Differences in a participant's state/feature leads to disconnected pathway in biopax/sbgn

[jvwong]

In examining several SBGN versions of pathways derived from Biofactoid, have noticed when a state-change is involved, it leads to a 'disjoint' or break in the set of interactions. Clearly, this is because assigning state (even explicitly assigning the absence of a feature/modification) creates distinct pools of the entity. At best it looks odd to have a single binary network (in biofactoid/SIF) look like multiple disjoint interaction sets (e.g. in PC/SBGN).

Illustrate this with an example for Waters et al. Cell Rep (2021):

The corresponding BioPAX/SBGN version(viewed in pc apps)

Note that BCAR1 above is the official symbol for p130Cas (in biofactoid).

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While this seems technically correct, it appears strange to take each interaction 'out of context' from other interactions. I wonder if there is a better way to handle this type of conversion.

[gbader]

A reaction/interaction would be needed to link these entities. One could be created automatically by biofactoid. We'd need to analyze examples to see what interaction types are needed.

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On Mon., Jun. 27, 2022, 5:52 p.m. Jeffrey, ***@***.***> wrote: In examining several SBGN versions of pathways derived from Biofactoid, have noticed when a state-change is involved, it leads to a 'disjoint' or break in the set of interactions. Clearly, this is because assigning state (even explicitly assigning the absence of a feature/modification) creates distinct pools of the entity. At best it looks odd to have a single binary network (in biofactoid/SIF) look like multiple disjoint interaction sets (e.g. in PC/SBGN). Illustrate this with an example for Waters et al. Cell Rep (2021) <https://biofactoid.org/document/69e71b02-82db-4f12-ac5b-0fd3d68dba48>: [image: Screen Shot 2022-06-27 at 5 47 02 PM] <https://user-images.githubusercontent.com/4706307/176041367-12af9f16-93f0-4934-aab0-b7062381dec7.png> The corresponding BioPAX/SBGN version(viewed in pc apps) <https://appsbeta.pathwaycommons.org/pathways?uri=http%3A%2F%2Fpathwaycommons.org%2Fpc13%2FPathway_81ca40a63b8cd13eac953b56331918ad> [image: pcapps_Targetingp130Cas] <https://user-images.githubusercontent.com/4706307/176041484-4a341b41-cdcc-4323-be58-d7b1218f6e12.png> Note that BCAR1 above is the official symbol for p130Cas (in biofactoid). ------------------------------ While this seems technically correct, it appears strange to take each interaction 'out of context' from other interactions. I wonder if there is a better way to handle this type of conversion. — Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHRPZ5J37MJCRBV4IMSZ5TVRIPA7ANCNFSM5Z76TNEQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jvwong]

A reaction/interaction would be needed to link these entities.

I can post more examples below.

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For the above example, it occurs to me that the author intended to say that "Phosphorylated form of p130Cas (BCAR1-p) activates DOCK1" so perhaps there's indeed something lost in the translation.

[jvwong]

Example with modifications splitting a pathway in 3 chunks Zheng et al. Theranostics (2019):

Biofactoid doc:

BioPAX/SBGN

[jvwong]

Example with seemingly duplicate entity (UBE2A) Cell Rep 31 2020:

Biofactoid:

BioPAX/SBGN:

[gbader]

Could you link to the biopax?

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On Tue., Jun. 28, 2022, 2:09 p.m. Jeffrey, ***@***.***> wrote: Example with seemingly duplicate entity (UBE2A) Cell Rep 31 2020 <https://www.doi.org/10.1016/j.celrep.2020.107542>: Biofactoid <https://biofactoid.org/document/2753be81-1b79-4582-adaa-aea258ba24b2>: BioPAX/SBGN: [image: factoid] <https://user-images.githubusercontent.com/4706307/176252739-050a5115-c4b7-4aaf-b535-3728c768e108.png> [image: SBGN] <https://user-images.githubusercontent.com/4706307/176252693-b7b4c013-216c-453b-99f7-629330fd50ab.png> — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHRPZ4UZPU2PHZO4FNH73LVRM5WXANCNFSM5Z76TNEQ> . You are receiving this because you commented.Message ID: ***@***.***>

[jvwong]

I linked it above and in #30

[jvwong]

I think there's two separate issues in the previous discussion worth distinguishing:

1. Participant is assigned some state and is inferred from the Biofactoid based on the type of interaction. For instance, a modification in Biofactoid translates to a BioPAX control/conversion where the controlled participant gets some state via the converter. This, in fact, is by design, and was discussed in the "Factoid binary interaction types" Google Doc.

e.g. #28 (comment)

2. Duplicate. This seems to be a bug.

e.g. #30