cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/inscriptifact-ouc111157644
title: Record (fields owned by individuals), KTU 4.399

description: [Text or Publication Number Note:] KTU 4.399, KTU2 4.399, KTU3 4.399, CTU 4.399, CAT 4.399 ❧ [Excavation Description:] Found during excavations at Ras Shamra. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform ❧
DOI: 10.25549/inscriptifact-ouc111111902
title: Receipt of animal sacrifice, UT 1599-8

description: [Text Description:] Receipt of animal sacrifice to the goddess Nana. ❧ [Text or Publication Number Note:] UT 1599-8 ❧ [Excavation Description:] Drehem ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Small rectangular clay tablet, pink-beige color. Shows fingerprints. LABEL: "1599" in black ink, "8" in red ink. 3 x 2.5cm. ❧ [Physical Object Note:] Reign of Shulgi, second dynastic king.
DOI: 10.15468/dl.4ajn6k
title: Occurrence Download

description: A dataset containing 3499 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Geometry POLYGON((-169.10156 70.14036,-168.39844 67.06743,-169.10156 59.17593,-173.32031 54.16243,-123.39844 17.97873,-77.69531 -28.92163,-87.77481 -60.35224,-36.68894 -56.97397,-37.61778 -39.24118,-30.1871 -17.37524,-37.61778 18.25951,-49.69262 45.41349,-36.91406 51.61802,-33.05072 65.16474,-9.87229 71.19014,-2.46094 83.59903,-66.44531 84.40594,-127.61719 81.09321,-149.41406 75.84517,-169.10156 70.14036))",
 "HasGeospatialIssue is false",
 "TaxonKey is Quadrella J.Presl",
 "Year 1980-2021"
 ]
}

 The dataset includes 3499 records from 128 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194281-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111353482
title: Record, teams of oxen, ploughmen and other personnel by royal farm or town, KTU 4.618

description: [Text Description:] Ugaritic Tablet KTU 4.618 ❧ [Text or Publication Number Note:] KTU 4.618; KTU2 4.618; KTU3 4.618; CTU 4.618; CAT 4.618; RS 19.045; DO 5032 ❧ [Excavation Description:] Found during excavations at Ras Shamra. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform
DOI: 10.25549/inscriptifact-ouc111157544
title: List (persons grouped by unidentifiable criteria), KTU 4.393

description: [Text or Publication Number Note:] KTU 4.393, KTU2 4.393, KTU3 4.393, CTU 4.393, CAT 4.393 ❧ [Excavation Description:] Found during excavations at Ras Shamra. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform ❧
DOI: 10.15468/dl.659ahj
title: Occurrence Download

description: A dataset containing 41741 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Biscutella laevigata L., Blysmus compressus (L.) Panz. ex Link, Bothriochloa ischaemum (L.) Keng)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 41741 records from 274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158083-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111157504
title: List (persons grouped by unidentifiable criteria), KTU 4.393

description: [Text or Publication Number Note:] KTU 4.393, KTU2 4.393, KTU3 4.393, CTU 4.393, CAT 4.393 ❧ [Excavation Description:] Found during excavations at Ras Shamra. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform ❧
DOI: 10.25549/inscriptifact-ouc111157505
title: List (persons grouped by unidentifiable criteria), KTU 4.393

description: [Text or Publication Number Note:] KTU 4.393, KTU2 4.393, KTU3 4.393, CTU 4.393, CAT 4.393 ❧ [Excavation Description:] Found during excavations at Ras Shamra. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform ❧
DOI: 10.15468/dl.6cuq9b
title: Occurrence Download

description: A dataset containing 895328 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sorbus aucuparia L."
 ]
}

 The dataset includes 895328 records from 1577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061556-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfxbt6
title: Occurrence Download

description: A dataset containing 1280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Opuntia sulphurea G.Don ex Loudon)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1280 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011778-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2xb763
title: Occurrence Download

description: A dataset containing 316 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ottelia alismoides (L.) Pers.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Japan"
 ]
}

 The dataset includes 316 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001982-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14161275
title: An integrated transcriptomic cell atlas of human neural organoids: Cleaned datasets

description: This deposition includes the datasets in h5ad format for the following publication: 



He, Z., Dony, L., Fleck, J.S. et al. An integrated transcriptomic cell atlas of human neural organoids. Nature 635, 690–698 (2024). https://doi.org/10.1038/s41586-024-08172-8


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.

