@bgicli/bgicli 2.1.0 → 2.2.0

package/data/skills/pyzotero/SKILL.md

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+---
+name: pyzotero
+description: Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
+allowed-tools: Read Write Edit Bash
+license: MIT License
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# Pyzotero
+
+Pyzotero is a Python wrapper for the [Zotero API v3](https://www.zotero.org/support/dev/web_api/v3/start). Use it to programmatically manage Zotero libraries: read items and collections, create and update references, upload attachments, manage tags, and export citations.
+
+## Authentication Setup
+
+**Required credentials** — get from https://www.zotero.org/settings/keys:
+- **User ID**: shown as "Your userID for use in API calls"
+- **API Key**: create at https://www.zotero.org/settings/keys/new
+- **Library ID**: for group libraries, the integer after `/groups/` in the group URL
+
+Store credentials in environment variables or a `.env` file:
+```
+ZOTERO_LIBRARY_ID=your_user_id
+ZOTERO_API_KEY=your_api_key
+ZOTERO_LIBRARY_TYPE=user  # or "group"
+```
+
+See [references/authentication.md](references/authentication.md) for full setup details.
+
+## Installation
+
+```bash
+uv add pyzotero
+# or with CLI support:
+uv add "pyzotero[cli]"
+```
+
+## Quick Start
+
+```python
+from pyzotero import Zotero
+
+zot = Zotero(library_id='123456', library_type='user', api_key='ABC1234XYZ')
+
+# Retrieve top-level items (returns 100 by default)
+items = zot.top(limit=10)
+for item in items:
+    print(item['data']['title'], item['data']['itemType'])
+
+# Search by keyword
+results = zot.items(q='machine learning', limit=20)
+
+# Retrieve all items (use everything() for complete results)
+all_items = zot.everything(zot.items())
+```
+
+## Core Concepts
+
+- A `Zotero` instance is bound to a single library (user or group). All methods operate on that library.
+- Item data lives in `item['data']`. Access fields like `item['data']['title']`, `item['data']['creators']`.
+- Pyzotero returns 100 items by default (API default is 25). Use `zot.everything(zot.items())` to get all items.
+- Write methods return `True` on success or raise a `ZoteroError`.
+
+## Reference Files
+
+| File | Contents |
+|------|----------|
+| [references/authentication.md](references/authentication.md) | Credentials, library types, local mode |
+| [references/read-api.md](references/read-api.md) | Retrieving items, collections, tags, groups |
+| [references/search-params.md](references/search-params.md) | Filtering, sorting, search parameters |
+| [references/write-api.md](references/write-api.md) | Creating, updating, deleting items |
+| [references/collections.md](references/collections.md) | Collection CRUD operations |
+| [references/tags.md](references/tags.md) | Tag retrieval and management |
+| [references/files-attachments.md](references/files-attachments.md) | File retrieval and attachment uploads |
+| [references/exports.md](references/exports.md) | BibTeX, CSL-JSON, bibliography export |
+| [references/pagination.md](references/pagination.md) | follow(), everything(), generators |
+| [references/full-text.md](references/full-text.md) | Full-text content indexing and retrieval |
+| [references/saved-searches.md](references/saved-searches.md) | Saved search management |
+| [references/cli.md](references/cli.md) | Command-line interface usage |
+| [references/error-handling.md](references/error-handling.md) | Errors and exception handling |
+
+## Common Patterns
+
+### Fetch and modify an item
+```python
+item = zot.item('ITEMKEY')
+item['data']['title'] = 'New Title'
+zot.update_item(item)
+```
+
+### Create an item from a template
+```python
+template = zot.item_template('journalArticle')
+template['title'] = 'My Paper'
+template['creators'][0] = {'creatorType': 'author', 'firstName': 'Jane', 'lastName': 'Doe'}
+zot.create_items([template])
+```
+
+### Export as BibTeX
+```python
+zot.add_parameters(format='bibtex')
+bibtex = zot.top(limit=50)
+# bibtex is a bibtexparser BibDatabase object
+print(bibtex.entries)
+```
+
+### Local mode (read-only, no API key needed)
+```python
+zot = Zotero(library_id='123456', library_type='user', local=True)
+items = zot.items()
+```

package/data/skills/radgpt-radiology-reporter/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: radgpt-radiology-reporter
+description: Radiology Reporter
+keywords:
+  - radiology
+  - report-generation
+  - patient-friendly
+  - summarization
+  - explanation
+measurable_outcome: Generate a patient-friendly explanation of a radiology report with <1% hallucination rate within 30 seconds.
