Send gene lists to over-representation, not ReactomeGSA

src/evaluation/answer_sweep.py

@@ -74,10 +74,20 @@ class Expectation:
         question="I have a gene list do you have a tool I can use to analyse where in "
         "reactome those genes are involved",
         why="Answered 'Reactome does not provide a specific tool' -- false, and about "
-        "its flagship feature.",
-        must=("ReactomeGSA",),
+        "its flagship feature. Then, until 2026-09-29, this expected ReactomeGSA: the "
+        "wrong tool for a list, which needs no measurements. A gene list is an "
+        "over-representation analysis; this gate was requiring the wrong answer.",
+        must_match=(r"over-?represent|analy[sz]e\s+data",),
         must_not=("does not provide", "not currently available"),
     ),
+    Expectation(
+        question="here is my gene list TP53, ERBB3 and JAX9. how can I analyse it?",
+        why="Reported 2026-09-29: told to paste the list into ReactomeGSA at "
+        "reactome.org/gsa -- a URL the user guide does not contain, for a tool that "
+        "needs a matrix.",
+        must_match=(r"over-?represent|analy[sz]e\s+data",),
+        must_not=("reactome.org/gsa",),
+    ),
     # --- gene set analysis should prefer the tool needing no install --------
     Expectation(
         question="How do I run a GSEA in Reactome?",

src/retrievers/userguide/prompt.py

@@ -16,7 +16,8 @@
    - If multiple excerpts support the same fact, cite them together (space-separated).
 3. How-to focus: Give clear, actionable steps when the user asks how to perform a task. Name UI elements accurately (buttons, panels, tabs) as they appear in the context.
    - When several Reactome tools can do the same job, **lead with the one that needs the least setup** — a web tool on reactome.org before a desktop application, a plugin, or an R package. Mention the others afterwards as alternatives.
-   - Concretely: gene set analysis is **ReactomeGSA** (web, at reactome.org/gsa, nothing to install). ReactomeFIViz also performs GSEA, but it is a Cytoscape plugin and requires installing Cytoscape first, so it is the alternative rather than the answer.
+   - Concretely: gene set analysis on expression data is **ReactomeGSA** (web, at reactome.org/gsa, nothing to install). ReactomeFIViz also performs GSEA, but it is a Cytoscape plugin and requires installing Cytoscape first, so it is the alternative rather than the answer.
+   - A **list of genes or identifiers** — names only, no measurements for each sample — is not that: it is an **over-representation analysis**, run with *Analyze Data* in the Pathway Browser by pasting the list. Never send a gene list to ReactomeGSA.
    - Do not pick a tool because its page happens to contain the most step-by-step text. The most detailed instructions are often for the most involved tool, which is rarely what someone asking "can you run this for me" wants.
 4. Tone and style:
    - Write in a clear, friendly, and conversational tone.