Obsidian Integration

MOSAIC can write paper notes directly into an Obsidian vault. Each paper becomes one .md file with:

• YAML frontmatter — Obsidian Properties (title, authors, year, DOI, …)
• Abstract callout — > [!abstract] block
• Metadata table — human-readable field/value pairs
• See also — [[wikilinks]] to other papers exported in the same batch

Notes already present in the vault are never overwritten, preserving any manual edits.

Setup

Add the vault path to your config file:

# ~/.config/mosaic/config.toml
[obsidian]
vault_path = "/path/to/your/vault"   # required
subfolder  = "papers"                # optional, default: "papers"

Or use the full reference below to customise every option.

Usage

Add --obsidian to any search, similar, or get command:

# Export search results as Obsidian notes
mosaic search "transformer attention" --obsidian

# Export and also download PDFs
mosaic search "BERT NLP" --obsidian --download

# Find similar papers and export them
mosaic similar 10.48550/arxiv.1706.03762 --obsidian

# Download a paper by DOI and create a note
mosaic get 10.1234/example --obsidian

# Write notes to a different subfolder this run
mosaic search "diffusion models" --obsidian --obsidian-folder "AI/diffusion"

Note format

A generated note looks like this:

---
title: Attention Is All You Need
authors:
  - Ashish Vaswani
  - Noam Shazeer
year: 2017
doi: 10.48550/arxiv.1706.03762
arxiv_id: 1706.03762
journal: NeurIPS
source: arXiv
open_access: true
citation_count: 50000
pdf_url: https://arxiv.org/pdf/1706.03762
tags:
  - paper
---

# Attention Is All You Need

> [!abstract]
> We propose a new simple network architecture, the Transformer, …

## Metadata

| Field | Value |
|-------|-------|
| Authors | Ashish Vaswani, Noam Shazeer |
| Year | 2017 |
| DOI | 10.48550/arxiv.1706.03762 |
| Source | arXiv |
| Open Access | yes |
| Citations | 50000 |
| URL | [link](https://arxiv.org/abs/1706.03762) |
| PDF | [link](https://arxiv.org/pdf/1706.03762) |

## See also

- [[2019_Devlin_BERT pre-training of deep bidirectional transformers]]
- [[2020_Brown_Language models are few-shot learners]]

Plugin compatibility

Plugin	Compatible	Notes
Obsidian Properties (core)	✅	YAML frontmatter is standard Obsidian property format
Dataview (community)	✅	Query by year, doi, source, citation_count, etc.
Templates (core)	✅	Notes contain no {{…}} syntax — not processed as templates
Templater (community)	✅	Notes contain no <%…%> syntax — not processed as templates

Configuration reference

[obsidian]
# Absolute path to the Obsidian vault root directory (required)
vault_path = "/home/you/my-vault"

# Subfolder within the vault where paper notes are written
# Use "" to write notes directly to the vault root
subfolder = "papers"

# Filename pattern — same placeholders as the PDF filename pattern:
#   {year}    publication year (0000 if unknown)
#   {author}  first author last name
#   {title}   title slug, truncated to 60 chars
#   {source}  source name (arXiv, Scopus, …)
#   {doi}     DOI with special chars replaced by _
#   {journal} journal name slug (no_journal if unknown)
filename_pattern = "{year}_{author}_{title}"

# Tags added to every note's frontmatter
tags = ["paper"]

# When true, a "See also" section with [[wikilinks]] is added to each note,
# linking to the other papers exported in the same command invocation
wikilinks = true

Deduplication

Notes are never overwritten. If a note file for a paper already exists (matched by filename), it is silently skipped. This means any annotations, links, or edits you have added to the note are preserved across future exports.

The export_papers call returns (added, skipped) counts, which MOSAIC prints after each run:

Obsidian: 8 note(s) added, 2 skipped (already exist) → /home/you/my-vault/papers

Wikilinks

When wikilinks = true (the default), each exported note gets a See also section listing [[wikilinks]] to the other papers exported in the same command invocation. Links are not added across separate runs — MOSAIC does not scan the whole vault.

To disable wikilinks entirely:

[obsidian]
wikilinks = false

Dataview queries

Because each note's frontmatter is standard Obsidian Properties, you can query your paper collection with the Dataview community plugin. Examples:

```dataview
TABLE year, authors, citation_count AS "Citations"
FROM "papers"
WHERE source = "arXiv"
SORT citation_count DESC
```

```dataview
LIST
FROM "papers"
WHERE year >= 2022 AND open_access = true
SORT year DESC
```