claw-semantic-sim
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
npx skills add BioTender-max/awesome-bio-agent-skills --skill claw-semantic-sim --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🦖 Semantic Similarity Index Measure how isolated or connected disease research is across the global biomedical literature, using PubMedBERT embeddings on PubMed abstracts spanning 175 GBD diseases. ## What it does 1. Takes a disease list (GBD taxonomy) as input 2. Retrieves PubMed abstracts (2000-2025) for each disease with quality filtering 3. Generates 768-dimensional PubMedBERT embeddings for every abstract 4. Computes four semantic equity metrics per disease: - **Semantic Isolation Index (SII)**: average cosine distance to k-nearest disease neighbours; higher = more isolated, less connected research - **Knowledge Transfer Potential (KTP)**: cross-disease centroid similarity; higher = more potential for research spillover - **Research Clustering Coefficient (RCC)**: within-disease embedding variance; higher = more diverse research approaches - **Temporal Semantic Drift**: cosine distance between yearly centroids; measures how research focus evolves 5. Generates publication-quality multi-panel figures: - **Panel A**: Semantic isolation by disease category (boxplot) - **Panel B**: Top 20 most semantically isolated diseases (bar chart, NTD/Global South colour-coded) - **Panel C*
- What it does
- Why this exists
- Key Finding
- Pipeline
- Demo (works out of the box)
- Example Output
- Interpretation Guide
- Citation
python semantic_sim.py --demo --output demo_report
What does the claw-semantic-sim skill do?
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill claw-semantic-sim --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.