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

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera pardus (Linnaeus, 1758)",
 "Year is greater than or equal to 2014",
 "TaxonKey is Vicugna pacos (Linnaeus, 1758)",
 "Year is greater than or equal to 2014"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020175-241107131044228/datasets/export for details.
DOI: 10.15468/dl.zs9d8x
title: Occurrence Download

description: A dataset containing 662 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pycnonotus cafer (Linnaeus, 1766)",
 "Country is New Caledonia",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 662 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020173-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzpkuw
title: Occurrence Download

description: A dataset containing 730 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera pardus (Linnaeus, 1758)",
 "Year is greater than or equal to 2014"
 ]
}

 The dataset includes 730 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020174-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rdrqgn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera pardus (Linnaeus, 1758)",
 "Year is greater than or equal to 2014",
 "TaxonKey is Vicugna pacos (Linnaeus, 1758)",
 "Year is greater than or equal to 2014",
 "TaxonKey is Attacus atlas (Linnaeus, 1758)",
 "Year is greater than or equal to 2014"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020176-241107131044228/datasets/export for details.
DOI: 10.15468/dl.pbwkuw
title: Occurrence Download

description: A dataset containing 2180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pycnonotus cafer (Linnaeus, 1766)",
 "Country is French Polynesia",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 2180 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020177-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13316338
title: xeno-canto America: xeno-canto America - archive

description: original archive, circa 2010, 5000 spp.
DOI: 10.5281/zenodo.13316339
title: xeno-canto America: xeno-canto America - archive

description: original archive, circa 2010, 5000 spp.
DOI: 10.15468/dl.mcz8ve
title: Occurrence Download

description: A dataset containing 406696 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Observation.org, Nature data from around the World)",
 "TaxonKey is Carabidae"
 ]
}

 The dataset includes 406696 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020122-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3y4y6m
title: Occurrence Download

description: A dataset containing 8784 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pycnonotus jocosus (Linnaeus, 1758)",
 "Country is Réunion",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 8784 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020178-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14179775
title: RAW PARKINSON METABOLOMICS DATA
DOI: 10.5281/zenodo.14179776
title: RAW PARKINSON METABOLOMICS DATA
DOI: 10.5281/zenodo.14181586
title: COMPARATIVE EVALUATION OF COMPLICATIONS OF DIABETES MELLITUS - NEUROPATHY AND ANGIOPATHY.
DOI: 10.5281/zenodo.14181587
title: COMPARATIVE EVALUATION OF COMPLICATIONS OF DIABETES MELLITUS - NEUROPATHY AND ANGIOPATHY.
DOI: 10.15468/dl.dq385x
title: Occurrence Download

description: A dataset containing 3050 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pycnonotus sinensis (Gmelin, 1789)",
 "Country is Japan",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 3050 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020179-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvwfxg
title: Occurrence Download

description: A dataset containing 10287 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.6463 40.6246,-8.6483 40.6335,-8.6599 40.6320,-8.6579 40.6231,-8.6463 40.6246))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 10287 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020180-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25810/yzb8-wx26
title: FIRED Rwanda Nov 2000 - July 2024

description: This is event-level polygons for the fire event delineation (FIRED) product for RWANDA from November 2000 to July 2024. It is derived from the MODIS MCD64A1 burned area product (see https://lpdaac.usgs.gov/products/mcd64a1v061/ for more details). The MCD64A1 is a monthly raster grid of estimated burned dates. Firedpy (https://github.com/earthlab/firedpy) is an algorithm that converts these rasters into events by stacking the entire time series into a spatial-temporal data cube, then uses an algorithm to assign event identification numbers to pixels that fit into the same 3-dimensional spatial temporal window. This particular dataset was created using a spatial parameter of 1 pixels and 5 days. Daily polygons are included and the event identification numbers are the same for both files, but the event-level product has only single polygons for each entire event, while the daily product has separate polygons for each date per event. See the associated paper for more details on the methods and more:

Balch, J.K.; St. Denis, L.A.; Mahood, A.L.; Mietkiewicz, N.P.; Williams, T.M.; McGlinchy, J.; Cook, M.C. FIRED (Fire Events Delineation): An Open, Flexible Algorithm and Database of US Fire Events Derived from the MODIS Burned Area Product (2001–2019). Remote Sens. 2020, 12, 3498. https://doi.org/10.3390/rs12213498
DOI: 10.5281/zenodo.14181415
title: Small BAM files for practising RNA-seq and WES visualization (human)

description: Two sets of BAM files for teaching RNA-seq and whole exome sequence (WES) visualization. 

All data was processed from open access SRA datasets. 




