cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17207156
title: Minimal Dataset for "Reframing Anthropomorphism in Trust Recovery: Warmth, Competence, and the Limits of Attribution"

description: This dataset contains the minimal data supporting the article “Reframing Anthropomorphism in Trust Recovery: Warmth, Competence, and the Limits of Attribution.”The study was conducted in Japan with N = 400 participants, using an online experiment with a 2×2 factorial design.All responses are fully anonymized and contain no personally identifiable information.

Contents:





data_JTAER.csv: Survey dataset.




README_JTAER.docx: Documentation with details on variables, coding, and usage.



The dataset is intended for replication and validation purposes and can be directly imported into SmartPLS 4 or other statistical software.
DOI: 10.15468/dl.nfdhb3
title: Occurrence Download

description: A dataset containing 222295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((77.47137 13.23605,77.46911 13.1385,77.58084 13.14072,77.58235 13.23532,77.47137 13.23605))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2014-2025"
 ]
}

 The dataset includes 222295 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018949-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pmuhfz
title: Occurrence Download

description: A dataset containing 630 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Colchicum cupanii)"
 ]
}

 The dataset includes 630 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019024-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95scat
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mortonagrion selenion",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019025-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qyrku
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Annona montana",
 "Country is Bolivia (Plurinational State of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 101 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019026-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.24mxvn
title: Occurrence Download

description: A dataset containing 1496 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Patella caerulea"
 ]
}

 The dataset includes 1496 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019028-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/0cgr-7745
title: "Causality-Informed Large-Small Model Collaborative Framework for Time Series Forecasting: Dataset"

description: "We propose a causality-informed collaborative framework that integrates large pre-trained models with small auxiliary models for time series forecasting. The architecture leverages the strong baseline predictions of large models while introducing two complementary enhancements: (i) residual correction guided by domain-specific signals, and (ii) causal denoising with external instrumental variables to mitigate spurious correlations. Comprehensive experiments on real-world financial and environmental datasets demonstrate that the framework consistently improves out-of-sample forecasting accuracy over large model baselines. Notably, incorporating instrumental-variable\u2013based denoising yields additional gains, showing that exogenous signals can further enhance predictive performance. Moreover, the improvements scale with model size, as larger pre-trained models benefit more from the collaborative design. Overall, the study demonstrates that causality-aware auxiliary modules can systematically boost large pre-trained models, delivering interpretable and scalable improvements for time-series forecasting in noisy real-world environments."
DOI: 10.15468/dl.fp63uz
title: Occurrence Download

description: A dataset containing 24091493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2020-2025"
 ]
}

 The dataset includes 24091493 records from 244 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018978-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vyk8sb
title: Occurrence Download

description: A dataset containing 9555 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ulmus alata"
 ]
}

 The dataset includes 9555 records from 193 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019027-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9bajr
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Colchicum speciosum)"
 ]
}

 The dataset includes 431 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019030-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17189994
title: Pharmacogenomic Knowledge Graph (PGx-KG) Dataset

description: Pharmacogenomic Knowledge Graph (PGx-KG) Dataset

This repository contains the processed pharmacogenomic knowledge graph (PGx-KG) prepared for benchmarking link prediction models. The graph integrates curated relationships from PharmGKB, ClinVar, SIDER, and Reactome to standard biomedical vocabularies so that entities and relations align across resources.

Contents



nodes.csv: Consolidated catalogue of biomedical entities with harmonized identifiers, semantic types, and source provenance.

edges.csv: Full edge list covering all relation types with integer IDs referencing the node maps.

triples/: Relation-specific subject–predicate–object triples in CSV format, named as <REL>__HEADTYPE__TAILTYPE.

relations/: Per-relation tables with descriptive metadata, confidence scores, and source annotations.

id_maps/: Mapping tables that link integer IDs to canonical biomedical identifiers (HGNC, RxNorm, MeSH, ChEBI, etc.).

degree/: Per-relation in/out degree distributions for downstream analysis or sampling.

splits/: Stratified train/validation/test partitions for each relation type, with only CSV versions (including reproducible random/ test/train/val).

stats.json: Summary statistics computed after harmonization (entity counts, relation counts,).


