Obsidian Vault Template

A Copier template for scaffolding a structured Obsidian knowledge vault with a pre-built domain model for life sciences and operational workflows.

What's included

Scientific entities

• Genes — Ensembl ID, species, chromosome, transcripts, pathways, diseases
• Transcripts — Ensembl transcript ID, gene, proteins, tissues, canonical flag
• Proteins — UniProt ID, gene, transcripts, species, domains, pathways, diseases
• Enzymes — EC number, gene, transcripts, substrates, products, cofactors, inhibitors
• Pathways — KEGG ID, Reactome ID, genes, proteins, enzymes, diseases, drugs
• Diseases — OMIM ID, ICD code, genes, proteins, pathways, drugs
• Drugs — DrugBank ID, ChEMBL ID, SMILES, targets, indications, approval status
• Experimental Models — unified view across:
  • Model Organisms — taxonomy ID, common/scientific name, genes, diseases
  • Cell Lines — Cellosaurus ID, species, tissue, disease, culture type

Operational entities

• Meetings — date, attendees, type, org
• Jira Tickets — URL, project, status, assignee, priority, sprint
• Teams — lead, members, domain, purpose
• Roles — responsibilities, accountabilities, domain
• Workflows — domains, tools, owners, users
• Tools / Software / Equipment / Repositories — unified view with type-based filtering
• Projects — type, year, status, URL
• People — birthday, org, meetings backlink
• Companies — URL, people

Plugins included

• DB Folder — powers the .base database views
• Excalidraw — sketching and diagrams
• Git — version control from within Obsidian

Prerequisites

• Git
• Copier — install with pip install copier or uv tool install copier

Quick start

copier copy https://github.com/<your-org>/<this-repo>.git ~/my-vault

Then open ~/my-vault in Obsidian. See README.md inside the vault for full setup instructions.

Updating your vault

When new entity types or domain changes are released:

cd ~/my-vault
git status  # must be clean before updating
copier update
git add . && git commit -m "Update domain model to vX.Y.Z"

Contributing

See CONTRIBUTING.md.