cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.m6xhqc
title: Occurrence Download

description: A dataset containing 3313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Procyon Storr, 1780"
 ]
}

 The dataset includes 3313 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032012-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2u38w9
title: Occurrence Download

description: A dataset containing 96984 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Parapolybia indica (de Saussure, 1854), Fanjinga digitata Yu & Yang, 2020, Cerceris californica Cresson, 1865, Leucoptera oxyphyllella (Kuroko, 1964), Encarsia brimblecombei (Girault, 1933), Varieganecroscia sineocula sineocula, Haemulon aurolineatum Cuvier, 1830, Pleuronectes quadrituberculatus Pallas, 1814, Rothschildia tucumani Dognin, 1901, Spragueia apicalis (Herrich-Schäffer, 1868), Bucculatrix eupatoriella Braun, 1918, Aristotelia eupatoriella Busck, 1934, Actinote carycina, Epistrophe nitidicollis (Meigen, 1822), Saptha libanota Meyrick, 1910, Pygarctia murina Stretch, 1885, Simyra dentinosa Freyer, 1839, Promalactis isothea Meyrick, 1930, Singhalia cymogramma Meyrick, 1933, Chamaesphecia cyanopasta (Hampson, 1910), Platypleura chalybaea Villet, 1989, Psychonotis caelius (Felder, 1860), Formica moki Wheeler, 1906, Camponotus micans (Nylander, 1856), Phytometra viridaria (Clerck, 1759), Tenthredo bifasciata O.F.Muller, 1766, Trichopoda indivisa Townsend, 1897, Adela australis Herrich-Schäffer, 1855, Stomorhina discolor (Fabricius, 1794), Baryscapus euphorbiae Graham, 1991, Bruchophagus bajariae (Erds, 1957), Leptomastix tanasijtshuki Sharkov, 1983, Eretmocerus evansi Myartseva, 2006, Homoporus verticalis Dzhanokmen, 1999, Aprostocetus capitigenae Graham, 1987, Coccobius euphorbiae (Risbec, 1957), Metaphycus sigillatus Annecke & Mynhardt, 1981, Encarsia peltata (Cockerell, 1911), Leucospis biguetina Jurine, 1807, Viscum minimum Harv., Hydnora africana Thunb., Lasioglossum pallens (Brullé, 1832), Aphthona melancholica Weise, 1888, Aphthona atrocaerulea (Stephens, 1831), Chamaesphecia iranica Le Cerf, 1937, Aphthona euphorbiae (Schrank, 1781), Dasymutilla monticola (Cresson, 1865) Cresson, 1865, Chamaesphecia guriensis (Emich von Emöke, 1872), Uromyces tinctoriicola Magnus, Trichomalus posticus (Walker, 1834))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 96984 records from 854 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031997-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3-acxa-a965
title: BoardEx Reports - Director Profiles - Set 1 - 2019 April

description: Director Profiles provide data on individual directors by ID number including: age, gender, education, number of boards on, achievements, board role ( current and historic), and other activities (current and historic). Data back to 1999 when available. Includes: North America (NA) - Director Profile - Characteristics (2 files); North America (NA) - Director Profile - Education & Achievements; North America (NA) - Director Profile - Employment Current Board; North America (NA) - Employment Current NonBoard; North America (NA) - Director Profile - Employment Historical Board (2 files); North America (NA) - Director Profile - Employment Historical NonBoard (2 files); North America (NA) - Director Profile - Other Activities.
DOI: 10.5281/zenodo.11398546
title: RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing

description: This dataset accompanies the study "RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing". The study introduces RepliChrom, a computational framework designed to predict enhancer–promoter interactions (EPIs) by leveraging multi-scale replication timing (RT) signals. This approach addresses the fundamental challenge of distinguishing gene targets regulated by distal enhancers from those activated by proximal transcriptional activity-a key problem in understanding the causal basis of complex diseases.

