bioskills-index

name	bioskills-index
description	Permanent, updatable EDAM-annotated index of all bioskills available online. Provides semantic search, UMAP cluster visualization, and composition playlists for assembling bioskill workflows.
triggers	["find bioskills for [task]","what bioskills are available for [domain]","search bioskills index","compose a bioskill workflow for","update bioskills index","add a bioskill to the index","import EDAM","annotate skill with EDAM"]
prerequisites	["TypeDB running (make db-start)","VOYAGE_API_KEY set for search/embed commands (dash.voyageai.com)",{"EDAM imported":"run import-edam --namespace operation && import-edam --namespace topic"}]

Bioskills Index

Permanent, EDAM-annotated index of bioskills — SKILL.md-pattern skills, MCP servers, Nextflow workflows, Python API wrappers.

Quick Start

# Create an index
uv run python .claude/skills/bioskills-index/bioskills_index.py create-index \
    --name "Bio AI Skills v1"

# Import EDAM ontology (one-time setup)
uv run python .claude/skills/bioskills-index/bioskills_index.py import-edam \
    --namespace operation
uv run python .claude/skills/bioskills-index/bioskills_index.py import-edam \
    --namespace topic

# Seed from prior investigation
uv run python .claude/skills/bioskills-index/bioskills_index.py update \
    --index <id>

# Search
uv run python .claude/skills/bioskills-index/bioskills_index.py search \
    --index <id> --query "protein structure prediction"

# Compose a workflow
uv run python .claude/skills/bioskills-index/bioskills_index.py compose \
    --index <id> --task "analyze single-cell RNA from IPF lung samples"

Read USAGE.md before executing commands.