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

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aspidistra marginella D.Fang & L.Zeng)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023795-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mr3h34
title: Occurrence Download

description: A dataset containing 575 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia fraterna Hance"
 ]
}

 The dataset includes 575 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023796-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rw9pm8
title: Occurrence Download

description: A dataset containing 321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "TaxonKey is Chilabothrus striatus (Fischer, 1856)"
 ]
}

 The dataset includes 321 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023798-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7wfuk
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia longissima Hung T.Chang & S.Y.Liang"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023797-241107131044228/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.27865398
title: A Radiograph Dataset for the Classification, Localization, and Segmentation of Primary Bone Tumors

description: Primary malignant bone tumors are the third highest cause of cancer-related mortality among patients under the age of 20. X-ray scan is the primary tool for detecting bone tumors. However, due to the varyingmorphologies of bone tumors, it is challenging for radiologists to make a definitive diagnosis based on radiographs. With the recent advancement in deep learning algorithms, there is a surge of interest in computer-aided diagnosis of primary bone tumors. Nonetheless, the development in this field has been hindered by the lack of publicly available X-ray datasets for bone tumors. To tackle this challenge, we established the Bone Tumor X-ray Radiograph dataset (termed BTXRD) in collaboration with multiple medical institutes and hospitals. The BTXRD dataset comprises 3,746 bone images (1,879 normal and 1,867 tumor), with clinical information and global labels available for each image, and distinct mask and annotated bounding box for each tumor instance. This publicly available dataset can support the development and evaluation of deep learning algorithms for the diagnosis of primary bone tumors.
DOI: 10.15468/dl.v9sjxg
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia achrysantha Hung T.Chang & S.Y.Liang"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023799-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/9961490
title: MushR-Annotated-Dataset (Oyster Mushrooms)
DOI: 10.15468/dl.jjubn6
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia longzhouensis J.Y.Luo"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023800-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7yns8y
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia acuticalyx Hung T.Chang"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023802-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7cjb3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aspidistra marginella D.Fang & L.Zeng)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023804-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3z66h7
title: Occurrence Download

description: A dataset containing 1579805 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2000-2020"
 ]
}

 The dataset includes 1579805 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023790-241107131044228/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.27865287
title: HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y)

description: This dataset contains 172 100ns pMHC Molecular Dynamics simulation trajectories of Knapp et al. 2014/2016<br>The trajectories were converted in the following way:- Periodic boundary condition artefacts were removed with the options “whole”, “cluster”, and “no jump”.- The pMHC complexes were centred in the box.- The pMHC complexes were superimposed rotationally and transnationally onto the first frame of each simulation.- Each trajectory contains 800 equally distributed simulation frames.- Water molecules were removed.<br><br>When using these data please acknowledge the source and use the following cites:<br>1) pMHC simulations:B. Knapp, C. M. Deane. (2016) T-cell receptor binding effects the dynamics of the peptide/MHCI complex. J. Chem. Inf. Model. 2016, 56, 1, 46–53<br>2) TCRpMHC simulations:B. Knapp, J. Dunbar, C. M. Deane (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. PLoS Comput Biol 10[8], e1003748. <br>
DOI: 10.6084/m9.figshare.27865287.v1
title: HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y)

description: This dataset contains 172 100ns pMHC Molecular Dynamics simulation trajectories of Knapp et al. 2014/2016<br>The trajectories were converted in the following way:- Periodic boundary condition artefacts were removed with the options “whole”, “cluster”, and “no jump”.- The pMHC complexes were centred in the box.- The pMHC complexes were superimposed rotationally and transnationally onto the first frame of each simulation.- Each trajectory contains 800 equally distributed simulation frames.- Water molecules were removed.<br><br>When using these data please acknowledge the source and use the following cites:<br>1) pMHC simulations:B. Knapp, C. M. Deane. (2016) T-cell receptor binding effects the dynamics of the peptide/MHCI complex. J. Chem. Inf. Model. 2016, 56, 1, 46–53<br>2) TCRpMHC simulations:B. Knapp, J. Dunbar, C. M. Deane (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. PLoS Comput Biol 10[8], e1003748. <br>
DOI: 10.15468/dl.8x6675
title: Occurrence Download

description: A dataset containing 10048 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carphophis amoenus (Say, 1825)"
 ]
}

