Prefer the Reactome tool that needs no installation

[adamjohnwright]

Asked "can you run gsea for me", beta answered with ReactomeFIViz — the Cytoscape plugin — and gave steps for installing Cytoscape. ReactomeGSA is a web tool at reactome.org/gsa that needs nothing installed, and is what someone asking that question wants.

Not a retrieval failure

The top four passages were the ReactomeGSA page:

1. [analysis/gsa]  2. [analysis/gsa]  3. [analysis/gsa]
4. [analysis/gsa]  5. [reactome-fiviz]

The FIViz page arrives fifth because the rephrase expands "gsea" into "Gene Set Enrichment Analysis (GSEA)", and that page carries a "Perform GSEA Analysis" menu item.

The model then led with it — because the prompt asks for "clear, actionable steps" and FIViz has by far the most step-by-step text.

The general trap, now named in the prompt

The most detailed instructions are usually for the most involved tool, which is rarely what someone asking "can you run this for me" wants.

Where several Reactome tools do the same job: lead with the one needing least setup — web before desktop application, plugin, or R package — and offer the rest as alternatives.

Verified both ways

Leads with ReactomeGSA now:

Q: Can you perform Gene Set Enrichment Analysis (GSEA) for me?
   You can perform GSEA using ReactomeGSA, which is a web-based tool that
   requires no installation...

Q: How do I run a GSEA in Reactome?
   To run a GSEA in Reactome using ReactomeGSA... click "Analyse gene expression"

And FIViz isn't buried — asked for by name, or asked about Cytoscape, it still answers with FIViz and its install steps:

ok [asks for FIViz by name] To use ReactomeFIViz in Cytoscape... 1. Install Cytoscape
ok [asks about Cytoscape]   With the ReactomeFIViz Cytoscape plugin, you can...
ok [unrelated how-to]       To use the Pathway Browser in Reactome...

One test pins the prompt wording, including the named trap, so a later edit can't quietly reintroduce it.

🤖 Generated with Claude Code

[adamjohnwright]

Checked for over-correction

The risk with this change is that it trades one wrong answer for another: pushing ReactomeGSA at someone who genuinely wants the Cytoscape plugin. I ran six questions against the branch — three where the least-setup rule should lead with ReactomeGSA, three where ReactomeFIViz is the honest answer.

question	leads with
Can you run GSEA for me?	ReactomeGSA
How do I do gene set enrichment analysis with Reactome?	ReactomeGSA
What is the easiest way to run pathway enrichment on my expression data?	ReactomeGSA
How do I use ReactomeFIViz?	ReactomeFIViz (install Cytoscape 3.7.0+, then the app)
I already have Cytoscape installed. How do I explore the FI network in it?	ReactomeFIViz (Apps > Reactome FI)
How do I build a functional interaction network from a gene list and cluster it?	ReactomeFIViz (Gene Set/Mutation Analysis)

6/6. The three FIViz questions are answered with FIViz and are not deflected to the web tool — the rule is scoped to "when several tools can do the same job" and stays out of the way when they cannot.

That direction is guarded permanently by the expectation in #223: "Preferring the web tool must not bury the plugin for someone who wants it."

🤖 Generated with Claude Code