+license: MIT
+metadata:
+  author: Stanford Medicine
+  version: "1.0.0"
+compatibility:
+  - system: Python 3.9+
+allowed-tools:
+  - run_shell_command
+  - read_file
+---
+
+# RadGPT (Radiology Report Assistant)
+
+An LLM-based agent designed to summarize and explain complex radiology reports for patients and clinicians.
+
+## When to Use
+
+*   **Patient Communication**: Converting technical findings into plain language.
+*   **Clinician Review**: Highlighting critical findings (e.g., "Pneumothorax detected").
+*   **Follow-up**: Suggesting appropriate next steps based on findings.
+
+## Core Capabilities
+
+1.  **Simplification**: Translates "bilateral opacity" to "cloudiness in both lungs".
+2.  **Entity Extraction**: Identifies key anatomical structures and pathologies.
+3.  **Q&A**: Answers follow-up questions about the report.
+
+## Workflow
+
+1.  **Input**: Raw text of the radiology report.
+2.  **Process**: LLM summarizes and identifies key findings.
+3.  **Output**: Structured summary or conversational explanation.
+
+## Example Usage
+
+**User**: "Explain this chest X-ray report to the patient."
+
+**Agent Action**:
+```bash
+python -m radgpt.explain --report ./report.txt --target_audience patient
+```
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/radiomics-pathomics-fusion-agent/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: 'radiomics-pathomics-fusion-agent'
+description: 'AI-powered multimodal fusion of radiology (CT/MRI/PET) and pathology (H&E/IHC) imaging with clinical and genomic data for comprehensive cancer diagnostics and treatment prediction.'
+measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
+allowed-tools:
+  - read_file
+  - run_shell_command
+---
+
+
+# Radiomics Pathomics Fusion Agent
+
+The **Radiomics Pathomics Fusion Agent** integrates multimodal medical imaging data from radiology (CT, MRI, PET) and digital pathology (H&E, IHC whole slide images) with clinical and genomic data using deep learning fusion architectures. It enables comprehensive cancer phenotyping, treatment response prediction, and prognostic modeling.
+
+## When to Use This Skill
+
+* When predicting treatment response using multimodal imaging.
+* For comprehensive tumor phenotyping combining macro and micro views.
+* To identify imaging biomarkers correlated with genomic features.
+* When building prognostic models from combined radiology-pathology.
+* For AI-powered second opinion integrating all imaging modalities.
+
+## Core Capabilities
+
+1. **Cross-Modal Fusion**: Integrate radiology and pathology features using attention.
+
+2. **Radiomics Extraction**: Compute 3D texture, shape, intensity features from CT/MRI.
+
+3. **Pathomics Extraction**: Extract histopathological features from WSI.
+
+4. **Clinical Integration**: Combine imaging with clinical variables and genomics.
+
+5. **Treatment Response Prediction**: Predict chemotherapy, immunotherapy response.
+
+6. **Survival Prediction**: Multi-modal prognostic modeling.
+
+## Supported Imaging Modalities
+
+| Modality | Features Extracted | Resolution |
+|----------|-------------------|------------|
+| CT | Texture, shape, density | Volumetric 3D |
+| MRI | Multi-sequence, perfusion | Volumetric 3D |
+| PET | SUV, metabolic features | Volumetric 3D |
+| H&E WSI | Nuclear, tissue architecture | 40x magnification |
+| IHC WSI | Marker quantification | 20-40x |
+| Multiplexed IF | Spatial protein patterns | Subcellular |
+
+## Fusion Architectures
+
+| Architecture | Method | Strengths |
+|--------------|--------|-----------|
+| Early Fusion | Concatenate features | Simple, baseline |
+| Late Fusion | Combine predictions | Modular |
+| Attention Fusion | Cross-modal attention | Interpretable |
+| Multimodal Transformer | Self-attention across modalities | State-of-art |
+| Graph Fusion | GNN for relationships | Spatial awareness |
+
+## Workflow
+
+1. **Input**: CT/MRI DICOM, pathology WSI, clinical data, optional genomics.
+
+2. **Segmentation**: Tumor ROI extraction from radiology.
+
+3. **Radiomics**: Extract 3D radiomic features.
+
+4. **Pathomics**: Extract histopathology features via foundation models.
+
+5. **Fusion**: Multimodal feature integration.
+
+6. **Prediction**: Treatment response, survival, biomarker prediction.
+
+7. **Output**: Integrated predictions, attention maps, explanations.
+
+## Example Usage
+
+**User**: "Predict immunotherapy response for this lung cancer patient using their CT scan and biopsy pathology."
