J0nasW/science-datalake

Science Data Lake

A unified, portable science data lake integrating 6 scholarly datasets (~523 GB Parquet) with cross-dataset DOI normalization, 13 scientific ontologies (1.3M terms), and a reproducible ETL pipeline.

Note: Two additional sources (Semantic Scholar S2AG and Reliance on Science) are supported by the pipeline but are not redistributed here pending license clarification. See Not Included in This Upload below.

What's Unique

This dataset enables queries that are impossible with any single source:

-- "Top disruptive papers with open-source code, checking for retractions"
SELECT doi, title, year,
       sciscinet_disruption,      -- from SciSciNet
       oa_cited_by_count,         -- from OpenAlex
       has_pwc,                   -- from Papers With Code
       has_retraction             -- from Retraction Watch
FROM unified_papers
WHERE has_pwc AND sciscinet_disruption > 0.5
ORDER BY oa_cited_by_count DESC
LIMIT 20

Datasets Included

Dataset	Papers/Records	License	Key Contribution
OpenAlex	479M works	CC0 1.0 (public domain)	Broadest coverage, topics, FWCI
SciSciNet v2	250M papers	CC BY 4.0	Disruption index, atypicality, team size
Papers With Code	513K papers	CC BY-SA 4.0	Method-task-dataset-code links
Retraction Watch	69K records	Open (via Crossref)	Retraction flags + reasons
Preprint-to-Paper	146K pairs	CC BY 4.0	bioRxiv preprint to published paper
13 Ontologies	1.3M terms	Various (see below)	CSO, MeSH, GO, DOID, ChEBI, NCIT, HPO, EDAM, AGROVOC, UNESCO, STW, MSC2020, PhySH

Ontology Licenses

Ontology	License
MeSH	Public Domain (US government work)
GO, ChEBI, NCIT, EDAM, CSO, PhySH, STW	CC BY 4.0
DOID	CC0 1.0
AGROVOC	CC BY 3.0 IGO
UNESCO Thesaurus	CC BY-SA 3.0 IGO
HPO	Custom (free for research use)
MSC2020	CC BY-NC-SA 4.0 (non-commercial)

Snapshot Dates

Each source was downloaded at a specific point in time:

Dataset	Snapshot / Release	Notes
OpenAlex	2026-02-03	S3 snapshot
SciSciNet v2	2024-11-01	GCS bucket
Papers With Code	2025-07	Archived JSON
Retraction Watch	2025-02	Crossref CSV
Preprint-to-Paper	2025-06	Zenodo record
13 Ontologies	2026-02	Official sources

All snapshots can be refreshed using the update pipeline — see below.

Not Included in This Upload

The following sources are supported by the full pipeline (GitHub) but are not redistributed here due to license restrictions or pending clarification:

Dataset	Reason	How to obtain
S2AG (Semantic Scholar, 231M papers)	License requires individual agreement with Semantic Scholar	Semantic Scholar Datasets API
Reliance on Science (548K patent-paper pairs)	CC BY-NC 4.0 — non-commercial restriction	Zenodo record

After downloading these sources locally, run the full pipeline to integrate them.

Key Tables

unified_papers (293M rows)

The headline table: one row per unique DOI, joining all sources.

Column	Type	Description
doi	VARCHAR	Normalized DOI (lowercase, no prefix)
title	VARCHAR	Best available title (OpenAlex > S2AG)
year	BIGINT	Publication year
openalex_id	VARCHAR	OpenAlex work ID
sciscinet_paperid	VARCHAR	SciSciNet paper ID
has_openalex	BOOLEAN	Present in OpenAlex
has_sciscinet	BOOLEAN	Present in SciSciNet
has_pwc	BOOLEAN	Has code on Papers With Code
has_retraction	BOOLEAN	Flagged in Retraction Watch
oa_cited_by_count	BIGINT	OpenAlex citation count
sciscinet_disruption	DOUBLE	Disruption index (CD index)
sciscinet_atypicality	DOUBLE	Atypicality score
oa_fwci	DOUBLE	Field-Weighted Citation Impact

Note: The locally-built version of unified_papers includes additional columns from S2AG and RoS (s2ag_corpusid, s2ag_citationcount, has_s2ag, has_patent). These columns are present in the uploaded file but will contain NULL values for users who have not integrated those sources locally.

topic_ontology_map

Maps OpenAlex's 4,516 topics to terms in 13 scientific ontologies via embedding-based semantic similarity (BGE-large-en-v1.5, 1024-dim) + exact matching for large ontologies (MeSH, ChEBI, NCIT). 16,150 mappings covering 99.8% of topics. Columns include similarity (cosine, 0-1) and match_type (label/synonym/exact) for quality filtering.

ontology_bridges

Cross-ontology links discovered via shared external IDs (UMLS, Wikidata, MESH, etc.).

Usage with DuckDB

import duckdb

# Query directly from HuggingFace
con = duckdb.connect()
con.execute("INSTALL httpfs; LOAD httpfs;")

df = con.execute("""
    SELECT doi, title, year, sciscinet_disruption, oa_cited_by_count
    FROM 'hf://datasets/J0nasW/science-datalake/xref/unified_papers/*.parquet'
    WHERE sciscinet_disruption IS NOT NULL
    ORDER BY sciscinet_disruption DESC
    LIMIT 100
""").df()

Keeping the Data Current

The full pipeline supports incremental updates. When upstream sources release new snapshots:

# Update a single dataset
python scripts/datalake_cli.py update openalex

# Update all datasets and rebuild cross-reference tables
python scripts/datalake_cli.py update
python scripts/materialize_unified_papers.py

See the GitHub repository for full pipeline documentation.

LLM & AI Agent Integration

This data lake ships with SCHEMA.md — a structured reference file optimized for LLM-based coding agents (Claude Code, Cursor, Copilot, etc.). It contains every table, column, type, join strategy, and performance tier in a format that AI agents can use to write correct DuckDB SQL without prior schema knowledge.

Point your AI assistant at SCHEMA.md and ask it to query across all 6+ datasets and 13 ontologies using natural language.

Building the Full Instance (All 8 Sources)

Clone the GitHub repository and run the pipeline to integrate all sources including S2AG and RoS:

git clone https://github.com/J0nasW/science-datalake
cd science-datalake
python scripts/datalake_cli.py download --all
python scripts/datalake_cli.py convert --all
python scripts/create_unified_db.py
python scripts/materialize_unified_papers.py

Citation

@dataset{wilinski2026sciencedatalake,
  title={Science Data Lake: A Unified, Portable Data Lake for Full-Lifecycle Scholarly Analysis},
  author={Wilinski, Jonas},
  year={2026},
  publisher={HuggingFace},
  url={https://huggingface.co/datasets/J0nasW/science-datalake},
  doi={10.57967/hf/7850}
}

License

This dataset aggregates multiple sources, each with its own license. Users must comply with the most restrictive license applicable to the sources they use.

Component	License
Integration code (scripts, pipeline)	MIT
OpenAlex data	CC0 1.0 (public domain)
SciSciNet v2 data	CC BY 4.0
Papers With Code data	CC BY-SA 4.0
Retraction Watch data	Open (via Crossref)
Preprint-to-Paper data	CC BY 4.0
Cross-reference tables (unified_papers, topic_ontology_map)	Derived work — most restrictive source license applies
Ontologies	Various — see table above; note MSC2020 is CC BY-NC-SA 4.0