[BUG] False Positive: Legitimate bioinformatics project blocked - agr_automated_information_extraction

Description

Claude Code is incorrectly blocking access to a legitimate scientific research project with the error:
API Error: Claude Code is unable to respond to this request, which appears to violate our Usage Policy (https://www.anthropic.com/legal/aup). Please double press esc to edit
your last message or start a new session for Claude Code to assist with a different task.

Project Context

• Project Name: agr_automated_information_extraction
• Organization: Alliance of Genome Resources (AGR) - https://www.alliancegenome.org
• Purpose: This is a bioinformatics tool that processes scientific literature metadata from PubMed and Model Organism Databases (MODs) for genomics research
• Repository Type: Academic/scientific software for public research

Why This is a False Positive

1. "Automated Information Extraction" in this context refers to:

• Parsing structured metadata from scientific publications (titles, authors, abstracts)
• Extracting gene/protein mentions from research papers
• Processing PubMed XML files and DOI metadata
• All data sources are public academic databases

1. Legitimate Scientific Use:

• Part of the AGR suite of tools used by researchers worldwide
• Processes only publicly available scientific literature
• Similar to tools like PubMed's E-utilities or Europe PMC's text mining services
• Used by academic institutions for genomics research

1. Not Related to Prohibited Activities:

• Does NOT scrape personal data
• Does NOT bypass authentication or security measures
• Does NOT extract credentials or private information
• Only processes academic publications with proper attribution

Impact

This false positive prevents development of important scientific software that helps researchers:

• Track publications related to specific genes/proteins
• Build knowledge graphs for biomedical research
• Support curation of genomics databases
• Advance understanding of disease mechanisms

Reproduction Steps

1. Navigate to a project directory named agr_automated_information_extraction
2. Attempt to use Claude Code for any operation
3. Receive the usage policy violation error

Suggested Resolution

• Whitelist academic/scientific terminology like "automated information extraction" when used in bioinformatics contexts
• Consider the full path/context (e.g., presence of "agr", "literature", "pubmed" indicates scientific use)
• Allow users to flag false positives directly in the interface

Additional Context

This project works alongside agr_literature_service (which Claude Code can access without issues) as part of a larger scientific data pipeline. Both repositories are part of
the same legitimate research infrastructure.

Environment

• Platform: Linux
• Claude Code version: v1.0.102
• Working directory contains standard Python scientific libraries (pandas, scikit-learn, spacy) for NLP on scientific text