Practical diagram guide
How to prepare a scientific pathway diagram
A useful pathway diagram starts with a list of supported relationships. Decide what you need to explain, draw only that mechanism, and verify every label and arrow before sharing.
By PathwayFig · Reviewed
1. Define the question your figure answers
Write one sentence describing the process and audience: for example, “Show where compound X is hypothesized to inhibit the pathway in our cell model.” Record the organism, tissue or cell type, and experimental condition. Keep an established interaction separate from a proposed mechanism.
2. Build a relationship list from your sources
For each interaction, record the source molecule, target, direction, relationship, compartment, and supporting reference. Add identifiers such as a DOI or PMID to your own source notes. Do not treat a generated diagram as the source of biological evidence.
| Source | Relationship | Target | Evidence note |
|---|---|---|---|
| Ligand A | Binds | Receptor B | Add your source and experimental context |
| Receptor B | Activates | Kinase C | Specify direct or indirect evidence |
| Compound X | Proposed inhibition | Kinase C | Mark the relationship as hypothetical |
This table is a writing template, not a claim about an actual biological pathway.
3. Choose your starting point
AI-assisted editable graphs: enter your mechanism description in the AI workspace. Review and correct the extracted molecules and relationships, then open them as editable nodes and arrows. This analyzes text; it does not vectorize an existing image. The graph preview is free within its account and site limits and does not use image credits.
Editable examples: open the research example library, choose a starting diagram, rename labels, move nodes, and adjust the connections in the browser. Use the example to explain a question in your own model; do not copy its scope or implied claims into a different experiment.
AI image drafts: enter a mechanism description to request a generated image when generation is available on your account. The output is a raster image; its labels and molecules are not automatically converted into editable canvas objects.
4. Write a prompt that limits ambiguity
Specify the required labels, the direction of each interaction, the layout, and what must be excluded. Here is a reusable prompt structure with placeholders to replace using your sources:
Purpose: explain [one mechanism] in [organism / cell type]. Include exactly these labels: [list]. Relationships: [A activates B]; [C inhibits B]. Compartments: [extracellular / membrane / cytoplasm / nucleus]. Distinguish supported and hypothetical relationships in the legend. Layout: left to right, with minimal line crossings. Do not add molecules or connections that are not listed.
A precise prompt reduces ambiguity; it does not make generated content scientifically reliable by itself.
A practical handoff: your lab-meeting mechanism slide
Start with a slide that answers one question: “Which branch could explain the change in our measured readout?” Keep the measured readout, the intervention, and the proposed connecting steps separate in your notes. A lower signal in an assay does not by itself prove direct inhibition of its upstream protein.
- List the relationships supported by your references and mark the proposed step as “hypothesis” in the relationship label.
- Choose Editable diagram in the workspace and build the graph. In the review step, remove any molecule that was not in your notes and check the direction and type of every connection.
- Open the editor, shorten labels, arrange the branches, and include uncertainty in the labels. If a compartment is important, name it explicitly rather than relying on color alone.
- Save the editable JSON file before leaving. Export SVG for a collaborator who will edit the figure, or PNG for a slide. Keep the evidence table and original description with those files.
For a one-panel research summary, use the graphical abstract planning workflow. For costs and saving behavior, read the product facts and pricing.
5. Review the diagram at its final size
- Check spelling, symbols, isoforms, arrows, and cellular compartments.
- Use a legend to explain arrow conventions and abbreviations.
- Make labels readable at the width at which the figure will be shown.
- Ask a subject-matter colleague to check the mechanism, then keep the source notes alongside the exported file.
Continue with the export and publication review guide.