+
+**Agent Action**:
+```bash
+python3 Skills/Oncology/Radiomics_Pathomics_Fusion_Agent/fusion_predict.py \
+    --ct_dicom ct_scan/ \
+    --wsi_path biopsy.svs \
+    --clinical_data patient_clinical.json \
+    --genomic_data tumor_wes.vcf \
+    --task immunotherapy_response \
+    --cancer_type nsclc \
+    --fusion_method attention \
+    --output fusion_prediction/
+```
+
+## Radiomic Feature Categories
+
+| Category | Features | Count |
+|----------|----------|-------|
+| Shape | Volume, surface area, sphericity | 14 |
+| First-Order | Mean, variance, skewness, entropy | 18 |
+| GLCM | Contrast, correlation, homogeneity | 24 |
+| GLRLM | Run length, gray level emphasis | 16 |
+| GLSZM | Zone size, gray level variance | 16 |
+| GLDM | Dependence features | 14 |
+| NGTDM | Texture features | 5 |
+| **Total** | | **~107** |
+
+## Pathomics Feature Categories
+
+| Category | Source | Features |
+|----------|--------|----------|
+| Nuclear | Segmentation | Size, shape, texture |
+| Cellular | Detection | Density, clustering |
+| Tissue | Architecture | Glandular, stromal ratios |
+| Foundation Model | CONCH, TITAN, UNI | Deep embeddings |
+| Spatial | Graph analysis | Neighborhood patterns |
+
+## Output Components
+
+| Output | Description | Format |
+|--------|-------------|--------|
+| Prediction | Response/outcome probability | .json |
+| Confidence | Prediction uncertainty | .json |
+| Attention Maps | Cross-modal importance | .npy, .png |
+| Feature Importance | Shapley values | .csv |
+| ROI Highlights | Predictive regions | DICOM-SEG, GeoJSON |
+| Report | Clinical summary | .pdf |
+
+## Clinical Applications
+
+| Application | Modalities Used | Performance |
+|-------------|-----------------|-------------|
+| NSCLC Immunotherapy | CT + H&E | AUC 0.82-0.88 |
+| HCC Survival | MRI + H&E | C-index 0.78 |
+| Breast Neoadjuvant | MRI + H&E | AUC 0.85 |
+| HNSCC HPV/Response | CT + H&E | AUC 0.89 |
+| CRC MSI Prediction | CT + H&E | AUC 0.86 |
+
+## AI/ML Components
+
+**Radiomics Pipeline**:
+- PyRadiomics for feature extraction
+- 3D-CNN for learned features
+- Transformer for volumetric analysis
+
+**Pathomics Pipeline**:
+- Foundation models (CONCH, UNI, TITAN)
+- MIL (Multiple Instance Learning) for WSI
+- Graph networks for spatial patterns
+
+**Fusion Models**:
+- Cross-attention transformers
+- Multimodal variational autoencoders
+- Contrastive learning for alignment
+
+## Prerequisites
+
+* Python 3.10+
+* PyRadiomics, SimpleITK
+* OpenSlide, HistoEncoder
+* PyTorch, transformers
+* CONCH/TITAN model weights
+* GPU with 16GB+ VRAM
+
+## Related Skills
+
+* Pathology_AI/CONCH_Agent - Pathology foundation model
+* Radiology_AI agents - Modality-specific analysis
+* Pan_Cancer_MultiOmics_Agent - Genomic integration
+* TMB_Estimation_Agent - Tumor mutational burden
+
+## Multimodal Integration Strategies
+
+| Strategy | Description | Use Case |
+|----------|-------------|----------|
+| Feature-Level | Combine extracted features | Limited data |
+| Embedding-Level | Fuse latent representations | Moderate data |
+| Decision-Level | Ensemble predictions | Interpretability |
+| End-to-End | Joint training | Large data |
+
+## Special Considerations
+
+1. **Data Alignment**: Ensure imaging from same timepoint
+2. **Missing Modalities**: Handle incomplete multimodal data
+3. **Class Imbalance**: Balance training across outcomes
+4. **Interpretability**: Attention maps for clinical trust
+5. **Validation**: External multi-site validation essential
+
+## Quality Control
+
+| QC Check | Threshold | Action |
+|----------|-----------|--------|
+| CT coverage | >90% tumor | Rescan if needed |
+| WSI quality | Blur score <X | Re-scan slide |
+| Segmentation | Dice >0.85 | Manual review |
+| Feature stability | ICC >0.8 | Robust features only |
+
+## Regulatory Considerations
+
+| Aspect | Status |
+|--------|--------|
+| FDA Clearance | Individual modality tools cleared |
+| Multimodal Fusion | Research use only (RUO) |
+| Clinical Integration | PACS/LIS integration pathways |
+| Explainability | Required for clinical adoption |
+
+## Author
+
+AI Group - Biomedical AI Platform
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->