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
Editable templates: open the template library, choose a starting diagram, rename labels, move nodes, and adjust activation or inhibition connections in the browser. The canvas contains discrete objects that can be edited.
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.
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.