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README.md
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@@ -6,6 +6,7 @@ license:
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- cc-by-4.0
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- cc-by-sa-4.0
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- cc-by-nc-sa-4.0
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size_categories:
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- 100M<n<1B
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task_categories:
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data_files: "retwatch/retraction_watch/*.parquet"
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- config_name: p2p_preprint_to_paper
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data_files: "p2p/preprint_to_paper/*.parquet"
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# Ontologies (various licenses, see below)
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- config_name: ontology_terms
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data_files: "ontologies/*_terms.parquet"
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| **SciSciNet** v2 | 250M papers | **CC BY 4.0** | Disruption index, atypicality, team size |
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| **Papers With Code** | 513K papers | **CC BY-SA 4.0** | Method-task-dataset-code links |
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| **Retraction Watch** | 69K records | **Open** (via Crossref) | Retraction flags + reasons |
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| **Preprint-to-Paper** | 146K pairs | **CC BY 4.0** | bioRxiv preprint to published paper |
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| **13 Ontologies** | 1.3M terms | Various (see below) | CSO, MeSH, GO, DOID, ChEBI, NCIT, HPO, EDAM, AGROVOC, UNESCO, STW, MSC2020, PhySH |
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| `has_sciscinet` | BOOLEAN | Present in SciSciNet |
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| `has_pwc` | BOOLEAN | Has code on Papers With Code |
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| `has_retraction` | BOOLEAN | Flagged in Retraction Watch |
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| `oa_cited_by_count` | BIGINT | OpenAlex citation count |
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| `sciscinet_disruption` | DOUBLE | Disruption index (CD index) |
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| `sciscinet_atypicality` | DOUBLE | Atypicality score |
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| `oa_fwci` | DOUBLE | Field-Weighted Citation Impact |
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> **Note:** The
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### `topic_ontology_map`
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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.
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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.
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Point your AI assistant at `SCHEMA.md` and ask it to query across all
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## Building the Full Instance (All 8 Sources)
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Clone the GitHub repository and run the pipeline to integrate all sources including S2AG
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```bash
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git clone https://github.com/J0nasW/science-datalake
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| SciSciNet v2 data | CC BY 4.0 |
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| Papers With Code data | CC BY-SA 4.0 |
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| Retraction Watch data | Open (via Crossref) |
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| Preprint-to-Paper data | CC BY 4.0 |
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| Cross-reference tables (`unified_papers`, `topic_ontology_map`) | Derived work — most restrictive source license applies |
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| Ontologies | Various — see table above; note **MSC2020 is CC BY-NC-SA 4.0** |
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- cc-by-4.0
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- cc-by-sa-4.0
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- cc-by-nc-sa-4.0
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- cc-by-nc-4.0
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size_categories:
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- 100M<n<1B
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task_categories:
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data_files: "retwatch/retraction_watch/*.parquet"
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- config_name: p2p_preprint_to_paper
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data_files: "p2p/preprint_to_paper/*.parquet"
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# Reliance on Science (CC BY-NC 4.0)
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- config_name: ros_patent_paper_pairs
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data_files: "ros/patent_paper_pairs/*.parquet"
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- config_name: ros_patent_paper_pairs_plus
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data_files: "ros/patent_paper_pairs_plus/*.parquet"
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- config_name: ros_pcs_oa
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data_files: "ros/pcs_oa/*.parquet"
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# Ontologies (various licenses, see below)
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- config_name: ontology_terms
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data_files: "ontologies/*_terms.parquet"
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| **SciSciNet** v2 | 250M papers | **CC BY 4.0** | Disruption index, atypicality, team size |
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| **Papers With Code** | 513K papers | **CC BY-SA 4.0** | Method-task-dataset-code links |
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| **Retraction Watch** | 69K records | **Open** (via Crossref) | Retraction flags + reasons |
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| **Reliance on Science** | 47.8M pairs | **CC BY-NC 4.0** | Patent-to-paper citation pairs (global) |
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| **Preprint-to-Paper** | 146K pairs | **CC BY 4.0** | bioRxiv preprint to published paper |
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| **13 Ontologies** | 1.3M terms | Various (see below) | CSO, MeSH, GO, DOID, ChEBI, NCIT, HPO, EDAM, AGROVOC, UNESCO, STW, MSC2020, PhySH |
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| `has_sciscinet` | BOOLEAN | Present in SciSciNet |
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| `has_pwc` | BOOLEAN | Has code on Papers With Code |
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| `has_retraction` | BOOLEAN | Flagged in Retraction Watch |
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| `has_s2ag` | BOOLEAN | Present in Semantic Scholar |
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| `has_patent` | BOOLEAN | Cited by at least one patent (RoS) |
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| `s2ag_corpusid` | BIGINT | Semantic Scholar corpus ID |
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| `s2ag_citationcount` | INTEGER | S2AG citation count |
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| `oa_cited_by_count` | BIGINT | OpenAlex citation count |
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| `sciscinet_disruption` | DOUBLE | Disruption index (CD index) |
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| `sciscinet_atypicality` | DOUBLE | Atypicality score |
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| `oa_fwci` | DOUBLE | Field-Weighted Citation Impact |
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> **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.
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### `topic_ontology_map`
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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.
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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.
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Point your AI assistant at `SCHEMA.md` and ask it to query across all 7 hosted datasets and 13 ontologies using natural language.
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## Building the Full Instance (All 8 Sources)
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Clone the GitHub repository and run the pipeline to integrate all sources including S2AG:
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```bash
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git clone https://github.com/J0nasW/science-datalake
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| SciSciNet v2 data | CC BY 4.0 |
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| Papers With Code data | CC BY-SA 4.0 |
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| Retraction Watch data | Open (via Crossref) |
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| Reliance on Science data | CC BY-NC 4.0 |
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| Preprint-to-Paper data | CC BY 4.0 |
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| Cross-reference tables (`unified_papers`, `topic_ontology_map`) | Derived work — most restrictive source license applies |
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| Ontologies | Various — see table above; note **MSC2020 is CC BY-NC-SA 4.0** |
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