cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.wsck3c
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinoneoida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261119-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ymfkx
title: Occurrence Download

description: A dataset containing 778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cenchrus pilosus Kunth)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 778 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066901-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.csh66k
title: Occurrence Download

description: A dataset containing 3341810 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "PublishingOrg is e2e717bf-551a-4917-bdc9-4fa0f342c530",
 "TaxonKey is one of (Bubo bubo (Linnaeus, 1758), Bubulcus ibis (Linnaeus, 1758), Burhinus oedicnemus (Linnaeus, 1758), Buteo buteo (Linnaeus, 1758), Buteo rufinus (Cretzschmar, 1829))"
 ]
}

 The dataset includes 3341810 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265788-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p45mdq
title: Occurrence Download

description: A dataset containing 200362 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chroicocephalus ridibundus (Linnaeus, 1766)",
 "HasCoordinate is true",
 "Country is Norway",
 "DatasetKey is Norwegian Species Observation Service",
 "Year is greater than or equal to 1990",
 "Year is less than or equal to 2022",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 200362 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0253953-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cb6wqb
title: Occurrence Download

description: A dataset containing 223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cidaroida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 223 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261112-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jsmn3b
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron ferrugineum L."
 ]
}

 The dataset includes 106 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265758-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vc79sc
title: Occurrence Download

description: A dataset containing 11236 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((389.53245 44.98627,389.45361 44.94467,389.60193 44.82727,389.67142 44.89925,389.53245 44.98627))"
 ]
}

 The dataset includes 11236 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010511-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdner4
title: Occurrence Download

description: A dataset containing 1304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1304 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010513-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e3mbs4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Spizella passerina)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010514-250711103210423/datasets/export for details.
DOI: 10.6084/m9.figshare.29558105.v1
title: modified IEEE 24-bus electric system and Belgian 20-node natural gas system

description: modified IEEE 24-bus electric system and Belgian 20-node natural gas system
DOI: 10.15468/dl.35e9cu
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADE2445"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010517-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cervq9
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Poland, Finland)",
 "TaxonKey is Mutatoderma mutatum"
 ]
}

 The dataset includes 41 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010516-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcj8rf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ctenopharyngodon idella",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010520-250711103210423/datasets/export for details.
DOI: 10.5281/zenodo.15719002
title: Dataset: Finite groups of symplectic birational transformations of IHS manifolds of OG10 type

description: Dataset for the finite symplectic birational actions on IHS manifolds of OG10 type.

Contains the data related to the paper, a list of Jupyter notebooks for demonstrating some of the computations, two extra tables recording information about the entries of the dataset, and a file containing a list of exceptional lattices (in the wording of the paper). 

Read the README.md for more information.
DOI: 10.5281/zenodo.10039504
title: Dataset: Finite groups of symplectic birational transformations of IHS manifolds of OG10 type

description: Dataset for the finite symplectic birational actions on IHS manifolds of OG10 type.

Contains the data related to the paper, a list of Jupyter notebooks for demonstrating some of the computations, two extra tables recording information about the entries of the dataset, and a file containing a list of exceptional lattices (in the wording of the paper). 

Read the README.md for more information.
DOI: 10.15468/dl.y3u2xv
title: Occurrence Download

description: A dataset containing 5513 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crataegus mollis"
 ]
}

 The dataset includes 5513 records from 185 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010519-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/sg5spw
title: Swedish Bird Survey: Swedish coastal bird monitoring programme (Nationella kustfågelövervakningen)

description: The Swedish coastal bird monitoring programme (aka the ”Archipelago squares”/”Kustfågelrutorna”) is one of several schemes within the Swedish Bird Survey (see below), run by the Department of Biology at Lund University.The survey scheme was initiated in 2015 as a standardized method for detecting and reporting changes in the abundance of coastal and archipelagic birds and their distributions in Sweden over time.The 200 archipelago squares are distributed along the Swedish coastline and are surveyed during the breeding season.In this dataset, some information is placed in the table ExtendedMeasurementOrFacts (eMoF), which is part of the Source Archive available to download directly from the dataset’s page here on gbif.org. The Source Archive contains the data exactly as uploaded to gbif (verbatim). Should you choose to download the dataset as GBIF Annotated Archive instead, the data has been interpreted and quality controlled by gbif, but, the data in the eMoF will not be included as the eMoF extension is not yet supported by gbif.
DOI: 10.6084/m9.figshare.29558105
title: modified IEEE 24-bus electric system and Belgian 20-node natural gas system

description: modified IEEE 24-bus electric system and Belgian 20-node natural gas system
DOI: 10.25592/uhhfdm.17709
title: Literature Dataset for Technology Adoption and Platform & Ecosystems

description: Those two datasets consisting of publications in the context of technology adoption research as well as research in the context of digital platforms and ecosystems. The datasets were used for a bibliometrics analysis.
DOI: 10.25592/uhhfdm.17708
title: Literature Dataset for Technology Adoption and Platform & Ecosystems

description: Those two datasets consisting of publications in the context of technology adoption research as well as research in the context of digital platforms and ecosystems. The datasets were used for a bibliometrics analysis.
DOI: 10.15468/dl.v2yqr2
title: Occurrence Download

description: A dataset containing 11640921 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is China"
 ]
}

