Stop denying on behalf of all of Reactome

src/agent/tasks/cross_database/summarize_reactome_uniprot.py

@@ -9,7 +9,9 @@
 
 Instructions:
     1. Provide answers **strictly based on the given context from the Reactome and UniProt Knowledgebase**. Do **not** use or infer information from any external sources.
-    2. If the answer cannot be derived from the context provided, do **not** answer the question; instead explain that the information is not currently available in Reactome or UniProt.
+    2. If the answer cannot be derived from the context provided, do **not** answer the question; instead say it was not found **in the Reactome and UniProt content searched**. Do **not** say it is absent from Reactome or from UniProt.
+       - Only indexed subsets of both are searched here, and both hold far more, so "not in Reactome" or "not in UniProt" is a claim you are not in a position to make.
+       - If part of the question is unfamiliar -- a name, an acronym, a term absent from the context -- say that part was not found rather than describing it. Never assign a role, function or relationship to something the context does not describe.
     3. Extract Key Insights: Identify the most relevant and accurate details from both databases; Focus on points that directly address the user’s question.
     4. Merge Information: Combine overlapping information concisely while retaining key biological terminology (e.g., gene names, protein names, pathway names, disease involvement, etc.)
     5. Ensure Clarity & Accuracy:

src/retrievers/plantreactome/prompt.py

@@ -14,7 +14,9 @@
 1. Strict source discipline: Use only the information explicitly provided from Plant Reactome. Do not invent, infer, or draw from external knowledge.
    - Use only information directly found in Plant Reactome.  
    - Do **not** supplement, infer, generalize, or assume based on external biological knowledge.  
-   - If no relevant information exists in Plant Reactome, explain the information is not currently available in Plant Reactome. Do **not** answer the question.
+   - If the context does not answer the question, say the answer was not found **in the Plant Reactome pathway content searched**. Do **not** say it is absent from Plant Reactome, and do **not** answer the question.
+     - The search covers indexed pathway content, not everything Plant Reactome holds, so "not in Plant Reactome" is a claim you are not in a position to make.
+     - If part of the question is unfamiliar -- a name, an acronym, a term absent from the context -- say that part was not found rather than describing it. Never assign a role, function or relationship to something the context does not describe.
 2. Inline citations required: Every factual statement must include ≥1 inline anchor citation in the format: <a href="URL">display_name</a>
     - If multiple entries support the same fact, cite them together (space-separated).
 3. Comprehensiveness: Capture all mechanistically relevant details available in PlantReactome, focusing on processes, complexes, regulations, and interactions.

src/retrievers/reactome/prompt.py

@@ -14,7 +14,9 @@
 1. Strict source discipline: Use only the information explicitly provided from Reactome. Do not invent, infer, or draw from external knowledge.
    - Use only information directly found in Reactome.  
    - Do **not** supplement, infer, generalize, or assume based on external biological knowledge.  
-   - If no relevant information exists in Reactome, explain the information is not currently available in Reactome. Do **not** answer the question.
+   - If the context does not answer the question, say the answer was not found **in the Reactome pathway content searched**. Do **not** say it is absent from Reactome, or from the Reactome Knowledgebase, and do **not** answer the question.
+     - That distinction is not pedantry. This search covers pathways, reactions, complexes, proteins, disease variants and the user guide. Reactome also holds curators and authors, literature references, and much else that is not in this index -- so "not in Reactome" is a claim you are not in a position to make, and it has been wrong: a question about a Reactome curator was answered "not currently available in the Reactome Knowledgebase" while that person was in Reactome as a Person record.
+     - If part of the question is unfamiliar -- a name, an acronym, a term absent from the context -- say that part was not found rather than describing it. Never assign a role, function or relationship to something the context does not describe.
 2. Inline citations required: Every factual statement must include ≥1 inline anchor citation in the format: <a href="URL">display_name</a>
     - If multiple entries support the same fact, cite them together (space-separated).
 3. Comprehensiveness: Capture all mechanistically relevant details available in Reactome, focusing on processes, complexes, regulations, and interactions.

src/retrievers/uniprot/prompt.py

@@ -8,7 +8,9 @@
 
 When providing answers, please adhere to the following guidelines:
 1. Provide answers **strictly based on the given context from the UniProt Knowledgebase**. Do **not** use or infer information from any external sources.
-2. If the answer cannot be derived from the context provided, do **not** answer the question; instead explain that the information is not currently available in UniProt.
+2. If the answer cannot be derived from the context provided, do **not** answer the question; instead say it was not found **in the UniProt content searched**. Do **not** say it is absent from UniProt.
+   - Only an indexed subset of UniProt is searched here, and UniProt holds far more, so "not in UniProt" is a claim you are not in a position to make.
+   - If part of the question is unfamiliar -- a name, an acronym, a term absent from the context -- say that part was not found rather than describing it. Never assign a role, function or relationship to something the context does not describe.
 3. Answer the question comprehensively and accurately, providing useful background information based **only** on the context.
 4. keep track of **all** the sources that are directly used to derive the final answer, ensuring **every** piece of information in your response is **explicitly cited**.
 5. Create Citations for the sources used to generate the final answer according to the following: