cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4y85wp
title: Occurrence Download

description: A dataset containing 33232 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Petaurus breviceps Waterhouse, 1838"
 ]
}

 The dataset includes 33232 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0354234-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rz7x6g
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Pseudacris illinoensis Smith, 1951)"
 ]
}

 The dataset includes 34 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003755-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvjgy3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Magnoliopsida, Liliopsida)",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Geometry MULTIPOLYGON (((-48.24051 1.565064, -48.149 2.092, -48.409 2.334, -48.685 2.319072, -48.792 1.824052, -48.24051 1.565064)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0176519-210914110416597/datasets/export for details.
DOI: 10.15468/dl.gqs32w
title: Occurrence Download

description: A dataset containing 320 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trogoderma variabile Ballion, 1878"
 ]
}

 The dataset includes 320 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016364-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pc7jdm
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-84.24874 -19.40385,-34.75126 -19.40385,-34.75126 0.40385,-84.24874 0.40385,-84.24874 -19.40385))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amburana acreana (Ducke) A.C.Sm."
 ]
}

 The dataset includes 51 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380686-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbwk93
title: Occurrence Download

description: A dataset containing 211244 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Saisie naturaliste opportuniste dans SICEN Occitanie-Données opportunistes du CEN Midi-Pyrénées"
 ]
}

 The dataset includes 211244 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0281996-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7bnfrc
title: Occurrence Download

description: A dataset containing 5566273 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris)"
 ]
}

 The dataset includes 5566273 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018631-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5xt4w
title: Occurrence Download

description: A dataset containing 2194326 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Geometry POLYGON((-82.43649 -20.06478,-67.60491 -20.06478,-67.60491 0.86298,-82.43649 0.86298,-82.43649 -20.06478))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1000-2022"
 ]
}

 The dataset includes 2194326 records from 475 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069179-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xtjw6f
title: Occurrence Download

description: A dataset containing 2501 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phylloscopus claudiae (La Touche, 1922)",
 "Year 1972-2022"
 ]
}

 The dataset includes 2501 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0353179-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mpwvz
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ambystoma mexicanum (Shaw & Nodder, 1798)"
 ]
}

 The dataset includes 247 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012197-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aj2gvs
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus trigonus DC.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069176-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e6g5ve
title: Occurrence Download

description: A dataset containing 3001 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Galerina paludosa (Fr.) Kühner, Galerina stylifera (G.F.Atk.) A.H.Sm. & Singer)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 3001 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0165901-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xdjdda
title: Occurrence Download

description: A dataset containing 2914 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Xylosandrus E.Reitter, 1913)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2914 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010901-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9d8n2j
title: Occurrence Download

description: A dataset containing 2604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Porites lutea Milne Edwards & Haime, 1851"
 ]
}

 The dataset includes 2604 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0435530-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7q2uja
title: Occurrence Download

description: A dataset containing 2344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aythya americana (Eyton, 1838)",
 "Year 2011-2018"
 ]
}

 The dataset includes 2344 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0171276-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mprq68
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dactyloctenium geminatum Hack."
 ]
}

 The dataset includes 392 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019472-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uuav5f
title: Occurrence Download

description: A dataset containing 8680 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myiarchus apicalis P.L.Sclater & Salvin, 1881"
 ]
}

 The dataset includes 8680 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380675-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqtafp
title: Occurrence Download

description: A dataset containing 8590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "GadmGid is BRA.25_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 8590 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0266221-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.by4625
title: Occurrence Download

description: A dataset containing 593345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "GadmGid is ESP.1.8_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 593345 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012203-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5a35hw
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus chihuahuana Engelm."
 ]
}

 The dataset includes 542 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002422-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9qu8nn
title: Occurrence Download

description: A dataset containing 18840 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Vertebrate Zoology Division - Mammalogy, Yale Peabody Museum"
 ]
}

