cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29287496.v1
title: Data from: The number of days required for egg hatching under five different temperature conditions (15°C, 20°C, 25°C, 30°C and 32°C) in social spider mites

description: Dataset of the number of days required for egg hatching under five different temperature conditions (15°C, 20°C, 25°C, 30°C and 32°C) in social spider mites: <i>Stigmaeopsis miscanthi</i> mild aggression (ML) form, <i>Stigmaeopsis miscanthi</i> high aggression (HG) form and <i>Stigmaeopsis sabelisi</i>, which were used for analysis in the paper entitled "Phenotypic variability and thermal adaptation in social spider mites: Insights into speciation and local adaptation".
DOI: 10.5281/zenodo.17142258
title: Randomly generated Flatland environments with increasing difficulty

description: Randomly generated environments for Flatland with increasing difficulty. The set was created following the specifications from the Flatland 3 Challenge.
DOI: 10.5281/zenodo.17151039
title: Summary statistics for dementia WGS
DOI: 10.15468/dl.etmnam
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Satureja hortensis",
 "Country is Bulgaria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014712-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6dffj2
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platyceps plinii"
 ]
}

 The dataset includes 52 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014715-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qgug5d
title: Occurrence Download

description: A dataset containing 4681 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ptyas mucosa"
 ]
}

 The dataset includes 4681 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014717-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15782956
title: CaP cells: μCT geometry, OpenFOAM case

description: This archive contains the input data and OpenFOAM case needed to reproduce the permeability results reported in "A novel upscaling approach for efficient permeability estimation of tight sandstones from large digital rock models" 

All simulations were conducted using OpenFOAM v2406 (https://www.openfoam.com/news/main-news/openfoam-v2406) Geometry/sandstone_image.raw - 1000×1000×1000-voxel RAW volume,Geometry/sandstone_pore_surf.stl - STL surface mesh of the same volume, Geometry/cubic_subdivision - folder with cubic subdivision geometry in STL format Geometry/flow-parallel - folder with flow-parallel subdivision geometry in STL formatGeometry/flow-orthogonal - folder with flow-orthogonal subdivision geometry in STL format

Openfoam_case/ - complete steady-state single-phase flow case (OpenFOAM v2406)

How to run the case: 



Navigate to the OpenFOAM case directory cd $FOAM_RUN/CaP_cells_directory/Openfoam_case

Copy the STL file from a chosen geometry into constant/triSurface/, for example:cp ../Geometry/cubic_subdivision/cubic1.stl constant/triSurface/mv constant/triSurface/cubic1.stl constant/triSurface/test2.stl(The geometry file must be renamed to test2.stl — this is the expected name configured in snappyHexMeshDict)

Adjust blockMeshDict according to the bounding box of the selected geometry. 

Optionally, adjust boundary conditions in the 0/ directory.

Run the simulation using the provided script: ./run.sh
DOI: 10.5281/zenodo.16382051
title: CaP cells: μCT geometry, OpenFOAM case

description: This archive contains the input data and OpenFOAM case needed to reproduce the permeability results reported in "A novel upscaling approach for efficient permeability estimation of tight sandstones from large digital rock models" 

All simulations were conducted using OpenFOAM v2406 (https://www.openfoam.com/news/main-news/openfoam-v2406) Geometry/sandstone_image.raw - 1000×1000×1000-voxel RAW volume,Geometry/sandstone_pore_surf.stl - STL surface mesh of the same volume, Geometry/cubic_subdivision - folder with cubic subdivision geometry in STL format Geometry/flow-parallel - folder with flow-parallel subdivision geometry in STL formatGeometry/flow-orthogonal - folder with flow-orthogonal subdivision geometry in STL format

Openfoam_case/ - complete steady-state single-phase flow case (OpenFOAM v2406)

How to run the case: 



Navigate to the OpenFOAM case directory cd $FOAM_RUN/CaP_cells_directory/Openfoam_case

Copy the STL file from a chosen geometry into constant/triSurface/, for example:cp ../Geometry/cubic_subdivision/cubic1.stl constant/triSurface/mv constant/triSurface/cubic1.stl constant/triSurface/test2.stl(The geometry file must be renamed to test2.stl — this is the expected name configured in snappyHexMeshDict)

Adjust blockMeshDict according to the bounding box of the selected geometry. 

Optionally, adjust boundary conditions in the 0/ directory.

