Duplicate from J0nasW/science-datalake

Co-authored-by: Jonas Wilinski <J0nasW@users.noreply.huggingface.co>

.gitattributes

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+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
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+# Audio files - compressed
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+*.jpg filter=lfs diff=lfs merge=lfs -text
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+*.webp filter=lfs diff=lfs merge=lfs -text
+# Video files - compressed
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+datalake.duckdb filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+language:
+- en
+license:
+- cc0-1.0
+- cc-by-4.0
+- cc-by-sa-4.0
+- cc-by-nc-sa-4.0
+- cc-by-nc-4.0
+size_categories:
+- 100M<n<1B
+task_categories:
+- text-classification
+- feature-extraction
+tags:
+- scholarly
+- academic
+- citations
+- bibliometrics
+- science-of-science
+- openalex
+- sciscinet
+- papers-with-code
+- duckdb
+- parquet
+- ontologies
+- knowledge-graph
+pretty_name: Science Data Lake
+thumbnail: https://raw.githubusercontent.com/J0nasW/science-datalake/main/sdl_banner.jpg
+configs:
+  # Cross-reference tables
+  - config_name: unified_papers
+    data_files: "xref/unified_papers/*.parquet"
+  - config_name: topic_ontology_map
+    data_files: "xref/topic_ontology_map/*.parquet"
+  - config_name: ontology_bridges
+    data_files: "xref/ontology_bridges/*.parquet"
+  # OpenAlex (CC0 1.0)
+  - config_name: openalex_works
+    data_files: "openalex/works/*.parquet"
+  - config_name: openalex_authors
+    data_files: "openalex/authors/*.parquet"
+  - config_name: openalex_topics
+    data_files: "openalex/topics/*.parquet"
+  - config_name: openalex_works_topics
+    data_files: "openalex/works_topics/*.parquet"
+  - config_name: openalex_works_authorships
+    data_files: "openalex/works_authorships/*.parquet"
+  - config_name: openalex_works_referenced_works
+    data_files: "openalex/works_referenced_works/*.parquet"
+  - config_name: openalex_works_keywords
+    data_files: "openalex/works_keywords/*.parquet"
+  - config_name: openalex_institutions
+    data_files: "openalex/institutions/*.parquet"
+  # SciSciNet (CC BY 4.0)
+  - config_name: sciscinet_core
+    data_files: "sciscinet/core/*.parquet"
+  - config_name: sciscinet_large
+    data_files: "sciscinet/large/*.parquet"
+  # Papers With Code (CC BY-SA 4.0)
+  - config_name: pwc_papers
+    data_files: "pwc/papers/*.parquet"
+  - config_name: pwc_paper_has_code
+    data_files: "pwc/paper_has_code/*.parquet"
+  - config_name: pwc_methods
+    data_files: "pwc/methods/*.parquet"
+  - config_name: pwc_paper_has_task
+    data_files: "pwc/paper_has_task/*.parquet"
+  - config_name: pwc_datasets
+    data_files: "pwc/datasets/*.parquet"
+  # Other sources
+  - config_name: retwatch
+    data_files: "retwatch/retraction_watch/*.parquet"
+  - config_name: p2p_preprint_to_paper
+    data_files: "p2p/preprint_to_paper/*.parquet"
+  # Reliance on Science (CC BY-NC 4.0)
+  - config_name: ros_patent_paper_pairs
+    data_files: "ros/patent_paper_pairs/*.parquet"
+  - config_name: ros_patent_paper_pairs_plus
+    data_files: "ros/patent_paper_pairs_plus/*.parquet"
+  - config_name: ros_pcs_oa
+    data_files: "ros/pcs_oa/*.parquet"
+  # Ontologies (various licenses, see below)
+  - config_name: ontology_terms
+    data_files: "ontologies/*_terms.parquet"
+  - config_name: ontology_hierarchy
+    data_files: "ontologies/*_hierarchy.parquet"
+  - config_name: ontology_xrefs
+    data_files: "ontologies/*_xrefs.parquet"
+---
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/J0nasW/science-datalake/main/sdl_banner.jpg" alt="Science Data Lake" width="100%">
+</p>
+
+<p align="center">
+  <a href="https://arxiv.org/abs/2603.03126"><img src="https://img.shields.io/badge/arXiv-2603.03126-b31b1b" alt="arXiv"></a>
+  <a href="https://github.com/J0nasW/science-datalake"><img src="https://img.shields.io/badge/GitHub-Repository-181717?logo=github" alt="GitHub"></a>
+  <a href="https://doi.org/10.57967/hf/7850"><img src="https://img.shields.io/badge/DOI-10.57967%2Fhf%2F7850-blue" alt="DOI"></a>
+  <a href="https://github.com/J0nasW/science-datalake/blob/main/SCHEMA.md"><img src="https://img.shields.io/badge/LLM--Ready-SCHEMA.md-purple" alt="LLM-Ready"></a>
+  <a href="https://x.com/Jonas_H_W"><img src="https://img.shields.io/badge/Follow-%40Jonas__H__W-black?logo=x" alt="Follow on X"></a>
+  <a href="https://wilinski.me"><img src="https://img.shields.io/badge/Author-wilinski.me-orange" alt="Author website"></a>
+</p>
+
+# Science Data Lake
+