 The dataset includes 18840 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204049-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.azgfmp
title: Occurrence Download

description: A dataset containing 2764 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oreochromis niloticus (Linnaeus, 1758)",
 "Year 2020-2023"
 ]
}

 The dataset includes 2764 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016368-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5r8w5s
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Proechimys roberti Thomas, 1901"
 ]
}

 The dataset includes 483 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0354043-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zke82s
title: Occurrence Download

description: A dataset containing 6981999 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is China"
 ]
}

 The dataset includes 6981999 records from 4512 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175327-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wc4hrb
title: Occurrence Download

description: A dataset containing 916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (South Africa, Lesotho, Eswatini)",
 "TaxonKey is one of (Cisticola rufilatus (Hartlaub, 1870))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 916 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005043-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g66qty
title: Occurrence Download

description: A dataset containing 5457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (South Africa, Lesotho, Eswatini)",
 "TaxonKey is one of (Promerops gurneyi J.Verreaux, 1871)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 5457 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005045-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10574533
title: Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization.

description: The source data and code of the paper "Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization".



## KGDRP: Interpretable drug response prediction with biomedical networks accelerates phenotypic drug discovery and drug target prioritization


We present a knowledge graph-based multimodal data fusion framework for predicting drug responses, named KGDRP. This framework seamlessly integrates multiple omics data, including network data containing biological system information, gene expression data coupled with phenotypic information, and sequence data incorporating chemical molecular structures, within a heterogeneous graph structure.


## System Requirements


The source code developed in Python 3.6.13 using PyTorch 1.10.1. The required python dependencies are given below. KGDRP is supported for any standard computer and operating system with enough RAM to run. There is no additional non-standard hardware requirements.


```

torch = 1.10.1

dgl = 0.8.2

numpy = 1.19.5

scikit-learn = 0.24.2

pandas = 1.1.5

tqdm = 4.64.0

scipy = 1.5.4

optuna = 2.10.1

```


## Instructions for Use


##### Knowledge graph and drug response data used in this work provided in the ./data/ folder

+ Knowledge graph: dppc_kg.csv

+ CV folds of drug response data:

+ ./data/cv_mix/

+ ./data/cv_cell/

+ ./data/cv_drug/

+ ./data/cv_both/

+ Drug ID map file: cid_infor.csv

+ Feature of cell-lines: rna_input.csv

+ Edges of gene-cell-lines for KG construction: rna_triples.csv

+ Feature of drugs: bdki_db_gdsc_fp.csv

+ Negative samples of protein-pathway: pro_path_neg_sp.csv

+ Negative samples of protein-pathway: neg_dpi_df_t10.csv


#### Hyper-parameter

The hyper-parameter script is located in the ./src/ folder.

**Noted:** To implement heterogeneous message passing, replace the hetero.py file located at ./anaconda3/envs/env_name/lib/python3.6/site-packages/dgl/nn/pytorch/hetero.py with the version provided in the ./src/ folder.


The script is compatible with both CPU and GPU architectures. A single run of the script typically requires approximately 30 minutes to complete.


## License


[MIT](https://choosealicense.com/licenses/mit/)
DOI: 10.5281/zenodo.10657753
title: Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization.

description: The source data and code of the paper "Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization".



## KGDRP: Interpretable drug response prediction with biomedical networks accelerates phenotypic drug discovery and drug target prioritization


We present a knowledge graph-based multimodal data fusion framework for predicting drug responses, named KGDRP. This framework seamlessly integrates multiple omics data, including network data containing biological system information, gene expression data coupled with phenotypic information, and sequence data incorporating chemical molecular structures, within a heterogeneous graph structure.