You can find the minimal HNOCA and primary reference h5ad files for query-to-reference-mapping in a third 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: 10.4121/78b904c2-21ab-40a7-b017-21c545a6b2f6
title: Data underlying the publication: Effect of drying conditions on quality of primed cabbage (Brassica oleracea) seeds and ethanol degradation as promising quality parameter

description: This dataset contains data collected during seed drying experiments at Wageningen University & Research and Bejo Zaden B.V. as part of Julia Veser's PhD Thesis project. The purpose of these experiments was to investigate the effect of drying conditions on seed quality of primed <em>Brassica oleracea</em> (cabbage) seeds. The drying conditions were varied systematically from 25 to 60 °C drying air temperature, 5 - 50% air relative humidity and 0.5 - 24 hr drying time. During drying the weight, thus moisture content, of seeds and the surface seed temperature were measured. After drying, seed quality was analysed by several parameters including germination quality, germination speed and the newly proposed ethanol index as well as germination quality and speed after a storage treatment.
DOI: 10.4121/78b904c2-21ab-40a7-b017-21c545a6b2f6.v1
title: Data underlying the publication: Effect of drying conditions on quality of primed cabbage (Brassica oleracea) seeds and ethanol degradation as promising quality parameter

description: This dataset contains data collected during seed drying experiments at Wageningen University & Research and Bejo Zaden B.V. as part of Julia Veser's PhD Thesis project. The purpose of these experiments was to investigate the effect of drying conditions on seed quality of primed <em>Brassica oleracea</em> (cabbage) seeds. The drying conditions were varied systematically from 25 to 60 °C drying air temperature, 5 - 50% air relative humidity and 0.5 - 24 hr drying time. During drying the weight, thus moisture content, of seeds and the surface seed temperature were measured. After drying, seed quality was analysed by several parameters including germination quality, germination speed and the newly proposed ethanol index as well as germination quality and speed after a storage treatment.
DOI: 10.5281/zenodo.15004872
title: Cyberbullying Detection
DOI: 10.5281/zenodo.15004873
title: Cyberbullying Detection
DOI: 10.5281/zenodo.12536006
title: An integrated transcriptomic cell atlas of human neural organoids: Full Dataset

description: This deposition includes the full HNOCA dataset for the following pre-print: 



He, Z., Dony, L., Fleck, J.S. et al. An integrated transcriptomic cell atlas of human neural organoids. Nature 635, 690–698 (2024). https://doi.org/10.1038/s41586-024-08172-8


This file contains additional data representations and metadata from intermediate processing steps of the HNOCA. For day-to-day use of the HNOCA as a resource, we recommend using the cleaned-up HNOCA object that can be found together with the disease atlas and the extended version of HNOCA in the original 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.12536007
title: An integrated transcriptomic cell atlas of human neural organoids: Full Dataset

description: This deposition includes the full HNOCA 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


This file contains additional data representations and metadata from intermediate processing steps of the HNOCA. For day-to-day use of the HNOCA as a resource, we recommend using the cleaned-up HNOCA object that can be found together with the disease atlas and the extended version of HNOCA in the original 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.14160929
title: An integrated transcriptomic cell atlas of human neural organoids: Full Dataset

description: This deposition includes the full HNOCA dataset for the following pre-print: 



He, Z., Dony, L., Fleck, J.S. et al. An integrated transcriptomic cell atlas of human neural organoids. Nature 635, 690–698 (2024). https://doi.org/10.1038/s41586-024-08172-8


This file contains additional data representations and metadata from intermediate processing steps of the HNOCA. For day-to-day use of the HNOCA as a resource, we recommend using the cleaned-up HNOCA object that can be found together with the disease atlas and the extended version of HNOCA in the original 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: 10.15468/dl.9uj2pw
title: Occurrence Download

description: A dataset containing 1182530 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ranunculus repens L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1182530 records from 3229 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001966-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vdu86m
title: Occurrence Download

description: A dataset containing 4830 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 4830 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092610-200613084148143/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.24849774
title: Ningdong (ND) coal base

description: The annual maximum NDVI dataset of Ningdong (ND) coal base in China (2013-2022).<br>
DOI: 10.15468/dl.uczmvq
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bellevalia longipes Post"
 ]
}

 The dataset includes 70 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052769-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0pp4ol
title: Occurrence Download

description: A dataset listing the 127493 species recorded in GBIF matching the query:
{
 "Country" : [
 "is Spain"
 ]
}

 The dataset's 127493 records were derived from 1525 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002854-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1074955.10fu
title: SH1074955.10FU

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.