Despite recent advances in high-throughput technologies such as Hi-C, ChIA-PET, and Hi-TrAC that allow genome-wide reconstruction of 3D chromatin architecture, the role of DNA replication timing in mediating these spatial interactions remains underexplored. RepliChrom fills this gap by using cell-type-specific RT profiles as predictive features for chromatin interaction inference.

To support model development, training, and evaluation, we provide a comprehensive multi-omics dataset covering six human cell lines (K562, GM12878, HeLaS3, IMR90, NHEK, and HUVEC ), encompassing:

Hi-C datasets: Processed chromatin interaction loops used to define positive and negative enhancer–promoter interaction pairs.

ChIA-PET datasets: Interaction data anchored around transcription factor binding, including POLR2A and CTCF, used for model validation across different interaction types.

Hi-TrAC datasets: Targeted chromatin accessibility-derived interaction data, offering complementary validation of the model on alternate platforms.

Replication Timing (RT) data: Processed RT signal profiles for each cell line, used to extract multi-scale temporal features as inputs for RepliChrom.

These datasets enable reproducibility of the model training process and serve as benchmark resources for future research into DNA replication–mediated regulation of 3D genome architecture.

Included Files

Hi-C_datasets.zip (2.23 MB): Processed Hi-C interaction pairs for six cell types.

ChIA-PET_datasets.zip (818.18 KB): CTCF and POLR2A ChIA-PET interactions across multiple lines.

Hi-TrAC_datasets.zip (196 bytes): Hi-TrAC-based chromatin interaction training datasets across multiple lines.

Cellline_RT_data.zip (86.17 MB): Replication timing signal data across multiple human cell types for multi-scale replication timing feature extraction.

UsageAll datasets are intended for academic, non-commercial use. The provided files can be directly used to reproduce the training and evaluation of RepliChrom, and may also support broader applications in enhancer–promoter modeling, replication-timing analysis, and 3D genomics studies. For detailed usage instructions and code implementation, please refer to the GitHub repository: https://github.com/DaoFuying/RepliChrom
DOI: 10.5281/zenodo.11398547
title: RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing

description: This dataset accompanies the study "RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing". The study introduces RepliChrom, a computational framework designed to predict enhancer–promoter interactions (EPIs) by leveraging multi-scale replication timing (RT) signals. This approach addresses the fundamental challenge of distinguishing gene targets regulated by distal enhancers from those activated by proximal transcriptional activity-a key problem in understanding the causal basis of complex diseases.

Despite recent advances in high-throughput technologies such as Hi-C, ChIA-PET, and Hi-TrAC that allow genome-wide reconstruction of 3D chromatin architecture, the role of DNA replication timing in mediating these spatial interactions remains underexplored. RepliChrom fills this gap by using cell-type-specific RT profiles as predictive features for chromatin interaction inference.

To support model development, training, and evaluation, we provide a comprehensive multi-omics dataset covering six human cell lines (K562, GM12878, HeLaS3, IMR90, NHEK, and HUVEC ), encompassing:

Hi-C datasets: Processed chromatin interaction loops used to define positive and negative enhancer–promoter interaction pairs.

ChIA-PET datasets: Interaction data anchored around transcription factor binding, including POLR2A and CTCF, used for model validation across different interaction types.

Hi-TrAC datasets: Targeted chromatin accessibility-derived interaction data, offering complementary validation of the model on alternate platforms.

Replication Timing (RT) data: Processed RT signal profiles for each cell line, used to extract multi-scale temporal features as inputs for RepliChrom.

These datasets enable reproducibility of the model training process and serve as benchmark resources for future research into DNA replication–mediated regulation of 3D genome architecture.

Included Files

Hi-C_datasets.zip (2.23 MB): Processed Hi-C interaction pairs for six cell types.

ChIA-PET_datasets.zip (818.18 KB): CTCF and POLR2A ChIA-PET interactions across multiple lines.

Hi-TrAC_datasets.zip (196 bytes): Hi-TrAC-based chromatin interaction training datasets across multiple lines.

Cellline_RT_data.zip (86.17 MB): Replication timing signal data across multiple human cell types for multi-scale replication timing feature extraction.