NAME
RNA-EMT
WES-LUNG


SOURCE
Yang et al. https://doi.org/10.1128/mcb.00019-16, SRA: PRJNA304419
Ju et al. https://doi.org/10.1101/gr.133645.111; SRA: ERP001071)


DESCRIPTION
Human RNA-seq BAM files 
Human WES BAM files: Lung cancer


SEQUENCING TYPE
Illumina paired-end, stranded
Illumina paired-end


METHODS
Original data are from cell lines subjected to epthithelium-mesenchymal transition. We took replicates corresponding to Day 0 (uninduced cells) and Day 7 (7 days after induction). Reads were aligned with STAR. BAM files are restricted to chromosome 18. Gene of interest: CDH2, up in mesenchymal state.
WES were obtained from tumor and blood tissues from a non small cell lung cancer patient. Reads were aligned with BWA. A fraction of sequences corresponding to a panel of genes were retained. Genes of interest: DUSP27, KRAS


MAPPED_TO
HG19
HG19


SAMPLING RATE
0.50%
0.10%


FILE SIZE
2*40Mb
2*7Mb
DOI: 10.5281/zenodo.14181416
title: Small BAM files for practising RNA-seq and WES visualization (human)

description: Two sets of BAM files for teaching RNA-seq and whole exome sequence (WES) visualization. 

All data was processed from open access SRA datasets. 




NAME
RNA-EMT
WES-LUNG


SOURCE
Yang et al. https://doi.org/10.1128/mcb.00019-16, SRA: PRJNA304419
Ju et al. https://doi.org/10.1101/gr.133645.111; SRA: ERP001071)


DESCRIPTION
Human RNA-seq BAM files 
Human WES BAM files: Lung cancer


SEQUENCING TYPE
Illumina paired-end, stranded
Illumina paired-end


METHODS
Original data are from cell lines subjected to epthithelium-mesenchymal transition. We took replicates corresponding to Day 0 (uninduced cells) and Day 7 (7 days after induction). Reads were aligned with STAR. BAM files are restricted to chromosome 18. Gene of interest: CDH2, up in mesenchymal state.
WES were obtained from tumor and blood tissues from a non small cell lung cancer patient. Reads were aligned with BWA. A fraction of sequences corresponding to a panel of genes were retained. Genes of interest: DUSP27, KRAS


MAPPED_TO
HG19
HG19


SAMPLING RATE
0.50%
0.10%


FILE SIZE
2*40Mb
2*7Mb
DOI: 10.6073/pasta/d1ec25508b441066817e14b049085c91
title: Tree species, size class, and DBH in the University of Michigan Biological Station (UMBS) Burn Chronosequence established in 1957 and remeasured in 1979 and 1998

description: A complete survey of overstory vegetation and saplings in the Bob Farmer plots within the UM Biological Station clearut and burn chronosequence. Surveys were completed in 1979 and 1998 to measure the change in biomass and forest composition in the burn plots with forest succession.
DOI: 10.5281/zenodo.14176443
title: The IBIS Challenge 2024 Benchmarking Package

description: IBIS Challenge 2024

Benchmarking Package, 17 Nov 2024

https://ibis.autosome.org

This repository provides the IBIS benchmarking suite and the challenge 'answers', i.e. the labeled test data. This repository is accompanied by another ZENODO repo [doi:10.5281/zenodo.14174161] containing the complete data of the Codebook/GRECO-BIT open challenge in Inferring Binding Specificities of human transcription factors from multiple experimental data types. Both the Leaderboard stage and the Final stage data are included.

* Please refer to the supplied README for more details.
DOI: 10.5281/zenodo.14176442
title: The IBIS Challenge 2024 Benchmarking Package

description: IBIS Challenge 2024

Benchmarking Package, 17 Nov 2024

https://ibis.autosome.org

This repository provides the IBIS benchmarking suite and the challenge 'answers', i.e. the labeled test data. This repository is accompanied by another ZENODO repo [doi:10.5281/zenodo.14174161] containing the complete data of the Codebook/GRECO-BIT open challenge in Inferring Binding Specificities of human transcription factors from multiple experimental data types. Both the Leaderboard stage and the Final stage data are included.

* Please refer to the supplied README for more details.
DOI: 10.15468/dl.kk5cs2
title: Occurrence Download

description: A dataset containing 592 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Lithobates palmipes (Spix, 1824)"
 ]
}

 The dataset includes 592 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020182-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2495j
title: Occurrence Download

description: A dataset containing 9364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Python bivittatus Kuhl, 1820",
 "Country is United States of America",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 9364 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020183-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhpbfb
title: Occurrence Download

description: A dataset containing 16275 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Malaysia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bucerotiformes",
 "Year 2009-2017"
 ]
}

