Splitting outputs from logic operators

[hasanbalci]

Moved from sbgn/process-descriptions#159 since it is actually related to Activity Flow.

The issue was previously mentioned in this discussion:
https://groups.google.com/forum/#!msg/sbgn-discuss/JAiPkj883CM/7uwVwbv5DAAJ

[adrienrougny]

As mentioned in the discussion, while the issue is relevant, the example is not (it makes no sense to represent metabolic processes as the one above in AF).

[hasanbalci]

Augustin: Allow some of these but only in simple cases. Rupert is uncomfortable with potential implications.

[adrienrougny]

@cannin @rupertoverall What would be those allowed/not allowed and what could be the undesired implications?

[hasanbalci]

Related to this issue: https://groups.google.com/g/sbgn-discuss/c/d9Xsy_uos2w/m/cnrAQ10DCgAJ

[adrienrougny]

The example we talked about during HARMONY:
demerging_arcs.pdf

Sample network comes from Figure 2 https://pmc.ncbi.nlm.nih.gov/articles/PMC6070353/

[cannin]

@adrienrougny it seems like your figure is missing port lines for the logical operators?

[hasanbalci]

I have drawn the example with ports:

[hasanbalci]

Here is the link to community conversation about the proposal: https://groups.google.com/g/sbgn-discuss/c/xciT6orrioQ

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I wanted ChatGPT to summarize the pros and cons of the proposal based on email conversation:

Advantages
A. Visual Clarity & Layout

• Reduces Visual Redundancy: Allows merging of repeated logic gates with identical inputs, minimizing duplication and visual clutter.

• Improves Readability: Simplifies complex maps, making them easier to interpret for both human readers and visual analysis.

B. Flexibility & Compatibility

• Optional Use: This feature is not mandatory. Users may choose to apply it selectively or continue using the current representation style.

• Preserves Logical Meaning: The change is purely syntactic; it does not alter the semantics or biological interpretation of the network.

• Tool-Compatible with Minimal Adjustment: Software tools can process multi-output gates by replicating them internally, preserving compatibility with current models.

C. Conceptual Familiarity

• Aligns with Established Practices: Follows the standard "fan-out" concept used in logic circuits and other diagram types, making it intuitive for many users.

Disadvantages
A. Interpretation Risks

• Possible Misinterpretation: Users may mistake a single logic gate with multiple outputs as representing one event with multiple simultaneous outcomes, rather than distinct downstream processes.

• Increases Cognitive Load: Merged logic may require more mental effort to understand, especially for users accustomed to clearly separated elements.

B. Metadata and Modeling Concerns

• Loss of Metadata Clarity: Merging arcs could obscure or conflate annotations such as reaction priorities, timing, or associated enzymes.

• Breaks One-to-One Mapping with Models: Simplified visual structures may not align cleanly with elements in structured biological models (e.g., SBML), complicating annotation and traceability.

C. Automation & Standardization Issues

• Challenges for Automation: Parsing and processing diagrams with multi-output gates may increase complexity in automated pipelines or graph-based analyses.

• Inconsistency in Visual Representations: Optional merging introduces visual variability—multiple valid diagram layouts may exist for the same logic, reducing standardization and making visual comparison harder.

D. Alternative Approaches

• Layout Optimization as an Alternative: Some visual issues could potentially be addressed through improved layout techniques (e.g., aligning or overlaying repeated gates), without modifying the notation.

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I also asked ChatGPT's opinion on accepting or rejecting this proposal:

Recommendation: Accept the Proposal with Caution and Guidance
The proposal to allow logic gates with multiple outputs should be accepted as an optional visual simplification, provided that it is supported by clear guidance and tooling safeguards.

Rationale

• Improves clarity in complex diagrams by reducing visual redundancy.

• Preserves semantics—the change is syntactic only and does not alter biological meaning.

• Optional—users and tools can continue using the current style if preferred.

• Aligns with familiar patterns like fan-out in logic circuits.

However, to address valid concerns:

• Tools should warn or prevent metadata loss when merging.

• A mechanism to toggle between simplified and expanded views is recommended.

• Clear usage guidelines should be provided to avoid confusion or inconsistent interpretations.