Run the simulation using the provided script: ./run.sh
DOI: 10.15468/dl.bfhju2
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sinningia hirsuta"
 ]
}

 The dataset includes 33 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014716-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rgn7tc
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Satureja hortensis",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 36 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014721-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xf3uhy
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Satureja hortensis",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014720-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jg77gn
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Smithiantha canarina"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014722-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4644a7
title: Occurrence Download

description: A dataset containing 17715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "Year is 1989"
 ]
}

 The dataset includes 17715 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014719-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tz7ahr
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Satureja hortensis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014724-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9yg2c
title: Occurrence Download

description: A dataset containing 62010 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbarium – Boissier's Flora Orientalis (CJBG-G-BOIS) of Conservatoire et Jardin botaniques de Genève"
 ]
}

 The dataset includes 62010 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014705-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17152431
title: Effects of confluence angle and ice coverage on morphodynamics in ice-covered river confluences: insights from laboratory experiments
DOI: 10.5281/zenodo.17152430
title: Effects of confluence angle and ice coverage on morphodynamics in ice-covered river confluences: insights from laboratory experiments
DOI: 10.15468/dl.vjac94
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhabdophis plumbicolor"
 ]
}

 The dataset includes 354 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014729-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4eezgn
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-44.19966 -19.81544,-44.15782 -19.81544,-44.15782 -19.78895,-44.19966 -19.78895,-44.19966 -19.81544))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 81 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014725-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.njcvw8
title: Occurrence Download

description: A dataset containing 1285 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Python molurus"
 ]
}

 The dataset includes 1285 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014728-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2n0sdw
title: CCDC 2443618: Experimental Crystal Structure Determination

description: Related Article: Vladislav V. Fedin, Danil V. Syrovsky, Sergey A. Usachev, Dmitrii L. Obydennov, Vyacheslav Y. Sosnovskikh|2025|Org.Lett.|27|9657|doi:10.1021/acs.orglett.5c02822
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0sfx
title: CCDC 2443619: Experimental Crystal Structure Determination

description: Related Article: Vladislav V. Fedin, Danil V. Syrovsky, Sergey A. Usachev, Dmitrii L. Obydennov, Vyacheslav Y. Sosnovskikh|2025|Org.Lett.|27|9657|doi:10.1021/acs.orglett.5c02822
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0tdx
title: CCDC 2443649: Experimental Crystal Structure Determination

description: Related Article: Andrea Fermi, Sapna Gahlot, Eric Jorand, Simone d’Agostino, Yasi Dai, Fabrizia Negri, Corinne Moustrou, Marc Gingras, Paola Ceroni|2025|J.Am.Chem.Soc.|147|32309|doi:10.1021/jacs.5c07339
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0tfy
title: CCDC 2443650: Experimental Crystal Structure Determination

description: Related Article: Andrea Fermi, Sapna Gahlot, Eric Jorand, Simone d’Agostino, Yasi Dai, Fabrizia Negri, Corinne Moustrou, Marc Gingras, Paola Ceroni|2025|J.Am.Chem.Soc.|147|32309|doi:10.1021/jacs.5c07339
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0tgz
title: CCDC 2443651: Experimental Crystal Structure Determination

description: Related Article: Andrea Fermi, Sapna Gahlot, Eric Jorand, Simone d’Agostino, Yasi Dai, Fabrizia Negri, Corinne Moustrou, Marc Gingras, Paola Ceroni|2025|J.Am.Chem.Soc.|147|32309|doi:10.1021/jacs.5c07339
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n5174
title: CCDC 2447705: Experimental Crystal Structure Determination

description: Related Article: Satyajit Majumder, Debabrata Mondal, Abhishek Mondal, Souvik Pal, Alakesh Bisai|2025|J.Org.Chem.|90|12323|doi:10.1021/acs.joc.5c01480
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17152428
title: Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs Supplementary Dataset

description: Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs

This repository accompanies the manuscript "Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs".

 

Overview

We present a transformer-based framework for operon prediction that recasts gene-pair classification as a natural language processing task. By serializing genomic features into structured textual descriptions, our approach enables pre-trained language models to classify whether two adjacent genes belong to the same operon.

Directory Structure

Data

The folder includes CSV files containing gene-pair examples used for training and evaluation. Each row corresponds to a gene pair with serialized textual input and operon membership label. The structure is:

| genome_id | gene1         | gene2         | text                                                                                          | label ||-----------|---------------|---------------|------------------------------------------------------------------------------------------------|-------|| 169963    | 169963.11.peg.2 | 169963.11.peg.3 | "Gene A is 1146 bp long... Gene B is 1344 bp long..."                                          | 0     |

- `text`: the serialized paragraph describing the gene pair (as detailed in the paper’s Methods).- `label`: binary indicator (1 = same operon, 0 = not same operon).