 The dataset includes 16275 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020184-241107131044228/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.cc2jgtg9
title: CCDC 2337941: Experimental Crystal Structure Determination

description: Related Article: Daniel C. Schultz, Alejandra Chávez-Riveros, Michael G. Goertzen, Beau R. Brummel, Raphaella A. Paes, Natalia M. Santos, Srinivasarao Tenneti, Khalil A. Abboud, James R. Rocca, Gustavo Seabra, Chenglong Li, Debopam Chakrabarti, Robert W. Huigens|2024|Org.Biomol.Chem.|22|8423|doi:10.1039/D4OB00853G
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.cc2jht1x
title: CCDC 2338889: Experimental Crystal Structure Determination

description: Related Article: Daniel C. Schultz, Alejandra Chávez-Riveros, Michael G. Goertzen, Beau R. Brummel, Raphaella A. Paes, Natalia M. Santos, Srinivasarao Tenneti, Khalil A. Abboud, James R. Rocca, Gustavo Seabra, Chenglong Li, Debopam Chakrabarti, Robert W. Huigens|2024|Org.Biomol.Chem.|22|8423|doi:10.1039/D4OB00853G
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.cc2jht2y
title: CCDC 2338890: Experimental Crystal Structure Determination

description: Related Article: Daniel C. Schultz, Alejandra Chávez-Riveros, Michael G. Goertzen, Beau R. Brummel, Raphaella A. Paes, Natalia M. Santos, Srinivasarao Tenneti, Khalil A. Abboud, James R. Rocca, Gustavo Seabra, Chenglong Li, Debopam Chakrabarti, Robert W. Huigens|2024|Org.Biomol.Chem.|22|8423|doi:10.1039/D4OB00853G
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.cc2jht3z
title: CCDC 2338891: Experimental Crystal Structure Determination

description: Related Article: Daniel C. Schultz, Alejandra Chávez-Riveros, Michael G. Goertzen, Beau R. Brummel, Raphaella A. Paes, Natalia M. Santos, Srinivasarao Tenneti, Khalil A. Abboud, James R. Rocca, Gustavo Seabra, Chenglong Li, Debopam Chakrabarti, Robert W. Huigens|2024|Org.Biomol.Chem.|22|8423|doi:10.1039/D4OB00853G
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.cc2jht40
title: CCDC 2338892: Experimental Crystal Structure Determination

description: Related Article: Daniel C. Schultz, Alejandra Chávez-Riveros, Michael G. Goertzen, Beau R. Brummel, Raphaella A. Paes, Natalia M. Santos, Srinivasarao Tenneti, Khalil A. Abboud, James R. Rocca, Gustavo Seabra, Chenglong Li, Debopam Chakrabarti, Robert W. Huigens|2024|Org.Biomol.Chem.|22|8423|doi:10.1039/D4OB00853G
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.cc2js04h
title: CCDC 2346766: Experimental Crystal Structure Determination

description: Related Article: Han Yang, Tian Huang, Yu Chen, Yuan-Hua Wang, Yong-Dong Jin, Xiao-Chuan Chen, Chuan-Qin Xia|2024|Inorg.Chem.|63|20762|doi:10.1021/acs.inorgchem.4c03489
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.cc2d229w
title: CCDC 2206527: Experimental Crystal Structure Determination

description: Related Article: Yu-Juan Ma, Fei Xu, Xin-Ye Ren, Fan-Yao Chen, Jie Pan, Jin-Hua Li, Song-De Han, Guo-Ming Wang|2024|Chemical Science|15|17642|doi:10.1039/D4SC04632C
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.cc2js05j
title: CCDC 2346767: Experimental Crystal Structure Determination

description: Related Article: Han Yang, Tian Huang, Yu Chen, Yuan-Hua Wang, Yong-Dong Jin, Xiao-Chuan Chen, Chuan-Qin Xia|2024|Inorg.Chem.|63|20762|doi:10.1021/acs.inorgchem.4c03489
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.cc2d22bx
title: CCDC 2206528: Experimental Crystal Structure Determination

description: Related Article: Yu-Juan Ma, Fei Xu, Xin-Ye Ren, Fan-Yao Chen, Jie Pan, Jin-Hua Li, Song-De Han, Guo-Ming Wang|2024|Chemical Science|15|17642|doi:10.1039/D4SC04632C
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.cc2k35pk
title: CCDC 2356548: Experimental Crystal Structure Determination

description: Related Article: ChengLong Wen, Jun Yuan, Zhiguo Zhang, Dongxu Li, Yuqian Zhou, Wanqiang Liu, Zaichun Zhou, Yungui Li, Lihui Jiang, Yingping Zou|2024|Mater. Chem. Front.|8|3587|doi:10.1039/D4QM00465E
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: 10.15468/dl.ray24v
title: Occurrence Download

description: A dataset containing 7411408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.04372 39.1014,21.76988 39.1014,21.76988 46.45102,10.04372 46.45102,10.04372 39.1014))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7411408 records from 1508 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020125-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0193707.10fu
title: SH0193707.10FU

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/sh0193708.10fu
title: SH0193708.10FU

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.