Data Statistics

Total nodes: 3,744,727 Total edges: 9,645,367

Node types:



Variants,

Genes,

Diseases,

Drugs,

ADRs, 


Pathways Relation types:



VAR_ASSOC_DIS,

VAR_IN_GENE,

DRUG_CAUSES_ADR,

GENE_IN_PATH,

DRUG_IN_PATH,

GENE_AFFECTS_DRUG


How to Use



Load the relation-specific triples in triples/ (or the global edge list in edges.*) into your preferred graph ML framework (e.g., PyTorch Geometric, DGL).

Use the mapping tables in id_maps/ (e.g., GENE_ids.csv, DRUG_ids.csv) to translate integer IDs back to canonical biomedical identifiers.

Evaluate models on the curated train/validation/test splits under splits/<REL>/ and report metrics such as MRR, Hits@K, or AUROC.


Source Databases

This dataset was derived from the following resources (not redistributed here):



PharmGKB (https://www.pharmgkb.org/)

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/)

SIDER (http://sideeffects.embl.de/)

Reactome (https://reactome.org/)


License

This processed dataset is released under the CC BY 4.0 License. You are free to share and adapt, provided appropriate credit is given.

Citation

Citation

If you use this dataset, please cite both the dataset and the preprint:





Faruk, M.O. (2025). Pharmacogenomic Knowledge Graph (PGx-KG): Processed Dataset for Link Prediction. Zenodo. https://doi.org/10.5281/zenodo.17189995




Faruk, M.O. (2025). A large-scale pharmacogenomic knowledge graph for drug-gene-variant-disease discovery. medRxiv. https://doi.org/10.1101/2025.09.24.25336269v1
DOI: 10.5281/zenodo.17189995
title: Pharmacogenomic Knowledge Graph (PGx-KG) Dataset

description: Pharmacogenomic Knowledge Graph (PGx-KG) Dataset

This repository contains the processed pharmacogenomic knowledge graph (PGx-KG) prepared for benchmarking link prediction models. The graph integrates curated relationships from PharmGKB, ClinVar, SIDER, and Reactome to standard biomedical vocabularies so that entities and relations align across resources.

Contents



nodes.csv: Consolidated catalogue of biomedical entities with harmonized identifiers, semantic types, and source provenance.

edges.csv: Full edge list covering all relation types with integer IDs referencing the node maps.

triples/: Relation-specific subject–predicate–object triples in CSV format, named as <REL>__HEADTYPE__TAILTYPE.

relations/: Per-relation tables with descriptive metadata, confidence scores, and source annotations.

id_maps/: Mapping tables that link integer IDs to canonical biomedical identifiers (HGNC, RxNorm, MeSH, ChEBI, etc.).

degree/: Per-relation in/out degree distributions for downstream analysis or sampling.

splits/: Stratified train/validation/test partitions for each relation type, with only CSV versions (including reproducible random/ test/train/val).

stats.json: Summary statistics computed after harmonization (entity counts, relation counts,).


Data Statistics

Total nodes: 3,744,727 Total edges: 9,645,367

Node types:



Variants,

Genes,

Diseases,

Drugs,

ADRs, 


Pathways Relation types:



VAR_ASSOC_DIS,

VAR_IN_GENE,

DRUG_CAUSES_ADR,

GENE_IN_PATH,

DRUG_IN_PATH,

GENE_AFFECTS_DRUG


How to Use



Load the relation-specific triples in triples/ (or the global edge list in edges.*) into your preferred graph ML framework (e.g., PyTorch Geometric, DGL).

Use the mapping tables in id_maps/ (e.g., GENE_ids.csv, DRUG_ids.csv) to translate integer IDs back to canonical biomedical identifiers.

Evaluate models on the curated train/validation/test splits under splits/<REL>/ and report metrics such as MRR, Hits@K, or AUROC.


Source Databases

This dataset was derived from the following resources (not redistributed here):



PharmGKB (https://www.pharmgkb.org/)

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/)

SIDER (http://sideeffects.embl.de/)

Reactome (https://reactome.org/)


License

This processed dataset is released under the CC BY 4.0 License. You are free to share and adapt, provided appropriate credit is given.