> Note: Gene features were derived using the BV-BRC API and annotations. See the manuscript for full details.

Reproducibility

The experimental setup and evaluation regimes are described in detail in the manuscript. While we do not include the full training notebook here, all necessary data and preprocessing details are provided to support reproducibility.

Citation

If you use this code or dataset, please cite the paper.
DOI: 10.5281/zenodo.17152429
title: Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs Supplementary Dataset

description: Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs

This repository accompanies the manuscript "Transformer-Based Operon Prediction Using Textual Representations of Gene Pairs".

 

Overview

We present a transformer-based framework for operon prediction that recasts gene-pair classification as a natural language processing task. By serializing genomic features into structured textual descriptions, our approach enables pre-trained language models to classify whether two adjacent genes belong to the same operon.

Directory Structure

Data

The folder includes CSV files containing gene-pair examples used for training and evaluation. Each row corresponds to a gene pair with serialized textual input and operon membership label. The structure is:

| genome_id | gene1         | gene2         | text                                                                                          | label ||-----------|---------------|---------------|------------------------------------------------------------------------------------------------|-------|| 169963    | 169963.11.peg.2 | 169963.11.peg.3 | "Gene A is 1146 bp long... Gene B is 1344 bp long..."                                          | 0     |

- `text`: the serialized paragraph describing the gene pair (as detailed in the paper’s Methods).- `label`: binary indicator (1 = same operon, 0 = not same operon).

> Note: Gene features were derived using the BV-BRC API and annotations. See the manuscript for full details.

Reproducibility

The experimental setup and evaluation regimes are described in detail in the manuscript. While we do not include the full training notebook here, all necessary data and preprocessing details are provided to support reproducibility.

Citation

If you use this code or dataset, please cite the paper.
DOI: 10.6085/aa/isckxx_xxxitv2xmsr01_20180412.40.1
title: (:unkn)
DOI: 10.6085/aa/isckxx_xxxitv2xmsr01_20180412.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Scott Creek (ISCKXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Scott Creek by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/isbfxx_xxxitv2xmsr01_20180412.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Sandhill Bluff (ISBFXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Sandhill Bluff by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/isckxx_xxxitv2xmsr01_20171017.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Scott Creek (ISCKXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Scott Creek by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/isckxx_xxxitv2xmsr01_20171017.40.1
title: (:unkn)
DOI: 10.6085/aa/isbfxx_xxxitv2xmsr01_20180412.40.1
title: (:unkn)
DOI: 10.6085/aa/isbfxx_xxxitv2xmsr01_20171017.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Sandhill Bluff (ISBFXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Sandhill Bluff by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/isbfxx_xxxitv2xmsr01_20171017.40.1
title: (:unkn)
DOI: 10.6085/aa/ipvaxx_xxxitv2xmsr01_20170518.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Pacific Valley (IPVAXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Pacific Valley by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/irmoxx_xxxitv2xmsr01_20171026.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Rancho Marino Reserve (IRMOXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Rancho Marino Reserve by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/irmoxx_xxxitv2xmsr01_20171026.40.1
title: (:unkn)
DOI: 10.6085/aa/ipvaxx_xxxitv2xmsr01_20170518.40.1
title: (:unkn)
DOI: 10.6085/aa/ipurxx_xxxitv2xmsr01_20171128.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Purisima (IPURXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Purisima by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.6085/aa/iptpxx_xxxitv2xmsr01_20170424.50.1
title: MARINe/PISCO: Intertidal: site temperature data: Point Pinos (IPTPXX)

description: This metadata record describes a mix of intertidal seawater and air temperature data collected at Point Pinos by MARINe/PISCO. Measurements were collected using Temperature Loggers from Onset Computer Corp
DOI: 10.15468/dl.cskdyp
title: Occurrence Download

description: A dataset containing 222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cypripedium irapeanum Lex."
 ]
}

 The dataset includes 222 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011982-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.em83w3
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cissus dasyantha Gilg & M.Brandt"
 ]
}

 The dataset includes 40 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093549-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mta36k
title: Occurrence Download

description: A dataset containing 3643 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Chloephaga Eyton, 1838"
 ]
}

 The dataset includes 3643 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010245-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfsrb6
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hymenandra iteophylla (Ridl.) Furtado"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024467-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.