Complete bibliography for all published DANDI datasets in BibTeX and RIS formats.
- Dandisets: 327
- Published Versions: 801
- Total Records: 1125 (including "latest" entries)
3 records failed to fetch valid BibTeX:
# No valid BibTeX for 000029/0.230317.1553. Starts with <!DOCTYPE html># No valid BibTeX for 000029/0.231017.1955. Starts with <!DOCTYPE html># No valid BibTeX for 000029/0.231017.1959. Starts with <!DOCTYPE html>
- dandi.bib: BibTeX format bibliography
- dandi.ris: RIS format bibliography
This bibliography is synchronized to a public Zotero group library: https://www.zotero.org/groups/5774211/dandi/library
-
Dandisets: All DANDI dandisets (synced from
dandi.bib) https://www.zotero.org/groups/5774211/dandi/collections/T8I34DL3/collection -
Dandiset-citations: Citations to dandisets (from citations-collector, planned) https://www.zotero.org/groups/5774211/dandi/collections/UHK47FKX/collection
Each dataset has two citation keys:
- Versioned:
dandi.000027/0.210831.2033(specific version) - Latest:
dandi.000027(most recent published version)
\bibliographystyle{plain}
\bibliography{dandi}
Cite as: \cite{dandi.000027/0.210831.2033}Import dandi.bib directly into Zotero, or access the public collection above.
flowchart TD
%% Current Implementation (solid lines)
trigger[["⏰ GitHub Actions Trigger<br/>(Daily @ 3:22 AM UTC)"]]
trigger -.->|<a href='.github/workflows/update-bibliography.yml'>update-bibliography.yml</a>| fetch
subgraph current["🟢 Current Implementation"]
direction TB
fetch["📥 Fetch Dandiset Metadata<br/><a href='code/get-bibliography'>get-bibliography</a>"]
api[("🌐 DANDI Archive API<br/>dandiarchive.org")]
fetch -->|"Query published<br/>dandisets"| api
api -->|"DOI, title,<br/>authors, etc"| fetch
fetch --> bib["📄 dandi.bib<br/>(BibTeX)"]
fetch --> ris["📄 dandi.ris<br/>(RIS)"]
fetch --> cache["💾 cache/results.json"]
zotero_sync["🔄 Sync to Zotero<br/><a href='code/update-zotero-collection'>update-zotero-collection</a>"]
bib --> zotero_sync
commit["✅ Git Commit & Push"]
bib --> commit
ris --> commit
cache --> commit
readme --> commit
stats["📊 Update Statistics<br/><a href='code/update-readme-stats'>update-readme-stats</a>"]
bib --> stats
stats --> readme["📝 README.md"]
end
%% Planned Future Additions (dashed lines)
subgraph planned["🔵 WiP: Citation Discovery Pipeline <a href='citations/'>(citations/)</a>"]
direction TB
cc_config["⚙️ Configuration<br/><a href='citations/dandi-full.yaml'>dandi-full.yaml</a>"]
discover["🔍 Discover Citations<br/><a href='https://github.com/con/citations-collector'>citations-collector</a>"]
bib -->|"Input:<br/>dandiset DOIs"| cc_config
cc_config --> discover
sources[("🔬 Citation Sources<br/>OpenAlex | DataCite<br/>CrossRef | OpenCitations")]
discover -->|Query on Dandiset DOI| sources
sources -->|Citation DOIs| discover
merge["🔀 Merge Preprints<br/>(detect published versions)"]
discover --> merge
tsv["📊 dandi-full-citations.tsv"]
merge --> tsv
pdfs["📑 Fetch PDFs<br/>(unpaywall, OA sources)"]
tsv --> pdfs
pdf_dir["📁 citations/pdfs/"]
pdfs --> pdf_dir
pdf_dir -.->|establish reuse type| discover
zotero_citations["🔄 Sync Citations to Zotero<br/>(subcollection)"]
tsv -.-> zotero_citations
makefile["🛠️ Automation<br/><a href='citations/Makefile'>Makefile</a>"]
makefile -->|"make all"| discover
end
%% Zotero Group (external)
subgraph zotero_group["📚 Zotero Group: <a href='https://www.zotero.org/groups/5774211/dandi/library'>DANDI</a>"]
direction TB
zotero_dandisets["📁 Subcollection: Dandisets<br/><a href='https://www.zotero.org/groups/5774211/dandi/collections/T8I34DL3/collection'>(T8I34DL3)</a>"]
zotero_citations_coll["📁 Subcollection: Dandiset-citations<br/><a href='https://www.zotero.org/groups/5774211/dandi/collections/UHK47FKX/collection'>(UHK47FKX)</a>"]
end
%% Connections to Zotero
zotero_sync -->|"pyzotero API"| zotero_dandisets
zotero_citations -.->|"via citations-collector"| zotero_citations_coll
%% Connections between workflows
commit -.->|"Manually (TODO: add to CI)"| makefile
%% Styling
classDef implemented fill:#90EE90,stroke:#2d5016,stroke-width:2px,color:#000
classDef planned fill:#87CEEB,stroke:#1e3a5f,stroke-width:2px,stroke-dasharray: 5 5,color:#000
classDef external fill:#FFE4B5,stroke:#8B4513,stroke-width:2px,color:#000
class fetch,bib,ris,cache,stats,readme,zotero_sync,commit,zotero_dandisets implemented
class cc_config,discover,merge,tsv,pdfs,pdf_dir,zotero_citations,zotero_citations_coll,makefile planned
class api,sources,zotero_group external
- Daily Automation: GitHub Actions workflow runs daily at 3:22 AM UTC
- Metadata Fetch:
get-bibliographyqueries DANDI Archive API for all published dandisets - Format Generation: Creates both
dandi.bib(BibTeX) anddandi.ris(RIS) files - Statistics Update:
update-readme-statsupdates this README with current counts - Zotero Sync:
update-zotero-collectionsyncs dandisets to the Dandisets subcollection in the public DANDI Zotero group - Git Commit: Changes are automatically committed and pushed to the repository
The citations/ directory contains configuration and tooling for discovering citations to DANDI dandisets:
- Configuration:
dandi-full.yamlpoints todandi.bibas the source of dandiset DOIs - Citation Discovery: citations-collector queries multiple sources:
- Preprint Merging: Detects and merges preprint citations with their published versions
- Output: Results saved to
dandi-full-citations.tsv - PDF Fetching: Downloads open-access PDFs to
citations/pdfs/ - Zotero Subcollection: Syncs citations to the Dandiset-citations subcollection in the DANDI Zotero group
- Automation:
Makefileprovides targets for running the pipeline locally or via DataLad
See citations/README.md for detailed usage instructions.
Located in code/:
get-bibliography: Fetch bibliography from DANDI APIupdate-zotero-collection: Sync to Zotero collectionupdate-readme-stats: Update this README with statistics
The bibliography data is derived from DANDI Archive metadata and follows the same licenses as the individual datasets.