VibecoderMcSwaggins commited on
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fix: replace remaining bioRxiv refs with Europe PMC in docs

Browse files

Files updated:
- 09_phase_source_cleanup.md: Literal type in preview code
- 10_phase_clinicaltrials.md: Literal type in preview code
- 13_phase_modal_integration.md: MCP tools diagram
- 14_phase_demo_submission.md: Demo script, HF README template, social media

These are documentation files showing what the tool does.
The actual implementation uses Europe PMC (not bioRxiv).

docs/implementation/09_phase_source_cleanup.md CHANGED
@@ -62,7 +62,7 @@ sources_searched: list[Literal["pubmed", "web"]]
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  sources_searched: list[Literal["pubmed"]]
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  # AFTER (Phase 10-11)
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- sources_searched: list[Literal["pubmed", "clinicaltrials", "biorxiv"]]
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  ```
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  ### 2.4 DELETE: Tests for WebTool
 
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  sources_searched: list[Literal["pubmed"]]
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  # AFTER (Phase 10-11)
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+ sources_searched: list[Literal["pubmed", "clinicaltrials", "europepmc"]]
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  ```
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68
  ### 2.4 DELETE: Tests for WebTool
docs/implementation/10_phase_clinicaltrials.md CHANGED
@@ -90,7 +90,7 @@ InterventionName, StartDate, CompletionDate, BriefSummary
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  source: Literal["pubmed", "web"]
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  # AFTER
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- source: Literal["pubmed", "clinicaltrials", "biorxiv"]
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  ```
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  ### 3.2 Evidence from Clinical Trials
 
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  source: Literal["pubmed", "web"]
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  # AFTER
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+ source: Literal["pubmed", "clinicaltrials", "europepmc"]
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  ```
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  ### 3.2 Evidence from Clinical Trials
docs/implementation/13_phase_modal_integration.md CHANGED
@@ -1133,7 +1133,7 @@ Phase 13 is **COMPLETE** when:
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  β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
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  β”‚ Gradio App + MCP Server β”‚
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  β”‚ β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β” β”‚
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- β”‚ β”‚ MCP Tools: search_pubmed, search_trials, search_biorxiv β”‚ β”‚
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  β”‚ β”‚ search_all, analyze_hypothesis β”‚ β”‚
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  β”‚ β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜ β”‚
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  β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”¬β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
 
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  β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”
1134
  β”‚ Gradio App + MCP Server β”‚
1135
  β”‚ β”Œβ”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β” β”‚
1136
+ β”‚ β”‚ MCP Tools: search_pubmed, search_trials, search_europepmc β”‚ β”‚
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  β”‚ β”‚ search_all, analyze_hypothesis β”‚ β”‚
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  β”‚ β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜ β”‚
1139
  β””β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”¬β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”€β”˜
docs/implementation/14_phase_demo_submission.md CHANGED
@@ -86,7 +86,7 @@ to find new uses for existing drugs."
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  "When I ask about metformin for Alzheimer's, DeepBoner:
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  1. Searches PubMed for peer-reviewed papers
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  2. Queries ClinicalTrials.gov for active trials
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- 3. Scans bioRxiv for the latest preprints"
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  [Show search results streaming]
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@@ -189,7 +189,7 @@ AI-Powered Drug Repurposing Research Agent
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190
  ## Features
191
 
192
- - **Multi-Source Search**: PubMed, ClinicalTrials.gov, bioRxiv/medRxiv
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  - **MCP Integration**: Use our tools from Claude Desktop or any MCP client
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  - **Modal Sandbox**: Secure execution of AI-generated statistical code
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  - **LlamaIndex RAG**: Semantic search and evidence synthesis
@@ -204,7 +204,7 @@ https://your-space.hf.space/gradio_api/mcp/
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  Available tools:
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  - `search_pubmed` - Search peer-reviewed biomedical literature
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  - `search_clinical_trials` - Search ClinicalTrials.gov
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- - `search_biorxiv` - Search bioRxiv/medRxiv preprints
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  - `search_all` - Search all sources simultaneously
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  ## Team
@@ -240,7 +240,7 @@ MODAL_TOKEN_SECRET=...
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  🧬 Excited to submit DeepBoner to MCP's 1st Birthday Hackathon!
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  An AI agent that:
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- βœ… Searches PubMed, ClinicalTrials.gov & bioRxiv
244
  βœ… Exposes tools via MCP protocol
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  βœ… Runs statistical code in Modal sandboxes
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  βœ… Uses LlamaIndex for semantic search
 
86
  "When I ask about metformin for Alzheimer's, DeepBoner:
87
  1. Searches PubMed for peer-reviewed papers
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  2. Queries ClinicalTrials.gov for active trials
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+ 3. Scans Europe PMC for the latest preprints"
90
 
91
  [Show search results streaming]
92
 
 
189
 
190
  ## Features
191
 
192
+ - **Multi-Source Search**: PubMed, ClinicalTrials.gov, Europe PMC (incl. preprints)
193
  - **MCP Integration**: Use our tools from Claude Desktop or any MCP client
194
  - **Modal Sandbox**: Secure execution of AI-generated statistical code
195
  - **LlamaIndex RAG**: Semantic search and evidence synthesis
 
204
  Available tools:
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  - `search_pubmed` - Search peer-reviewed biomedical literature
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  - `search_clinical_trials` - Search ClinicalTrials.gov
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+ - `search_europepmc` - Search Europe PMC (preprints & papers)
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  - `search_all` - Search all sources simultaneously
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210
  ## Team
 
240
  🧬 Excited to submit DeepBoner to MCP's 1st Birthday Hackathon!
241
 
242
  An AI agent that:
243
+ βœ… Searches PubMed, ClinicalTrials.gov & Europe PMC
244
  βœ… Exposes tools via MCP protocol
245
  βœ… Runs statistical code in Modal sandboxes
246
  βœ… Uses LlamaIndex for semantic search