+A unified, portable science data lake integrating **7 scholarly datasets** (~525 GB Parquet) with cross-dataset DOI normalization, **13 scientific ontologies** (1.3M terms), and a reproducible ETL pipeline.
+
+> **Note:** One additional source (Semantic Scholar S2AG) is supported by the pipeline but is **not redistributed here** due to its API terms of service. See [Not Included in This Upload](#not-included-in-this-upload) below.
+
+## What's Unique
+
+This dataset enables queries that are **impossible with any single source**:
+
+```sql
+-- "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 |
+| **Reliance on Science** | 47.8M pairs | **CC BY-NC 4.0** | Patent-to-paper citation pairs (global) |
+| **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 |
+| Reliance on Science | v64 | Zenodo record |
+| Preprint-to-Paper | 2025-06 | Zenodo record |
+| 13 Ontologies | 2026-02 | Official sources |
+
+All snapshots can be refreshed using the [update pipeline](https://github.com/J0nasW/science-datalake) — see below.
+
+### Not Included in This Upload
+
+The following source is supported by the full pipeline ([GitHub](https://github.com/J0nasW/science-datalake)) but is **not redistributed here** due to its API terms of service:
+
+| Dataset | Reason | How to obtain |
+|---------|--------|---------------|
+| **S2AG** (Semantic Scholar, 231M papers) | License requires individual agreement with Semantic Scholar | [Semantic Scholar Datasets API](https://api.semanticscholar.org/api-docs/datasets) |
+
+After downloading S2AG locally, run the full pipeline to integrate it.
+
+## 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 |
+| `has_s2ag` | BOOLEAN | Present in Semantic Scholar |
+| `has_patent` | BOOLEAN | Cited by at least one patent (RoS) |
+| `s2ag_corpusid` | BIGINT | Semantic Scholar corpus ID |
+| `s2ag_citationcount` | INTEGER | S2AG citation count |
+| `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 S2AG columns (`s2ag_corpusid`, `s2ag_citationcount`, `s2ag_influentialcitationcount`, `s2ag_isopenaccess`, `has_s2ag`) are present in the uploaded file but will contain NULL/FALSE values unless S2AG has been integrated locally. All other columns (including `has_patent` from Reliance on Science) are fully populated.
+
+### `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
+
+### Option 1: Pre-built database file (recommended)
+
+This repository includes a ready-to-use DuckDB database file (`datalake.duckdb`, 274 KB) with 145 SQL views pre-configured to read directly from HuggingFace. Download just this one file and query all 7 datasets immediately — no pipeline setup required.
+
+```python
+import duckdb
+
+con = duckdb.connect()
+con.execute("INSTALL httpfs; LOAD httpfs;")
+con.execute("ATTACH 'hf://datasets/J0nasW/science-datalake/datalake.duckdb' AS lake")
+
+# Query using familiar schema.table syntax
+df = con.execute("""
+    SELECT doi, title, year, sciscinet_disruption, oa_cited_by_count
+    FROM lake.xref.unified_papers
+    WHERE sciscinet_disruption IS NOT NULL
+    ORDER BY sciscinet_disruption DESC
+    LIMIT 100
+""").df()
+
+# Cross-source joins work out of the box
+con.execute("""
+    SELECT t.display_name AS topic, o.ontology, o.term_name, o.similarity
+    FROM lake.xref.topic_ontology_map o
+    JOIN lake.openalex.topics t ON t.id = o.topic_id
+    WHERE o.similarity >= 0.85
+    ORDER BY o.similarity DESC
+    LIMIT 20
+""").df()
+```
+
+### Option 2: Direct Parquet queries
+
+You can also query individual Parquet files directly without the database file:
+
+```python
+import duckdb
+
+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:
+
+```bash
+# 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](https://github.com/J0nasW/science-datalake) for full pipeline documentation.
+
+## LLM & AI Agent Integration
+
+This data lake ships with **[SCHEMA.md](https://github.com/J0nasW/science-datalake/blob/main/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 7 hosted 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:
+
+```bash
+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
+
+If you use the Science Data Lake, please cite the paper:
+
+```bibtex
+@article{wilinski2026sciencedatalake,
+  title   = {The Science Data Lake: A Unified Open Infrastructure Integrating
+             293 Million Papers Across Eight Scholarly Sources with
+             Embedding-Based Ontology Alignment},
+  author  = {Wilinski, Jonas},
+  journal = {arXiv preprint arXiv:2603.03126},
+  year    = {2026},
+  url     = {https://arxiv.org/abs/2603.03126}
+}
+```
+
+Dataset DOI: [10.57967/hf/7850](https://doi.org/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) |
+| Reliance on Science data | CC BY-NC 4.0 |
+| 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** |

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