cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16983154
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB22973 and PRJEB57230 (cohort used in catalogue assembly) and PRNJNA609596 (independent cohort not used in assembly).
DOI: 10.15468/dl.2spbbz
title: Occurrence Download

description: A dataset containing 3770 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus microcephalus"
 ]
}

 The dataset includes 3770 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012952-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48577/jpl.t5hivj
title: Measuring the Masses of the TOI-700 Planets with ESPRESSO

description: No abstract available.
DOI: 10.48577/jpl.vwyzwe
title: Magnetic Shielding Concepts for Reaction Wheel Assembly on NASA Europa Clipper Spacecraft

description: No abstract available.
DOI: 10.5281/zenodo.17011293
title: ETIOPATHOGENETICALLY BASED DETECTION OF PERIODONTITIS ASSOCIATED WITH CANDIDA AMONG PATIENTS.
DOI: 10.5281/zenodo.17011294
title: ETIOPATHOGENETICALLY BASED DETECTION OF PERIODONTITIS ASSOCIATED WITH CANDIDA AMONG PATIENTS.
DOI: 10.15468/dl.w5fqk2
title: Occurrence Download

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

 The dataset includes 36 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012954-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hpx6fq
title: Occurrence Download

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

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012955-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7trtu
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012956-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48577/jpl.ccjv7j
title: Gravity science instrumentation for a Uranus Orbiter and Probe Mission

description: No abstract available.
DOI: 10.5281/zenodo.16983124
title: MicroReset: characterization of the rabbit (Oryctolagus cuniculus) fecal metagenome and resistome by deep shotgun sequencing

description: Data sourceThe dataset was generated from 30 rabbit fecal samples subjected to deep shotgun metagenomic sequencing. The sequencing data is available under the BioProject PRJEB50625.Metagenomic AssemblyRaw sequencing reads were first pre-processed using fastp for adapter removal and quality trimming. Host-derived reads were filtered out by mapping to the rabbit reference genome (GCF_000001635.27) using Bowtie2 and removing mapped reads with Samtools. Each sample was individually assembled using metaSPAdes. Contigs shorter than 1,500 bp were excluded from downstream analysis.
MAG RecoveryReads from each sample were mapped to all 30 assemblies (30×30 mappings) using Bowtie2. The resulting alignments were sorted and indexed with Samtools. Contig coverage across all samples was computed using `jgi_summarize_bam_contig_depths`. Binning was performed with MetaBAT 2 and SemiBin v1.3. MAG quality was assessed with CheckM. Only high-quality MAGs (≥70% completeness, ≤5% contamination, N50 ≥ 8 kb) were retained.Non-Redundant Gene CatalogGene prediction was carried out using Prodigal on all contigs from the current study (with `-m -p meta`). Genes shorter than 90 bp or lacking start/stop codons were discarded. The remaining genes from both sources were pooled and clustered using CD-HIT-EST (parameters: `-c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0`). The longest contigs were used to select representative genes.
MSP RecoveryShotgun reads from the 30 samples were aligned to the non-redundant gene catalog using the Meteor suite, generating a gene abundance matrix (5.7 million genes × 30 samples). Co-abundant genes were grouped into 1,053 Metagenomic Species Pan-genomes (MSPs) using MSPminer.
Taxonomic Annotation of MSPsMAGs representing each species were taxonomically annotated using GTDB-Tk with GTDB release r214. The resulting taxonomy was propagated to the corresponding MSPs.
Phylogenetic Tree ConstructionA set of 39 universal phylogenetic marker genes was extracted from the 1,053 MSPs (or their corresponding MAGs, when available) using fetchMGs. Each marker was independently aligned using MUSCLE, and the alignments were concatenated and trimmed using trimAl (parameter: `-automated1`). A maximum-likelihood phylogenetic tree was constructed with FastTreeMP (parameters: `-gamma -pseudo -spr -mlacc 3 -slownni`).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB50625 (cohort used in catalogue assembly).
DOI: 10.48577/jpl.5xpi1d
title: Novel Approach to Spacecraft System Level Magnetic Test at NASA Jet Propulsion Laboratory

description: A novel and unique spacecraft system level magnetic test method was conceptualized, designed, and developed to support two concurrent spacecrafts built at NASA JPL (Jet Propulsion Laboratory), Psyche and Europa Clipper, both equipped with science-grade magnetometers. This method did not require the use of a large three-axis Helmholtz/Braunbeck coils or a mu-metal shielded chamber, typically used by the majority of magnetic test facilities to remove Earth’s magnetic field. The method was accurate and robust, scalable from small electronic assemblies to large flight systems, portable, cost effective, and relatively risk-free to the spacecraft. The method underwent proof-of-concept testing with a known magnetic source as well as a mock-up spacecraft. Ultimately, it was successfully performed on the Psyche spacecraft and Europa Clipper spacecraft.
DOI: 10.48577/jpl.ty5v8m
title: JOINT POLARIMETRIC/TIME SERIES ANALYSIS OF INUNDATION DYNAMICS

description: No abstract available.
DOI: 10.48577/jpl.z9fg1r
title: 2.5/3D Package Microbump Metallurgy

description: No abstract available.
DOI: 10.15468/dl.qmmps8
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus mollis"
 ]
}

