cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7jue8w
title: Occurrence Download

description: A dataset containing 412 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate accuracy invalid, Coordinate precision/uncertainty mismatch, Footprint SRS invalid, Footprint WKT invalid, Country mismatch, Country invalid, Country derived from coordinates, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Continent derived from country, Continent derived from coordinates, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Recorded date unlikely, Taxon match aggregate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, The scientific name differs on the record from that found in the checklist, Taxon match none, The backbone match found using the taxon IDs differs from what would be found if using the scientific names, Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Identified date invalid, Basis of record invalid, Type status invalid, Multimedia date invalid, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status unparsable, Occurrence status inferred from individual count, Occurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy, Institution collection mismatch, Possibly on loan, Different owner institution)",
 "OccurrenceStatus is Present",
 "TaxonKey is Crithagra xanthopygia"
 ]
}

 The dataset includes 412 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015376-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b4vwsh
title: Occurrence Download

description: A dataset containing 26332 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhamnus alpina",
 "Year 1954-2022"
 ]
}

 The dataset includes 26332 records from 196 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015377-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kr6c7h
title: Occurrence Download

description: A dataset containing 8687 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atherina presbyter"
 ]
}

 The dataset includes 8687 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015375-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.64rbf9
title: Occurrence Download

description: A dataset containing 28974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arctotheca calendula",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28974 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015378-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30022240
title: crime_per_1000_pyc.dta

description: Neighborhood-level crime data in 2022, that is spatially disaggregated from municipal-level data from Seoul Metropolitan Police Agency.
DOI: 10.6084/m9.figshare.30022240.v1
title: crime_per_1000_pyc.dta

description: Neighborhood-level crime data in 2022, that is spatially disaggregated from municipal-level data from Seoul Metropolitan Police Agency.
DOI: 10.6084/m9.figshare.27643779.v1
title: <b>Tilapia primers -</b> <b>M</b><b>ulti-</b><b>l</b><b>ocus </b><b>e</b><b>nvironmental DNA </b><b>m</b><b>arkers and </b><b>taxon-s</b><b>pecific </b><b>p</b><b>rimers </b><b>e</b><b>nhance</b><b>d</b><b> </b><b>d</b><b>etection </b><b>rate </b><b>of </b><b>i</b><b>nvasive </b><b>t</b><b>ilapia</b>

description: This file contains amplicons of species specific tilapia primer from environmental DNA in China.
DOI: 10.6084/m9.figshare.30019297
title: Supporting Datasets for: Prediction of Charged Small Molecule Conformations in Solution using a Balanced ML/MM Potential

description: For each dataset, structures were generated by sampling every 1 ps from 20 ns molecular dynamics simulations in the aqueous phase using GAFF. For each structure, gas phase energies and Cartesian atomic forces were evaluated at the B3LYP-D3/6-31+G level of theory and unscaled partial atomic charges determined using the CM5 approach.For each dataset, energies in energies.txt are given in units of kcal/mol, Cartesian atomic forces in forces.txt are given in units of kcal/mol/ångstrom, coordinates in coords.txt are given in units of ångstrom and partial charges in charges.txt are given in units of elementary charge. Nuclear charges, which define the atom ordering, are provided in nuclear_charges.txt.In addition to the "ml_data" folder format used for PairFEQ-Net, datasets are also provided using comma separated values (CSV) format in the ml_data.csv file.
DOI: 10.6084/m9.figshare.30019297.v2
title: Supporting Datasets for: Prediction of Charged Small Molecule Conformations in Solution using a Balanced ML/MM Potential

description: For each dataset, structures were generated by sampling every 1 ps from 20 ns molecular dynamics simulations in the aqueous phase using GAFF. For each structure, gas phase energies and Cartesian atomic forces were evaluated at the B3LYP-D3/6-31+G level of theory and unscaled partial atomic charges determined using the CM5 approach.For each dataset, energies in energies.txt are given in units of kcal/mol, Cartesian atomic forces in forces.txt are given in units of kcal/mol/ångstrom, coordinates in coords.txt are given in units of ångstrom and partial charges in charges.txt are given in units of elementary charge. Nuclear charges, which define the atom ordering, are provided in nuclear_charges.txt.In addition to the "ml_data" folder format used for PairFEQ-Net, datasets are also provided using comma separated values (CSV) format in the ml_data.csv file.
DOI: 10.6084/m9.figshare.30019297.v1
title: Supporting Datasets for Prediction of Charged Small Molecule Conformations in Solution using a Balanced ML/MM Potential

description: For each dataset, structures were generated by sampling every 1 ps from 20 ns molecular dynamics simulations in the aqueous phase using GAFF. For each structure, gas phase energies and Cartesian atomic forces were evaluated at the B3LYP-D3/6-31+G level of theory and unscaled partial atomic charges determined using the CM5 approach.For each dataset, energies in energies.txt are given in units of kcal/mol, Cartesian atomic forces in forces.txt are given in units of kcal/mol/ångstrom, coordinates in coords.txt are given in units of ångstrom and partial charges in charges.txt are given in units of elementary charge. Nuclear charges, which define the atom ordering, are provided in nuclear_charges.txt.In addition to the "ml_data" folder format used for PairFEQ-Net, datasets are also provided using comma separated values (CSV) format in the ml_data.csv file.
DOI: 10.15468/dl.7d9764
title: Occurrence Download

description: A dataset containing 55101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ginkgo biloba"
 ]
}

