cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.x34bak
title: Occurrence Download

description: A dataset containing 4327 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagenorhynchus obliquidens"
 ]
}

 The dataset includes 4327 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009535-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j08w3bvc
title: CIL:46263, Homo sapiens. In Cell Image Library

description: Plate 25858 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j03777w0
title: CIL:10009, Didinium nasutum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: An image of the fibrous cortex of Didinium nasutum. Embedded within the fibrous layer are many extrusive organelles, called mucocysts, involved in cyst formation. In this view there is also a longitudinal section of a more prominent and long curved extrusome (called a cyrtocyst by Wessenberg and Antipa, 1968) in the proter of a dividing cell. The cyrtocyst is of unknown function. Extrusomes of Didinium typically have a bundle of myelin-like membrane material enclosed by their surrounding membrane. This may be stored membrane needed for extrusome discharge. TEM taken on 5/20/69 by R. Allen with a Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:4665) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j03x85s3
title: CIL:9971, Rattus, permanent cell line cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: ECFP
Processing history: unprocessed raw data
description: Normal Rat Kidney (NRK) cells grown in culture expressing Galactosyl Transferase-YFP (GalT-YFP) and p58-CFP. This file is the CFP time series demonstrating the organization of the early secretory pathway (Golgi and intermediate compartment). 

Images were collected on a Zeiss Spinning Disk confocal as a single z slice over time with CFP imaged using 445ht and YFP imaged using 515ht and a 63X oil objective. Images were collected every 2 minutes. Exposure time: 515 was 50ms; 445 was 200ms: for both channels, the gain was 3, the camera intensification was 200, the laser neutral density was 10.
DOI: 10.6075/j0hq3z4v
title: CIL:1031, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j09k4b9s
title: CIL:39619, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0571b38
title: CIL:21715, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
description: A view of the E-face of the fractured collecting canal of the contractile vacuole showing its association with microtubular ribbons and with the smooth spongiome. The E-fracture face of the smooth spongiome is highly pitted like that of the collecting canal. Thin filaments lie between the microtubules and the collecting canal membrane. TEM taken on 7/19/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 40,500X. Bar = 0.1µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:13126) is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j04m94qc
title: CIL:40135, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: The cerebral cortex of a wild type mouse immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
DOI: 10.5281/zenodo.17491840
title: Coretax Data

description: Coretax Data
DOI: 10.5281/zenodo.17491841
title: Coretax Data

description: Coretax Data
DOI: 10.15468/dl.q59qpe
title: Occurrence Download

description: A dataset containing 57449 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alchemilla vulgaris"
 ]
}

 The dataset includes 57449 records from 298 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009507-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dsc84h
title: Occurrence Download

description: A dataset containing 352433 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Latvia)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Literature Occurrence, Specimen, Unknown evidence, Machine Observation)",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2020",
 "HasCoordinate is true"
 ]
}

 The dataset includes 352433 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009485-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17482543
title: Short term effects of soil disturbance on greenhouse gas fluxes on a nutrient-rich peatland after clearcutting

description:  The data contains greenhouse gas flux (CO2,CH4, N2O ) data from the mounded and unprepared (control) surfaces measured with a portable gas analyzer in 2022-2024. The file "t05" contains the handmeasured soil temperatures in 2022-2024 and the file  "Tomst_data" the soil temperature and soil moisture measured by TOMST sensor 06/19/2024-02/10/2024. All data is collected from Ränskälänkorpi (N61°10.973' E25°15.761’), a nutrient-rich drained peatland.
DOI: 10.5281/zenodo.17482544
title: Short term effects of soil disturbance on greenhouse gas fluxes on a nutrient-rich peatland after clearcutting

description:  The data contains greenhouse gas flux (CO2,CH4, N2O ) data from the mounded and unprepared (control) surfaces measured with a portable gas analyzer in 2022-2024. The file "t05" contains the handmeasured soil temperatures in 2022-2024 and the file  "Tomst_data" the soil temperature and soil moisture measured by TOMST sensor 06/19/2024-02/10/2024. All data is collected from Ränskälänkorpi (N61°10.973' E25°15.761’), a nutrient-rich drained peatland.
DOI: 10.15468/dl.wvct32
title: Occurrence Download

description: A dataset containing 1702 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagenorhynchus obscurus"
 ]
}

 The dataset includes 1702 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009536-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17630/9f397e32-2121-48f7-b5d7-1f25669d345c
title: Biochemical and microscopical investigation of Heavy Metal Associated Isoprenylated Plant Protein 7 (HIPP7) as a component and regulator of plasmodesmata. (Thesis data)

description: The data files are embargoed until 24/01/2027
DOI: 10.5281/zenodo.17484991
title: Mafoko Companion Dataset for Mafoko Open Multilingual Terminologies Paper

description: The Mafoko project systematically aggregates, digitises, and standardises fragmented multilingual terminological resources for South Africa’s official languages. Sourced from government and academic repositories, these terminologies have historically been locked in non-machine-readable formats and inaccessible structures, limiting their use for linguistic research and NLP development.

This release provides the foundational Mafoko dataset, curated under the equitable Africa-centered NOODL licensing framework. Data is released in open, machine-readable formats (CSV/JSON) with provenance metadata and ISO language identifiers.

Author list



Vukosi Marivate (University of Pretoria; AfriDSAI; Lelapa AI)

Isheanesu Dzingirai (University of Pretoria)

Fiskani Banda (University of Pretoria)

Richard Lastrucci (University of Pretoria)

Thapelo Sindane (University of Pretoria)

Keabetswe Madumo (University of Pretoria)

Kayode Olaleye (University of Pretoria)

Abiodun Modupe (University of Pretoria)

Unarine Netshifhefhe (University of Pretoria)

Herkulaas Combrink (University of the Free State)

Mohlatlego Nakeng (University of Pretoria)

Matome Ledwaba (University of Pretoria)


Corresponding author: vukosi.marivate@cs.up.ac.za
DOI: 10.5281/zenodo.17484992
title: Mafoko Companion Dataset for Mafoko Open Multilingual Terminologies Paper

description: The Mafoko project systematically aggregates, digitises, and standardises fragmented multilingual terminological resources for South Africa’s official languages. Sourced from government and academic repositories, these terminologies have historically been locked in non-machine-readable formats and inaccessible structures, limiting their use for linguistic research and NLP development.

This release provides the foundational Mafoko dataset, curated under the equitable Africa-centered NOODL licensing framework. Data is released in open, machine-readable formats (CSV/JSON) with provenance metadata and ISO language identifiers.

Author list



Vukosi Marivate (University of Pretoria; AfriDSAI; Lelapa AI)

Isheanesu Dzingirai (University of Pretoria)

Fiskani Banda (University of Pretoria)

Richard Lastrucci (University of Pretoria)

Thapelo Sindane (University of Pretoria)

Keabetswe Madumo (University of Pretoria)

Kayode Olaleye (University of Pretoria)

Abiodun Modupe (University of Pretoria)

Unarine Netshifhefhe (University of Pretoria)

Herkulaas Combrink (University of the Free State)

Mohlatlego Nakeng (University of Pretoria)

Matome Ledwaba (University of Pretoria)


Corresponding author: vukosi.marivate@cs.up.ac.za
DOI: 10.15468/dl.rymmze
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagenorhynchus obscurus obscurus"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009539-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fu2hu
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagenorhynchus obscurus fitzroyi"
 ]
}

 The dataset includes 28 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009537-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyfcvu
title: Occurrence Download

description: A dataset containing 956862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((136.2409 48.25909,136.0935 49.71547,129.7755 51.96353,123.8523 56.6137,117.5179 53.38808,109.0445 44.53851,108.591 44.49731,109.0552 17.11032,109.8999 16.73974,119.429 22.45741,134.5339 44.40329,136.2409 48.25909))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year is 2021"
 ]
}

 The dataset includes 956862 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009518-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95rnac
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Takasagohadra"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009538-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17491658
title: Data related to the publication: Mortality of ground beetles (Coleoptera, Carabidae) in discarded containers - evidence from urban forests

description: Data associated with the article: Mortality of ground beetles (Coleoptera, Carabidae) in discarded containers - evidence from urban forests

 

DaneiNEXT.slsx and Species richness by iNext.R - files corresponding to sample size based rarefaction and extrapolation curves for species richness and sample coverage with 95% confidence intervals  for ground beetle assemblage collected by container sampling and pitfall traps (Fig.2)

PERMANOVA - Bary - proportions.R and PERMAOVA - Raup.R - files corresponding to two-way PERMANOVA for the effect of sampling method and site on the qualitative similarity (Raup-Crick distance for species presence/absence) and quantitative similarity (Bray-Curtis distance for relative species abundance) in species composition (Table 1, Fig. 3, Appendix Fig. 3-4).

Statistical analyses are described in detail in the article
DOI: 10.5281/zenodo.17491659
title: Data related to the publication: Mortality of ground beetles (Coleoptera, Carabidae) in discarded containers - evidence from urban forests

description: Data associated with the article: Mortality of ground beetles (Coleoptera, Carabidae) in discarded containers - evidence from urban forests

 

DaneiNEXT.slsx and Species richness by iNext.R - files corresponding to sample size based rarefaction and extrapolation curves for species richness and sample coverage with 95% confidence intervals  for ground beetle assemblage collected by container sampling and pitfall traps (Fig.2)

PERMANOVA - Bary - proportions.R and PERMAOVA - Raup.R - files corresponding to two-way PERMANOVA for the effect of sampling method and site on the qualitative similarity (Raup-Crick distance for species presence/absence) and quantitative similarity (Bray-Curtis distance for relative species abundance) in species composition (Table 1, Fig. 3, Appendix Fig. 3-4).

Statistical analyses are described in detail in the article