 The dataset includes 10048 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023803-241107131044228/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.27861678
title: LC13 + HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y)

description: LC13 + HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y). See also Knapp et al. Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study (https://pubmed.ncbi.nlm.nih.gov/25101830/)
DOI: 10.6084/m9.figshare.27861678.v1
title: LC13 + HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y)

description: LC13 + HLA–B*08:01 + all single point mutations of the peptide FLRGRAYGL (F1A, ... L9Y). See also Knapp et al. Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study (https://pubmed.ncbi.nlm.nih.gov/25101830/)
DOI: 10.15468/dl.fbv3wk
title: Occurrence Download

description: A dataset containing 6156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((12.94798 47.04566,12.99296 47.04566,12.99296 47.08327,12.94798 47.08327,12.94798 47.04566))",
 "PublishingOrg is 7a070ba0-bafb-11d9-8e53-b8a03c50a862"
 ]
}

 The dataset includes 6156 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023805-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7dueb7
title: Occurrence Download

description: A dataset containing 12695 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Swedish Bird Survey: Fixed routes (Standardrutterna)",
 "Geometry POLYGON((19.497540916362183 65.97964974979725,21.751173716405 65.97964974979725,21.751173716405 68.23328254984007,19.497540916362183 68.23328254984007,19.497540916362183 65.97964974979725))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12695 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023806-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ujze9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Aspidistra medusa Aver., K.S.Nguyen & Tillich)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023809-241107131044228/datasets/export for details.
DOI: 10.15468/dl.u6vajr
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia luteoflora Y.K.Li ex Hung T.Chang & F.A.Zeng"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023808-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13293807
title: early exports: 2019, Nov 11

description: all trait data exports from 2019
DOI: 10.5281/zenodo.14007119
title: Raw data for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy"

description: Raw NMR, IR and MS  data  for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy" published in  Angewandte Chemie, International Edition, DOI: 

https://doi.org/10.1002/anie.202417719

The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.
DOI: 10.5281/zenodo.14007120
title: Raw data for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy"

description: Raw NMR, IR and MS  data  for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy" published in  Angewandte Chemie, International Edition, DOI: 

https://doi.org/10.1002/anie.202417719

The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.
DOI: 10.5281/zenodo.11203685
title: An integrated transcriptomic cell atlas of human neural organoids: Cleaned datasets

description: This deposition includes the datasets in h5ad format dataset for the following pre-print: 



He, Z.; Dony, L.; Fleck, J. S. et al. An integrated transcriptomic cell atlas of human neural organoids. bioRxiv 2023.10.05.561097; doi: 10.1101/2023.10.05.561097


The file `hnoca_cleanedmeta.h5ad` is a cleaned up version of the HNOCA dataset. While it contains all cells, some metadata and representations originating from intermediate processing steps are removed. You can find the full (and significantly larger) object in a second Zenodo deposition.

 

Abstract:

Neural tissues generated from human pluripotent stem cells in vitro (known as neural organoids) are becoming useful tools to study human brain development, evolution and disease. The characterization of neural organoids using single-cell genomic methods has revealed a large diversity of neural cell types with molecular signatures similar to those observed in primary human brain tissue. However, it is unclear which domains of the human nervous system are covered by existing protocols. It is also difficult to quantitatively assess variation between protocols and the specific cell states in organoids as compared to primary counterparts. Single-cell transcriptome data from primary tissue and neural organoids derived with guided or unguided approaches and under diverse conditions combined with large-scale integrative analyses make it now possible to address these challenges. Recent advances in computational methodology enable the generation of integrated atlases across many data sets. Here, we integrated 36 single-cell transcriptomics data sets spanning 26 protocols into one integrated human neural organoid cell atlas (HNOCA) totaling over 1.7 million cells. We harmonize cell type annotations by incorporating reference data sets from the developing human brain. By mapping to the developing human brain reference, we reveal which primary cell states have been generated in vitro, and which are under-represented. We further compare transcriptomic profiles of neuronal populations in organoids to their counterparts in the developing human brain. To support rapid organoid phenotyping and quantitative assessment of new protocols, we provide a programmatic interface to browse the atlas and query new data sets, and showcase the power of the atlas to annotate new query data sets and evaluate new organoid protocols. Taken together, the HNOCA will be useful to assess the fidelity of organoids, characterize perturbed and diseased states and facilitate protocol development in the future.
DOI: 10.5281/zenodo.13293784
title: Mammal body size (EOL v3 test): mammal body size

description: A sample of data downloaded from the new EOL search interface. All available data for mammals for any measure of body size, with full metadata.

https://beta.eol.org/terms/search_results?term_query%5Bclade_id%5D=1642&term_query%5Bfilters_attributes%5D%5B0%5D%5Bop%5D=is_any&term_query%5Bfilters_attributes%5D%5B0%5D%5Bpred_uri%5D=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0100005&term_query%5Bresult_type%5D=record
DOI: 10.5281/zenodo.13293783
title: Mammal body size (EOL v3 test): mammal body size

description: A sample of data downloaded from the new EOL search interface. All available data for mammals for any measure of body size, with full metadata.

https://beta.eol.org/terms/search_results?term_query%5Bclade_id%5D=1642&term_query%5Bfilters_attributes%5D%5B0%5D%5Bop%5D=is_any&term_query%5Bfilters_attributes%5D%5B0%5D%5Bpred_uri%5D=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0100005&term_query%5Bresult_type%5D=record
DOI: 10.5281/zenodo.13293697
title: early exports: 2019, August 22

description: all trait data exports from 2019
DOI: 10.5281/zenodo.13293698
title: early exports: 2019, August 22

description: all trait data exports from 2019
DOI: 10.5281/zenodo.14192479
title: oligodon_sublineatus_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.14192480
title: oligodon_sublineatus_decontaminated_FSCR.fasta.gz
DOI: 10.15468/dl.qw7u8b
title: Occurrence Download

description: A dataset containing 349494 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is NatureMapr"
 ]
}

 The dataset includes 349494 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023779-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vrvxdy
title: Occurrence Download

description: A dataset containing 178693 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kazakhstan",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 178693 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023778-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ba6322
title: Occurrence Download

description: A dataset containing 15229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "Country is Mexico",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 15229 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023810-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7vj79v
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia macrosepala Hung T.Chang"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023811-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvueac
title: Occurrence Download

description: A dataset containing 461 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia furfuracea (Merr.) Cohen-Stuart"
 ]
}

 The dataset includes 461 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023812-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6mhrv
title: Occurrence Download

description: A dataset containing 548899 species occurrences available in GBIF matching the query:
{
 "PublishingCountry" : [
 "is Dominican Republic"
 ]
}

 The dataset includes 548899 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023807-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fj9w2c
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((12.94798 47.04566,12.99296 47.04566,12.99296 47.08327,12.94798 47.08327,12.94798 47.04566))",
 "PublishingOrg is 7a070ba0-bafb-11d9-8e53-b8a03c50a862",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 352 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023813-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d7bsc3
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia acutiserrata Hung T.Chang"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023814-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vu9nv5
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camellia ×maliflora Lindl."
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023815-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnhssy
title: Occurrence Download

description: A dataset containing 427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "Issue is Geodetic datum assumed WGS84",
 "TaxonKey is Psidium guajava L."
 ]
}

 The dataset includes 427 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000697-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zpq4bv
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Myzomela erythromelas Salvadori, 1881"
 ]
}

 The dataset includes 134 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051122-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.