 The dataset includes 55101 records from 436 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015281-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30022261
title: crime_prevention.dta

description: The number of police stations, police boxes, fire stations, and security centers in 2022, Seoul, South Korea.
DOI: 10.6084/m9.figshare.30022261.v1
title: crime_prevention.dta

description: The number of police stations, police boxes, fire stations, and security centers in 2022, Seoul, South Korea.
DOI: 10.34740/kaggle/dsv/12928716
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.16633987
title: Gene Regulatory Networks of early B cell differentation in Humans

description: Collection of computationally processed and analyzed data from matched transcriptomic (RNA-seq) and epigenomic (ATAC-seq) profiles across eight immune cell populations representing the early lymphoid hematopoietic differentiation cascade along the B-cell lineage in healthy individuals.

Datasets



RNA-seq data - Normalized data, metadata, and gene annotation.

ATAC-seq data - Normalized data, metadata, OCR annotation, and TFBS activity (computed by ChromVAR).

Gene Regulatory Networks - TF-OCR-gene predictions, GRN of B-cell differentiation, single-cell specific GRNs.

TF regulons - TF-target gene data, and TF regulon classification (clustering).


Public data acquisition

Public data used in this study was omitted and must be acquired through the corresponding platform.



Mouse data can be accessed from Gene Expression Omnibus (GEO) for Yoshida H. et al. under the accession GSE109125.

B-ALL data (Li dataset) can be accessed from European Genome-Phenome Archive under the accession EGAD00001002151, EGAD00001002692, and EGAD00001002704.

Additional public B-ALL datasets can be accessed through Gene Expression Omnibus (GEO) for Rainer J., Iacobucci I., Zinngrebe J., and Singh N., under accession GSE73578, GSE13204, GSE140556, and GSE153670, respectively.

Public single-cell data from Chen et al. can be accessed through HTAN (phs002371.v7.p2).

Hi-C data of naive B cells from Vilarrassa-Blasi et al. can be accessed under the accession EGAD00001006486.


Contact information



Núria Planell - nplanellpic@unav.es

David Gomez-Cabrero - david.gomezcabrero@kaust.edu.sa


Please cite our pre-print if you use this resource in your research.
DOI: 10.5281/zenodo.16633986
title: Gene Regulatory Networks of early B cell differentation in Humans

description: Collection of computationally processed and analyzed data from matched transcriptomic (RNA-seq) and epigenomic (ATAC-seq) profiles across eight immune cell populations representing the early lymphoid hematopoietic differentiation cascade along the B-cell lineage in healthy individuals.

Datasets



RNA-seq data - Normalized data, metadata, and gene annotation.

ATAC-seq data - Normalized data, metadata, OCR annotation, and TFBS activity (computed by ChromVAR).

Gene Regulatory Networks - TF-OCR-gene predictions, GRN of B-cell differentiation, single-cell specific GRNs.

TF regulons - TF-target gene data, and TF regulon classification (clustering).


Public data acquisition

Public data used in this study was omitted and must be acquired through the corresponding platform.



Mouse data can be accessed from Gene Expression Omnibus (GEO) for Yoshida H. et al. under the accession GSE109125.

B-ALL data (Li dataset) can be accessed from European Genome-Phenome Archive under the accession EGAD00001002151, EGAD00001002692, and EGAD00001002704.

Additional public B-ALL datasets can be accessed through Gene Expression Omnibus (GEO) for Rainer J., Iacobucci I., Zinngrebe J., and Singh N., under accession GSE73578, GSE13204, GSE140556, and GSE153670, respectively.

Public single-cell data from Chen et al. can be accessed through HTAN (phs002371.v7.p2).

Hi-C data of naive B cells from Vilarrassa-Blasi et al. can be accessed under the accession EGAD00001006486.


Contact information



Núria Planell - nplanellpic@unav.es

David Gomez-Cabrero - david.gomezcabrero@kaust.edu.sa


Please cite our pre-print if you use this resource in your research.
DOI: 10.15468/dl.x7dqeh
title: Occurrence Download

description: A dataset containing 540172 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vicia cracca",
 "Year 1956-2022"
 ]
}

 The dataset includes 540172 records from 2156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015330-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.20747521
title: 107 transconjugants of PromA plasmids

description: This dataset is constructed by 107 draft sequences that obtained by conjugation assay in CD methods with SMDBS harboring PromA plasmids and bacterial communities extracted from soil and/or lake water. <br> <br>
DOI: 10.15156/bio/sh1170607.08fu
title: SH1170607.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1170608.08fu
title: SH1170608.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh617927.07fu
title: SH617927.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh617928.07fu
title: SH617928.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh617929.07fu
title: SH617929.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.25549/one-c4-38877
title: Karen C., letters (1960)

description: Karen C., forms, letter requesting address for The Ladder, published by the Daughters of Bilitis (1960)
DOI: 10.15156/bio/sh1170609.08fu
title: SH1170609.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1170610.08fu
title: SH1170610.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1170611.08fu
title: SH1170611.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh617930.07fu
title: SH617930.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.