Commit
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a2ca5f6
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Parent(s):
e720905
fix: replace remaining bioRxiv refs with Europe PMC in docs
Browse filesFiles 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
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@@ -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", "
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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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### 2.4 DELETE: Tests for WebTool
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docs/implementation/10_phase_clinicaltrials.md
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@@ -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", "
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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
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docs/implementation/13_phase_modal_integration.md
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@@ -1133,7 +1133,7 @@ Phase 13 is **COMPLETE** when:
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βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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β Gradio App + MCP Server β
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β ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ β
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β β MCP Tools: search_pubmed, search_trials,
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β β search_all, analyze_hypothesis β β
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β ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ β
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βββββββββββββββββββββββββββββ¬ββββββββββββββββββββββββββββββββββββββ
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βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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β Gradio App + MCP Server β
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β ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ β
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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 ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ β
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βββββββββββββββββββββββββββββ¬ββββββββββββββββββββββββββββββββββββββ
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docs/implementation/14_phase_demo_submission.md
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@@ -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
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[Show search results streaming]
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## Features
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- **Multi-Source Search**: PubMed, ClinicalTrials.gov,
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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
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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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- `
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- `search_all` - Search all sources simultaneously
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## Team
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@@ -240,7 +240,7 @@ MODAL_TOKEN_SECRET=...
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𧬠Excited to submit DeepBoner to MCP's 1st Birthday Hackathon!
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An AI agent that:
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β
Searches PubMed, ClinicalTrials.gov &
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β
Exposes tools via MCP protocol
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β
Runs statistical code in Modal sandboxes
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β
Uses LlamaIndex for semantic search
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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 Europe PMC for the latest preprints"
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[Show search results streaming]
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## Features
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- **Multi-Source Search**: PubMed, ClinicalTrials.gov, Europe PMC (incl. preprints)
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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
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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_europepmc` - Search Europe PMC (preprints & papers)
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- `search_all` - Search all sources simultaneously
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## Team
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𧬠Excited to submit DeepBoner to MCP's 1st Birthday Hackathon!
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An AI agent that:
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+
β
Searches PubMed, ClinicalTrials.gov & Europe PMC
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β
Exposes tools via MCP protocol
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β
Runs statistical code in Modal sandboxes
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β
Uses LlamaIndex for semantic search
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