way that doesn't affect how the pathway diagram looks on our page, that step ordering is actually erroneously present in our internal representation of that pathway. I have just fixed this pathway so it is now represented correctly (so should not generate any next-step relationships at all), but the changes won't be available until after our next metacyc release. Thanks for reporting this.

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Hi Suzanne, Thanks for your answer. I've started to look into again and it appears that the topology is correctly represented in the various files pathways.dat, compounds.dat, ... In general are these files a more reliable source of truth than the exported .owl files?

JW Carlson gravatar imageJW Carlson ( 2020-04-02 18:05:23 -0500 )edit

Those files are closer to our internal representation of the data than are the owl files, so, to the extent that misrepresentations or loss of precision can creep in when converting our internal format to biopax, I would say they are more reliable. If we have errors in our data, they will appear in both places though (though perhaps they will manifest in different ways).

Suzanne Paley gravatar imageSuzanne Paley ( 2020-04-03 17:03:00 -0500 )edit
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answered 2020-02-18 19:19:20 -0500

JW Carlson gravatar image

Maybe I should have added (without expecting people to review the pathway) is that pathway-tools shows all reactions with a left component (2E,6E)-farnesyl diphosphate and right components diphosphate and a germacrene. There are no connections between the reactions.

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Asked: 2020-02-18 12:43:36 -0500

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Last updated: Mar 05