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  1. .DS_Store +0 -0
  2. .gitattributes +9 -0
  3. benchmark/LICENSE +41 -0
  4. benchmark/README.md +81 -0
  5. benchmark/croissant.json +112 -0
  6. benchmark/diffs/diff_t0_t1.json +59 -0
  7. benchmark/features/disease_features.csv +0 -0
  8. benchmark/features/drug_features.csv +0 -0
  9. benchmark/features/edge_index.pt +3 -0
  10. benchmark/features/edge_type.pt +3 -0
  11. benchmark/features/mol_dim.txt +1 -0
  12. benchmark/features/mol_features.pt +3 -0
  13. benchmark/features/node_has_mol.pt +3 -0
  14. benchmark/features/node_has_text.pt +3 -0
  15. benchmark/features/node_index_map.csv +0 -0
  16. benchmark/features/text_embeddings.pt +3 -0
  17. benchmark/features/vocab_sizes.json +1 -0
  18. benchmark/snapshots/kg_t0.csv +3 -0
  19. benchmark/snapshots/kg_t1.csv +3 -0
  20. benchmark/snapshots/t1_build_info.json +53 -0
  21. benchmark/statistics.json +85 -0
  22. benchmark/tasks/task_0_base/test.txt +3 -0
  23. benchmark/tasks/task_0_base/train.txt +3 -0
  24. benchmark/tasks/task_0_base/valid.txt +3 -0
  25. benchmark/tasks/task_1_disease_related/test.txt +0 -0
  26. benchmark/tasks/task_1_disease_related/train.txt +0 -0
  27. benchmark/tasks/task_1_disease_related/valid.txt +1700 -0
  28. benchmark/tasks/task_1_drug_related/test.txt +0 -0
  29. benchmark/tasks/task_1_drug_related/train.txt +0 -0
  30. benchmark/tasks/task_1_drug_related/valid.txt +0 -0
  31. benchmark/tasks/task_2_disease_related/test.txt +0 -0
  32. benchmark/tasks/task_2_disease_related/train.txt +0 -0
  33. benchmark/tasks/task_2_disease_related/valid.txt +0 -0
  34. benchmark/tasks/task_2_gene_protein/test.txt +3 -0
  35. benchmark/tasks/task_2_gene_protein/train.txt +3 -0
  36. benchmark/tasks/task_2_gene_protein/valid.txt +0 -0
  37. benchmark/tasks/task_3_gene_protein/test.txt +0 -0
  38. benchmark/tasks/task_3_gene_protein/train.txt +0 -0
  39. benchmark/tasks/task_3_gene_protein/valid.txt +0 -0
  40. benchmark/tasks/task_3_phenotype_related/test.txt +0 -0
  41. benchmark/tasks/task_3_phenotype_related/train.txt +0 -0
  42. benchmark/tasks/task_3_phenotype_related/valid.txt +0 -0
  43. benchmark/tasks/task_4_biological_process/test.txt +0 -0
  44. benchmark/tasks/task_4_biological_process/train.txt +0 -0
  45. benchmark/tasks/task_4_biological_process/valid.txt +0 -0
  46. benchmark/tasks/task_4_phenotype_related/test.txt +0 -0
  47. benchmark/tasks/task_4_phenotype_related/train.txt +0 -0
  48. benchmark/tasks/task_4_phenotype_related/valid.txt +0 -0
  49. benchmark/tasks/task_5_anatomy_pathway/test.txt +3 -0
  50. benchmark/tasks/task_5_anatomy_pathway/train.txt +3 -0
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+ benchmark/snapshots/kg_t1.csv filter=lfs diff=lfs merge=lfs -text
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+ benchmark/tasks/task_0_base/valid.txt filter=lfs diff=lfs merge=lfs -text
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+ benchmark/tasks/task_2_gene_protein/test.txt filter=lfs diff=lfs merge=lfs -text
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+ benchmark/tasks/task_2_gene_protein/train.txt filter=lfs diff=lfs merge=lfs -text
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+ benchmark/tasks/task_5_anatomy_pathway/test.txt filter=lfs diff=lfs merge=lfs -text
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+ benchmark/tasks/task_5_anatomy_pathway/train.txt filter=lfs diff=lfs merge=lfs -text
benchmark/LICENSE ADDED
@@ -0,0 +1,41 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ PrimeKG-CL Benchmark
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+ ====================
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+
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+ Code and benchmark configuration files in this release: MIT License.