 The dataset includes 11640921 records from 5256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010387-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mj4xpr
title: Occurrence Download

description: A dataset containing 3214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Mauritia flexuosa L.f."
 ]
}

 The dataset includes 3214 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089331-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a5dbma
title: Occurrence Download

description: A dataset containing 1310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rosa multiflora var. cathayensis Rehder & E.H.Wilson)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1310 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089332-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bmgnp
title: Occurrence Download

description: A dataset containing 3124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aruncus sylvester Kostel.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3124 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089333-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fephgq
title: Occurrence Download

description: A dataset containing 8967 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Prunus domestica subsp. domestica)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8967 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089334-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8fnfx5
title: Occurrence Download

description: A dataset containing 21209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, Svalbard and Jan Mayen, Portugal, Spain, France, Germany, Belgium, Netherlands, Denmark, Estonia, Latvia, Lithuania, Italy, Greece, Cyprus, Türkiye, Russian Federation, Ukraine, Romania, Bulgaria, Albania, Croatia, Austria, Slovakia, Poland)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phleum arenarium L."
 ]
}

 The dataset includes 21209 records from 272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089335-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgjzv7
title: Occurrence Download

description: A dataset containing 200488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cenchrus L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 200488 records from 1089 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089328-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nj3cna
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Seligeria tristichoides",
 "Country is one of (Norway)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1986",
 "Year is less than or equal to 2025",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "not" : {
 "BasisOfRecord" : [
 "is Machine Observation"
 ]
 }
 }
 ]
}

 The dataset includes 99 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023760-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10597357
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622

 

V5: Fixed bug in calculation of profile attribution scores causing them to be off by a factor of exactly 500. Genome-wide DeepSHAP tracks & TF-MoDISco tracks have been accordingly updated. I have not updated the individual examples, as these can be quickly fixed by simply multiplying by 500 when plotting. Additionally, I have uploaded profile and quantity motif calls, which contain genome-wide seqlet annotations. The columns in these files are [chrom, start, end, peak_idx, motif_annotation].

V4: Uploaded individual bigWigs. These have been lifted over using CrossMap from the original hg19 (GSE110638) to hg38 and RPM normalized.

V3: Final version prior to journal submission. Don't recall exact details of what's changed.

V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.
DOI: 10.5281/zenodo.10597358
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622
DOI: 10.5281/zenodo.13771189
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622

 

V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.
DOI: 10.5281/zenodo.14037372
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622

 

V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.
DOI: 10.5281/zenodo.14751249
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622

 

V4: Uploaded individual bigWigs. These have been lifted over using CrossMap from the original hg19 (GSE110638) to hg38 and RPM normalized.

V3: Final version prior to journal submission. Don't recall exact details of what's changed.

V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.
DOI: 10.5281/zenodo.15117438
title: Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)

description: This contains data necessary to reproduce the figures in the CLIPNET paper (preprint here) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: https://github.com/Danko-Lab/clipnet_paper/

 

Pretrained CLIPNET models are archived separately at DOI 10.5281/zenodo.10408622

 

V5: Fixed bug in calculation of profile attribution scores causing them to be off by a factor of exactly 500. Genome-wide DeepSHAP tracks & TF-MoDISco tracks have been accordingly updated. I have not updated the individual examples, as these can be quickly fixed by simply multiplying by 500 when plotting. Additionally, I have uploaded profile and quantity motif calls, which contain genome-wide seqlet annotations. The columns in these files are [chrom, start, end, peak_idx, motif_annotation].

V4: Uploaded individual bigWigs. These have been lifted over using CrossMap from the original hg19 (GSE110638) to hg38 and RPM normalized.

V3: Final version prior to journal submission. Don't recall exact details of what's changed.

V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.
DOI: 10.5281/zenodo.14039937
title: NBM: an Open Dataset for the Acoustic Monitoring of Nocturnal Migratory Birds in Europe

description: This is the dataset presented in the paper "NBM: an Open Dataset for the Acoustic Monitoring of Nocturnal Migratory Birds in Europe", which can be found here: https://arxiv.org/pdf/2412.03633.

 

File description

Files come in three directories: train_nbm_orig, train_nbm_xc and test.

Each is composed of a list of .wav files with its .txt annotations file in time and frequency.

The train dataset is composed of a total of  2,077 audio files and 13,359 annotations, for a total of ~38 hours of recording. Among these, 883 files were downloaded from Xeno-canto and finely hand-annotated.

 

Citation (Bibtex)

@article{airale2024nbm,
  title={NBM: an Open Dataset for the Acoustic Monitoring of Nocturnal Migratory Birds in Europe},
  author={Airale, Louis and Pajot, Adrien and Linossier, Juliette},
  journal={arXiv preprint arXiv:2412.03633},
  year={2024}
}