Citation

Citation

If you use this dataset, please cite both the dataset and the preprint:





Faruk, M.O. (2025). Pharmacogenomic Knowledge Graph (PGx-KG): Processed Dataset for Link Prediction. Zenodo. https://doi.org/10.5281/zenodo.17189995




Faruk, M.O. (2025). A large-scale pharmacogenomic knowledge graph for drug-gene-variant-disease discovery. medRxiv. https://doi.org/10.1101/2025.09.24.25336269v1
DOI: 10.15468/dl.t45qhb
title: Occurrence Download

description: A dataset containing 264 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudagrion microcephalum",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 264 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019032-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cdvmu8
title: Occurrence Download

description: A dataset containing 37778 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ulex minor"
 ]
}

 The dataset includes 37778 records from 843 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019031-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xgisor
title: Occurrence Download

description: A dataset containing 1076 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "TaxonKey is Beilschmiedia tarairi (A.Cunn.) Kirk"
 ]
}

 The dataset includes 1076 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010442-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6hwpd
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aeschynanthus hians C.B.Clarke"
 ]
}

 The dataset includes 30 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017405-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.me4h7f
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dracocephalum multicaule Montbret & Aucher ex Benth."
 ]
}

 The dataset includes 76 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025103-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h15i4t
title: Occurrence Download

description: A dataset containing 3374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Country is Guam"
 ]
}

 The dataset includes 3374 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46jfyv
title: Occurrence Download

description: A dataset containing 5205 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leontodon saxatilis subsp. saxatilis"
 ]
}

 The dataset includes 5205 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047097-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vpcy4e
title: Occurrence Download

description: A dataset containing 2802 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Phylloscopus laetus (Sharpe, 1902)"
 ]
}

 The dataset includes 2802 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025106-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u1ykaz
title: Occurrence Download

description: A dataset containing 1742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Archilochus alexandri (Bourcier & Mulsant, 1846)",
 "Country is Mexico"
 ]
}

 The dataset includes 1742 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxmd9s
title: Occurrence Download

description: A dataset containing 2433 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "TaxonKey is Libythea Fabricius, 1807",
 "Year 2015-2024"
 ]
}

 The dataset includes 2433 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047164-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vyq4qg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diplazium birgeri C.Chr."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025123-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4me9cd
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Succession of benthic hard-bottom communities abundance at station Errina2012_MDD3"
 ]
}

 The dataset includes 110 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a6pqm8
title: Occurrence Download

description: A dataset containing 114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((63.62952 8.85786,134.37048 8.85786,134.37048 37.14214,63.62952 37.14214,63.62952 8.85786))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Argynnis childreni Gray, 1831"
 ]
}

 The dataset includes 114 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047460-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yxrpns
title: Occurrence Download

description: A dataset containing 3067 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dracocephalum nutans L."
 ]
}

 The dataset includes 3067 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025170-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fci8uq
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Fig. 5a) Limacina dissolution index of sediment core GeoB2205-4"
 ]
}

 The dataset includes 30 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tspfqs
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((88.68019 38.77753,152.31981 38.77753,152.31981 64.22247,88.68019 64.22247,88.68019 38.77753))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Erebia ajanensis Ménétriés, 1855"
 ]
}

 The dataset includes 35 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047561-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ya2jxp
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Distephanus inhacensis (G.V.Pope) Boon & Glen"
 ]
}

 The dataset includes 49 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025325-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xk3gzb
title: Occurrence Download

description: A dataset containing 28294 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Francolinus capensis (J.F.Gmelin, 1789)"
 ]
}

 The dataset includes 28294 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4gvu2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Axis axis (Erxleben, 1777))",
 "Country is China",
 "HasCoordinate is true",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025323-240314170635999/datasets/export for details.
DOI: 10.15468/dl.xen743
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((21.68494 8.88730,177.31506 8.88730,177.31506 71.11270,21.68494 71.11270,21.68494 8.88730))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Erebia cyclopius Eversmann, 1844"
 ]
}

 The dataset includes 93 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047562-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpuug8
title: Occurrence Download

description: A dataset containing 10486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "TaxonKey is Beilschmiedia tawa (A.Cunn.) Kirk"
 ]
}

 The dataset includes 10486 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010443-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.