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+
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+ Data files derived from PrimeKG and downstream from the source databases:
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+ licensed under Creative Commons Attribution 4.0 International (CC BY 4.0),
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+ inheriting PrimeKG's license. Users must respect upstream-database licenses
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+ where applicable. The t_1 snapshot was reconstructed from these freely
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+ accessible upstream databases; restrictively licensed databases (DrugBank,
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+ UMLS, DrugCentral, SIDER, DisGeNET) are NOT re-queried for t_1 and the t_0
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+ edges from those sources are carried forward unchanged.
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+
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+ Upstream databases used for t_1 reconstruction:
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+ Bgee, CTD, Gene Ontology, Gene2GO, HPO, HPOA, MONDO, Uberon, HGNC.
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+
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+ Citation: see README.md.
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+
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+ ----------------------------------------------------------------------
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+
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+ MIT License (code components)
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+
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+ Copyright (c) 2026 The PrimeKG-CL authors
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
30
+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
benchmark/README.md ADDED
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1
+ # PrimeKG-CL Benchmark v1.0
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+
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+ A continual graph learning benchmark on a real biomedical knowledge graph
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+ with genuine temporal evolution.
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+
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+ ## Snapshots
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+ - `snapshots/kg_t0.csv` — June 2021 PrimeKG release. 8,100,498 triples, 129,375 nodes, 30 relations.
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+ - `snapshots/kg_t1.csv` — July 2023 reconstruction from nine upstream databases (Bgee, CTD, GO, Gene2GO, HPO, HPOA, MONDO, Uberon, HGNC). 13,001,666 triples, 134,211 nodes, 25 relations.
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+ - `snapshots/t1_build_info.json` — provenance / database versions used for the t_1 reconstruction.
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+
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+ ## Temporal diff (t_0 -> t_1)
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+ - Added: 5,760,234 new triples (driven by GO annotations, disease-phenotype refinement, drug-target updates)
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+ - Removed: 888,848 deprecated triples (retracted associations, ontology corrections)
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+ - Persistent: 7,208,624 triples unchanged across both snapshots
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+
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+ Full breakdown in `diffs/diff_t0_t1.json`.
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+
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+ ## Continual learning tasks
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+ 10 entity-type-grouped tasks (`tasks/task_*`). Each directory contains
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+ `train.txt`, `valid.txt`, `test.txt`, one tab-separated triple per line
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+ (`head_id<TAB>relation<TAB>tail_id`). 70/10/20 train/valid/test split.
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+
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+ ```
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+ task_0_base 8,100,498 triples (full t_0)
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+ task_1_disease_related 17,009
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+ task_1_drug_related 125,343
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+ task_2_disease_related 115,382
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+ task_2_gene_protein 2,850,593
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+ task_3_gene_protein 99,761
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+ task_3_phenotype_related 47,997
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+ task_4_biological_process 116,118
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+ task_4_phenotype_related 57,390
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+ task_5_anatomy_pathway 2,752,675
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+ ```
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+
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+ ## Stratified evaluation
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+ `test_stratification.json` — per-task partition of test triples into
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+ **persistent** (in both snapshots), **added** (new in t_1), and
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+ **removed** (only in t_0) strata, supporting stratified-MRR analysis of
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+ correct retention vs. correct forgetting.
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+
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+ Task 0's test split: 1,443,243 persistent + 176,856 removed = 1,620,099 total.
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+
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+ ## Multimodal features (`features/`)
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+ - `text_embeddings.pt` — BiomedBERT [CLS] embeddings projected to 256-d.
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+ Coverage: 36% of entities (those with textual descriptions).
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+ - `mol_features.pt` — Morgan fingerprints (radius 2, 1024 bits) for drugs
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+ with available SMILES. Coverage: 4% of entities.