 The dataset includes 26 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012957-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17008279
title: Widget-Based Environment Awareness: UX Evaluation on Air Quality Interface on Urban Mobile Application Creators
DOI: 10.5281/zenodo.17011198
title: Widget-Based Environment Awareness: UX Evaluation on Air Quality Interface on Urban Mobile Application Creators
DOI: 10.5281/zenodo.17011214
title: Dataset for "Nonreciprocal Entanglement by Dynamically Encircling a Nexus"
DOI: 10.5281/zenodo.17011215
title: Dataset for "Nonreciprocal Entanglement by Dynamically Encircling a Nexus"
DOI: 10.15468/dl.4c6fph
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012959-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5zmmp
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012958-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhpqug
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012960-250827131500795/datasets/export for details.
DOI: 10.15468/dl.pwcdfj
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus scaberrimus"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012961-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17009466
title: Unified Synthetic Ortophoto Shadow Dataset

description: This is a placeholder for the description.
DOI: 10.5281/zenodo.17009467
title: Unified Synthetic Ortophoto Shadow Dataset

description: This is a placeholder for the description.
DOI: 10.15468/dl.jja7au
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012963-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdk73p
title: Occurrence Download

description: A dataset containing 1008 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus bolanderi"
 ]
}

 The dataset includes 1008 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012964-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e99qyv
title: Occurrence Download

description: A dataset containing 9902009 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "DatasetKey is one of (Southern African Bird Atlas Project 2, Southern African Bird Atlas Project)",
 "Geometry POLYGON((26.10058 -26.77017,32.87732 -26.77017,32.87732 -24.06063,26.10058 -24.06063,26.10058 -26.77017))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 9902009 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012953-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17011206
title: Niqab Dataset for Occluded Face Detection

description: The Niqab Dataset is a curated collection of images designed to support research in face detection under conditions of heavy occlusion, particularly relevant for cultural and religious coverings such as the niqab, veil, and mask. The dataset contains approximately 10,000 images with 12,000 faces, where over 50% of the faces are covered. A subset of 5,175 images (5,343 faces) was employed in our experiments.

The dataset provides diverse occlusion styles of niqabs and veils, reflecting real-world variations in coverage, position, and texture. Each image is manually annotated with bounding boxes using a contextual labeling approach that incorporates surrounding head and shoulder regions, enabling models to capture auxiliary visual cues critical for detecting highly occluded faces.

This dataset was developed and utilized in the study:Alashbi AAS, Sunar MS. Occluded face detection, face in Niqab dataset. In: Saeed F, Mohammed F, Gazem N,editors. Emerging Trends in Intelligent Computing and Informatics. Cham, Switerland: Springer InternationalPublishing; 2020. p. 209–15. doi: 10.1007/978-3-030-33582-3_20. 

The dataset can support a wide range of applications in computer vision, security, surveillance, biometrics, and cultural AI research, serving as a benchmark for the development and evaluation of models handling highly occluded face scenarios.

Contents:





10,000+ images (niqab-covered faces, partially occluded faces, and non-faces).




Bounding box annotations (contextual labeling).




Training/testing split (approx. 80/20).



Intended Use:For research in face detection, occluded face recognition, and machine learning model benchmarking.
DOI: 10.5281/zenodo.17011207
title: Niqab Dataset for Occluded Face Detection

description: The Niqab Dataset is a curated collection of images designed to support research in face detection under conditions of heavy occlusion, particularly relevant for cultural and religious coverings such as the niqab, veil, and mask. The dataset contains approximately 10,000 images with 12,000 faces, where over 50% of the faces are covered. A subset of 5,175 images (5,343 faces) was employed in our experiments.

The dataset provides diverse occlusion styles of niqabs and veils, reflecting real-world variations in coverage, position, and texture. Each image is manually annotated with bounding boxes using a contextual labeling approach that incorporates surrounding head and shoulder regions, enabling models to capture auxiliary visual cues critical for detecting highly occluded faces.

This dataset was developed and utilized in the study:Alashbi AAS, Sunar MS. Occluded face detection, face in Niqab dataset. In: Saeed F, Mohammed F, Gazem N,editors. Emerging Trends in Intelligent Computing and Informatics. Cham, Switerland: Springer InternationalPublishing; 2020. p. 209–15. doi: 10.1007/978-3-030-33582-3_20. 

The dataset can support a wide range of applications in computer vision, security, surveillance, biometrics, and cultural AI research, serving as a benchmark for the development and evaluation of models handling highly occluded face scenarios.

Contents:





10,000+ images (niqab-covered faces, partially occluded faces, and non-faces).




Bounding box annotations (contextual labeling).




Training/testing split (approx. 80/20).



Intended Use:For research in face detection, occluded face recognition, and machine learning model benchmarking.
DOI: 10.5281/zenodo.16982908
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJNA46333 (cohort used in catalogue assembly) and PRJEB80549 (independent cohort not used in assembly).
DOI: 10.5281/zenodo.16982835
title: Updated Metagenomic Species Pan-genomes (MSPs) of the human gastrointestinal microbiota

description: Gene catalog constructionThe methodology for creating the IGC2 catalog is described in the original papers: Li et al., 2014 and Wen et al., 2017
MSP creationReads from publicly available human gut metagenomes were aligned against the IGC2 catalog with the Meteor to produce a raw gene abundance table (10.4M genes quantified in >2000 samples). Then, co-abundant genes were binned in 1,989 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationMSPs taxonomic annotation was performed by aligning MSP core and accessory genes against representative genomes of the Genome Taxonomy Database (GTDB r207) using blastn (task = megablast, word_size = 16). The 20 best hits for each gene were kept (--max-target-seq 20). Using an in-house pipeline, a species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). 
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB1786, PRJEB5224, PRJEB6337, PRJNA422434 (cohort used in catalogue assembly) and PRJEB11532, PRJEB33500, PRJEB37249, PRNJNA834801 (independent cohort not used in assembly).
DOI: 10.5281/zenodo.17011276
title: test

description: Test for personal publish service
DOI: 10.15468/dl.sff7yh
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus strumosus"
 ]
}

 The dataset includes 31 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012965-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6z34fq
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Turdus feae",
 "Year 2015-2025"
 ]
}

 The dataset includes 314 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012966-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.