Added phoenix guidelines to the gitbook#34
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Pull Request Overview
This PR introduces comprehensive documentation for interacting effectively with Phoenix, a chemistry-focused discovery agent. The guidelines help users formulate queries that leverage Phoenix's computational capabilities for molecular analysis, synthesis planning, and property prediction.
- Adds 8 best practice guidelines covering molecular inputs, output specifications, chemical terminology, query structure, and iteration strategies
- Provides a comparison table with 10 examples showing how to improve vague queries into specific, actionable ones
- Includes technical details on Phoenix's toolset capabilities (ADMET properties, synthesis routes, safety assessments, database searches)
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| ## 6. Request specific properties or analyses. | ||
| Instead of asking vaguely about a molecule, specify what you need. For example, request specific ADMET properties, synthetic accessibility scores, solubility predictions, or toxicity data. This allows Phoenix to use the most appropriate computational tools and provide quantitative, actionable results. |
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I understand the point of including this, but it seems redundant - all of htis is listed above. maybe put those as bullets on this one or remove this
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| ## 8. Iterate. |
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I get it...but I kinda hate it because we charge them per query. idk
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
Co-authored-by: Sam Cox <swrig30@ur.rochester.edu>
SamWright822
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keekz23
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| When asking about molecules, provide SMILES strings, CAS numbers, IUPAC names, or molecular formulas explicitly. Phoenix can work with multiple representation types, but being explicit helps ensure accurate results. A chemist familiar with your field should be able to unambiguously identify the molecule(s) you're asking about. | ||
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| ## 2. Specify desired outputs clearly. | ||
| Clearly state what you need from Phoenix. It can be a synthesis route, molecular property prediction, safety assessment, literature-backed answer, or a combination of these. The more specific you are about the outputs you need, the better Phoenix can select appropriate tools and provide actionable results. |
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Would it be helpful to include an example of a bad prompt vs. a good prompt? Just so people can get a feel for what you mean by "more specific" in this context.
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I see that you have a list of examples below in ## 7. I'm suggesting that each Best Practice bullet point should have a specific example of bad query vs. good query that connects to the Best Practice description.
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Yeah, I agree on that. I was just unsure if adding multiple tables would make the text harder to read. Let me add them so we see how it feels like
keekz23
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Nov 13, 2025
| | What's the latest on green chemistry? | Using literature search, find recent advances in green chemistry methods for esterification reactions. Focus on catalysts and reaction conditions that minimize environmental impact. | | ||
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| ## 8. Iterate. | ||
| Take some time to write your first Phoenix query so you can avoid the common pitfalls listed above. However, trial and error will be your best guide to develop a deep intuition on how to best use the system. Start with familiar molecules or reactions. While Phoenix can handle complex multi-step workflows, begin with simpler queries for faster results. Quicker iteration will help you learn how to use Phoenix more effectively and get the most out of the system. |
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Saying "While Phoenix can handle complex multi-step workflows, ..." again makes me think it's actually not good at handling multi-step workflows. Maybe just remove this line and have "Begin with simpler queries for faster results."
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* added phoenix guidelines * Fixed typos * Rewording some odd sentences * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Addressed PR comments Co-authored-by: Kiki <kiki@edisonscientific.com> --------- Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> Co-authored-by: Kiki <kiki@edisonscientific.com>
maykcaldas
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* added phoenix guidelines * Fixed typos * Rewording some odd sentences * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Update docs/phoenix_guidelines.md Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> * Addressed PR comments Co-authored-by: keekz23 <keekz23@users.noreply.github.com> --------- Co-authored-by: Sam Cox <swrig30@ur.rochester.edu> Co-authored-by: keekz23 <keekz23@users.noreply.github.com>
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