## System Requirements


The source code developed in Python 3.6.13 using PyTorch 1.10.1. The required python dependencies are given below. KGDRP is supported for any standard computer and operating system with enough RAM to run. There is no additional non-standard hardware requirements.


```

torch = 1.10.1

dgl = 0.8.2

numpy = 1.19.5

scikit-learn = 0.24.2

pandas = 1.1.5

tqdm = 4.64.0

scipy = 1.5.4

optuna = 2.10.1

```


## Instructions for Use


##### Knowledge graph and drug response data used in this work provided in the ./data/ folder

+ Knowledge graph: dppc_kg.csv

+ CV folds of drug response data:

+ ./data/cv_mix/

+ ./data/cv_cell/

+ ./data/cv_drug/

+ ./data/cv_both/

+ Drug ID map file: cid_infor.csv

+ Feature of cell-lines: rna_input.csv

+ Edges of gene-cell-lines for KG construction: rna_triples.csv

+ Feature of drugs: bdki_db_gdsc_fp.csv

+ Negative samples of protein-pathway: pro_path_neg_sp.csv

+ Negative samples of protein-pathway: neg_dpi_df_t10.csv


#### Hyper-parameter

The hyper-parameter script is located in the ./src/ folder.

**Noted:** To implement heterogeneous message passing, replace the hetero.py file located at ./anaconda3/envs/env_name/lib/python3.6/site-packages/dgl/nn/pytorch/hetero.py with the version provided in the ./src/ folder.


The script is compatible with both CPU and GPU architectures. A single run of the script typically requires approximately 30 minutes to complete.


## License


[MIT](https://choosealicense.com/licenses/mit/)
DOI: 10.5281/zenodo.8394247
title: Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization.

description: The source data and code of the paper "Graph deep learning paradigm integrating biomedical networks for phenotypic drug discovery and target prioritization".



## KGDRP: Interpretable drug response prediction with biomedical networks accelerates phenotypic drug discovery and drug target prioritization


We present a knowledge graph-based multimodal data fusion framework for predicting drug responses, named KGDRP. This framework seamlessly integrates multiple omics data, including network data containing biological system information, gene expression data coupled with phenotypic information, and sequence data incorporating chemical molecular structures, within a heterogeneous graph structure.


## System Requirements


The source code developed in Python 3.6.13 using PyTorch 1.10.1. The required python dependencies are given below. KGDRP is supported for any standard computer and operating system with enough RAM to run. There is no additional non-standard hardware requirements.


```

torch = 1.10.1

dgl = 0.8.2

numpy = 1.19.5

scikit-learn = 0.24.2

pandas = 1.1.5

tqdm = 4.64.0

scipy = 1.5.4

optuna = 2.10.1

```


## Instructions for Use


##### Knowledge graph and drug response data used in this work provided in the ./data/ folder

+ Knowledge graph: dppc_kg.csv

+ CV folds of drug response data:

+ ./data/cv_mix/

+ ./data/cv_cell/

+ ./data/cv_drug/

+ ./data/cv_both/

+ Drug ID map file: cid_infor.csv

+ Feature of cell-lines: rna_input.csv

+ Edges of gene-cell-lines for KG construction: rna_triples.csv

+ Feature of drugs: bdki_db_gdsc_fp.csv

+ Negative samples of protein-pathway: pro_path_neg_sp.csv

+ Negative samples of protein-pathway: neg_dpi_df_t10.csv


#### Hyper-parameter

The hyper-parameter script is located in the ./src/ folder.

**Noted:** To implement heterogeneous message passing, replace the hetero.py file located at ./anaconda3/envs/env_name/lib/python3.6/site-packages/dgl/nn/pytorch/hetero.py with the version provided in the ./src/ folder.


The script is compatible with both CPU and GPU architectures. A single run of the script typically requires approximately 30 minutes to complete.


## License


[MIT](https://choosealicense.com/licenses/mit/)
DOI: 10.15468/dl.x3swsy
title: Occurrence Download

description: A dataset containing 84462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myocastor coypus (Molina, 1782)",
 "Country is France",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 84462 records from 1707 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005044-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/fbq-9pa-yve
title: Lathyrus palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fbq-a08-81x
title: Lepidium densiflorum Schrad.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.