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+ - `edge_index.pt`, `edge_type.pt` — R-GCN message-passing tensors for the
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+ full t_0 graph (used by the structural encoder).
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+ - `node_has_text.pt`, `node_has_mol.pt` — boolean coverage masks.
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+ - `node_index_map.csv` — global entity_id <-> row_index map.
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+ - `vocab_sizes.json` — entity / relation vocab sizes.
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+
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+ ## Files
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+ ```
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+ LICENSE MIT (code) + CC BY 4.0 (data)
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+ croissant.json MLCommons Croissant metadata
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+ README.md this file
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+ statistics.json benchmark-level summary
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+ test_stratification.json per-task persistent/added/removed counts
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+ diffs/diff_t0_t1.json full t_0->t_1 diff with per-relation breakdown
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+ snapshots/ kg_t0.csv, kg_t1.csv, build provenance
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+ tasks/ 10 task directories with train/valid/test splits
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+ features/ multimodal node features
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+ ```
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+
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+ ## Citation
69
+ ```
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+ @inproceedings{primekgcl2026,
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+ title={PrimeKG-CL: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs},
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+ author={Anonymous},
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+ booktitle={NeurIPS Datasets and Benchmarks Track},
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+ year={2026}
75
+ }
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+ ```
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+
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+ ## License
79
+ - Code components: MIT.
80
+ - Data files: CC BY 4.0, inheriting PrimeKG's license; users must respect upstream-database licenses where applicable.
81
+ - See `LICENSE` for details.
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+ },
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+ "@type": "sc:Dataset",
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+ "name": "PrimeKG-CL",
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+ "description": "PrimeKG-CL is a continual graph learning benchmark on a real biomedical knowledge graph with genuine temporal evolution. It contains two temporal snapshots reconstructed from nine asynchronously updating biomedical databases (June 2021 and July 2023), with 129K+ entities, 8.1M+ edges, 10 entity-type-grouped continual learning tasks, multimodal node features (textual via BiomedBERT, molecular via Morgan fingerprints, structural via R-GCN), and three evaluation tracks (continual biomedical relationship prediction, biomedical entity classification, biomedical KGQA).",
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+ "license": "https://creativecommons.org/licenses/by/4.0/",
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+ "url": "https://github.com/yradwan147/Yousef_PrimeKG-CL_NeurIPS2026",
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+ "version": "1.0",
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+ "datePublished": "2026-04-25",
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+ "citeAs": "@inproceedings{primekgcl2026, title={{PrimeKG-CL}: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs}, author={Anonymous}, booktitle={NeurIPS Datasets and Benchmarks Track}, year={2026}}",
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+ "name": "kg_t0.csv",
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+ "description": "Snapshot t_0 (June 2021): 8,100,498 triples across 129,375 nodes and 30 relation types."
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+ },
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+ {
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+ "@type": "cr:FileObject",
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+ "@id": "snapshot-t1",
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+ "name": "kg_t1.csv",
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+ "contentUrl": "snapshots/kg_t1.csv",
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+ "encodingFormat": "text/csv",
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+ "description": "Snapshot t_1 (July 2023): 13,001,666 triples across 134,211 nodes and 25 relation types."
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+ },
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+ {
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+ "@type": "cr:FileSet",
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+ "@id": "task-files",
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+ },
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+ {
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+ "@type": "cr:FileSet",
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+ "@id": "features",
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+ "name": "features",
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+ "description": "Multimodal node features: text_embeddings.pt (BiomedBERT 768-d -> 256-d), mol_features.pt (Morgan 1024-bit), edge_index.pt and edge_type.pt for R-GCN message passing.",
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+ "encodingFormat": "application/octet-stream",
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+ "includes": "features/*"
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+ "@id": "triples-t0",
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+ "name": "triples-t0",
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+ "description": "Triples in snapshot t_0.",
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+ "field": [
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+ {"@type": "cr:Field", "@id": "triples-t0/relation", "name": "relation", "dataType": "sc:Text"},
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+ {"@type": "cr:Field", "@id": "triples-t0/x_id", "name": "x_id", "dataType": "sc:Text"},
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+ }
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+ ]
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+ }
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