UsageAll datasets are intended for academic, non-commercial use. The provided files can be directly used to reproduce the training and evaluation of RepliChrom, and may also support broader applications in enhancer–promoter modeling, replication-timing analysis, and 3D genomics studies. For detailed usage instructions and code implementation, please refer to the GitHub repository: https://github.com/DaoFuying/RepliChrom
DOI: 10.21227/2gjh-7278
title: "S3DIS"

description: "S3DIS is composed of five large-scale indoor areas from three different buildings, each covering approximately 1900, 450, 1700, 870 and 1100 square meters (total of 6020 square meters). These areas show diverse properties in architectural style and appearance and include mainly office areas, educational and exhibition spaces, and conference rooms, personal offices, restrooms, open spaces, lobbies, stairways, and hallways are commonly found therein. One of the areas includes multiple floors, whereas the rest have one. The entire point clouds are automatically generated without any manual intervention using the Matterport scanner. It has 12 semantic elements, which are structural elements (ceiling, floor, wall, beam, column, window and door) and commonly found items and furniture (table, chair, sofa, bookcase and board). "
DOI: 10.15468/dl.y99kgg
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bursera martae J.Jiménez Ram. & Cruz Durán"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032016-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pt8xwt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodiola litwinowii Boriss.",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032018-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcn3ua
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodiola gelida Schrenk ex Fisch. & C.A.Mey.",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)"
 ]
}

 The dataset includes 52 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032017-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c52z2u
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bursera mirandae C.A.Toledo"
 ]
}

 The dataset includes 186 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032021-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.68pkw5
title: Occurrence Download

description: A dataset containing 3349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bursera microphylla A.Gray"
 ]
}

 The dataset includes 3349 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032019-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dftgtt
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodiola recticaulis Boriss.",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032020-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3gm81r35
title: BoardEx Reports - Company Profiles - 2016 May

description: Company details include capitalization, revenue and auditors. Includes:<br> Europe - Company Details <br> North America (NA) - Company Details <br> Rest of World (ROW) - Company Details <br> UK - Company Details <br>
DOI: 10.15468/dl.fknezm
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Zamia soconuscensis Schutzman, Vovides & Dehgan"
 ]
}

 The dataset includes 56 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032023-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nzjnt
title: Occurrence Download

description: A dataset containing 363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bursera multijuga Engl."
 ]
}

 The dataset includes 363 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032026-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z4fcwc
title: Occurrence Download

description: A dataset containing 1036 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-140.44338 8.20101,-41.55662 8.20101,-41.55662 47.79899,-140.44338 47.79899,-140.44338 8.20101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dendroctonus frontalis Zimmermann, 1868"
 ]
}

 The dataset includes 1036 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032027-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nzz63f
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bursera multifolia (Rose) Engl."
 ]
}

 The dataset includes 67 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032025-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.reme69
title: Occurrence Download

description: A dataset containing 906 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Bursera morelensis Ramírez, Bursera morelense Ramirez)"
 ]
}

 The dataset includes 906 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032024-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15085088
title: Example outputs from a realistic global ocean configuration of MOM6, used to demonstrate calculations like Water Mass Transformation Budgets.

description: This data repository contains the following files:



`MOM6_global_example_diagnostics_zlevels_v0_0_6.nc`: Various outputs (including closed mass, heat, and salt budgets) from the Modular Ocean Model, version 6 (MOM6), conservatively binned (online) into depth coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_transports_zlevels_v0_0_6.nc`: Horizontal mass transport from the Modular Ocean Model, version 6 (MOM6) conservatively binned (online) into depth coordinates and averaged over 12 months.

`MOM6_global_example_potdensity_zlevels_v0_0_6.nc`: Potential density field (referenced to 2000 dbar) from the Modular Ocean Model, version 6 (MOM6) conservatively binned (online) into depth coordinates and averaged over 12 months.

`MOM6_global_example_vertically_integrated_mass_budget_v0_0_6.nc`: Vertically-integrated mass budget tendencies and mass transports from the Modular Ocean Model, version 6 (MOM6), averaged over 12 months.

