Improve response precision by refining system prompts for Reactome and UniProt retrievers

src/retrievers/reactome/prompt.py

@@ -11,16 +11,18 @@
 ## **Answering Guidelines**
 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.  
+   - Prefer retrieved pathway data over general biological background knowledge.
    - 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.
 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.
-4. Tone & Style:
+3. Where applicable, reference specific Reactome stable identifiers (e.g., R-HSA-109581) from the retrieved context.
+4. Comprehensiveness: Capture all mechanistically relevant details available in Reactome, focusing on processes, complexes, regulations, and interactions.
+5. Tone & Style:
     - Write in a clear, engaging, and conversational tone.
     - Use accessible language while maintaining technical precision.
     - Ensure the narrative flows logically, presenting background, mechanisms, and significance
-5. Source list at the end: After the main narrative, provide a bullet-point list of each unique citation anchor exactly once, in the same <a href="URL">Node Name</a> format.
+6. Source list at the end: After the main narrative, provide a bullet-point list of each unique citation anchor exactly once, in the same <a href="URL">Node Name</a> format.
     - Examples:
         - <a href="https://reactome.org/content/detail/R-HSA-109581">Apoptosis</a>
         - <a href="https://reactome.org/content/detail/R-HSA-1640170">Cell Cycle</a>

src/retrievers/uniprot/prompt.py

@@ -8,11 +8,13 @@
 
 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.
+   - Prefer retrieved UniProt entry data over general biological background knowledge.
 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.
 3. Answer the question comprehensively and accurately, providing useful background information based **only** on the context.
+   - Where applicable, reference specific UniProt accession identifiers (e.g., Q92908) from the retrieved 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 asnwer according to the following:
-     - For Reactome always format citations in the following format: <a href="citation">*short_protein_name*</a>.
+     - For Uniprot always format citations in the following format: <a href="citation">*short_protein_name*</a>.
             Examples:
                 -  <a href="https://www.uniprot.org/uniprotkb/Q92908">GATA6</a>
                 -  <a href="https://www.uniprot.org/uniprotkb/O00482">NR5A2</a>