`MOM6_global_example_vertically_integrated_heat_budget_v0_0_6.nc`: Vertically-integrated heat budget tendencies and heat transports from the Modular Ocean Model, version 6 (MOM6), averaged over 12 months.

`MOM6_global_example_surface_fluxes_v0_0_7.nc`: Surface heat, salt, and freshwater mass fluxes from the Modular Ocean Model, version 6 (MOM6), monthly-averaged on the native horizontal grid.

`MOM6_global_example_sigma2_budgets_v0_0_6.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) conservatively binned (offline) into density coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_sigma2_wmb_v0_0_6.nc`: Globally-integrated water mass budget as a function of potential density referenced to 2000 dbar, as computed by v0.2.3 of `xwmb` from the diagnostics provided in the budgets file above. The methdology for computing the water mass budgets is described in Drake et al. (2025).


These files are used to generate the iPython notebooks that serve as documentation for `xwmb` and several of its dependent packages, such as `sectionate`, `regionate`, `xbudget`, and `xwmt`.
DOI: 10.5281/zenodo.15085089
title: Example ocean mass, heat, and budget diagnostics, as required for Water Mass Transformation budget calculations

description: This data repository contains two files:



`MOM6_global_example_diagnostics.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) pre-binned into density coordinates, and conservatively coarsened in the horizontal and averaged in time

`MOM6_global_example_wmb.nc`: Globally-integrated water mass budget as a function of potential density referenced to 2000 dbar, as computed by v0.2.3 of `xwmb` from the diagnostics in the above file. The methdology for computing the water mass budgets is described in Drake et al. (2025).


These files are used to generate the iPython notebooks that serve as documentation for `xwmb` and several of its dependent packages, such as `sectionate`, `regionate`, `xbudget`, and `xwmt`.
DOI: 10.5281/zenodo.15086631
title: Example ocean mass, heat, and budget diagnostics, for example as required for Water Mass Transformation budget calculations

description: This data repository contains the following files:



`MOM6_global_example_diagnostics_zlevels.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) conservatively binned (online) into depth coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_diagnostics.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) conservatively binned (offline) into density coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_wmb.nc`: Globally-integrated water mass budget as a function of potential density referenced to 2000 dbar, as computed by v0.2.3 of `xwmb` from the diagnostics in the above file. The methdology for computing the water mass budgets is described in Drake et al. (2025).


These files are used to generate the iPython notebooks that serve as documentation for `xwmb` and several of its dependent packages, such as `sectionate`, `regionate`, `xbudget`, and `xwmt`.
DOI: 10.5281/zenodo.15117174
title: Example outputs from a realistic global ocean configuration of MOM6, used to demonstrate calculations like Water Mass Transformation Budgets.

description: This data repository contains the following files:



`MOM6_global_example_coasened_diagnostics_zlevels.nc`: Various outputs (including closed mass, heat, and salt budgets) from the Modular Ocean Model, version 6 (MOM6), conservatively binned (online) into depth coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_density_and_mass_transports_zlevels.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) conservatively binned (online) into depth coordinates and averaged over 12 months.

`MOM6_global_example_vertically_integrated_mass_budget.nc`: Vertically-integrated mass budget tendencies and mass transports from the Modular Ocean Model, version 6 (MOM6), averaged over 12 months.

`MOM6_global_example_coarsened_sigma2_budgets.nc`: Outputs from the Modular Ocean Model, version 6 (MOM6) conservatively binned (offline) into density coordinates, conservatively coarsened in the horizontal, and averaged over 12 months.

`MOM6_global_example_coarsened_sigma2_wmb.nc`: Globally-integrated water mass budget as a function of potential density referenced to 2000 dbar, as computed by v0.2.3 of `xwmb` from the diagnostics provided in the . The methdology for computing the water mass budgets is described in Drake et al. (2025).


These files are used to generate the iPython notebooks that serve as documentation for `xwmb` and several of its dependent packages, such as `sectionate`, `regionate`, `xbudget`, and `xwmt`.