cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1389394.10fu
title: SH1389394.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389395.10fu
title: SH1389395.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389398.10fu
title: SH1389398.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389400.10fu
title: SH1389400.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389405.10fu
title: SH1389405.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389407.10fu
title: SH1389407.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389408.10fu
title: SH1389408.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389413.10fu
title: SH1389413.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389415.10fu
title: SH1389415.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1389417.10fu
title: SH1389417.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.17138336
title: Data and Codes for the manuscript "Role of Intersections in Fracture Connectivity"

description: Networks of intersecting fractures often provide the flow paths through subsurface reservoirs.  Assessing network connectivity is challenging because fracture intersections compose a vanishingly small fraction of the network void volume.  In the paper "Role of Intersections in Fracture Connectivity" by L.J. Pyrak-Nolte and D.D. Nolte, we perform a percolation and finite-size scaling analysis to study the connectivity provided by fracture intersections that was motivated by 3D X-ray imaging of the simplest element of fracture network, i.e., two orthogonal fractures.  This repository contains the laboratory data, Monte Carlo simulation data and computer codes associated with the analysis and results presented in the paper "Role of Intersections in Fracture Connectivity".
DOI: 10.5281/zenodo.17138337
title: Data and Codes for the manuscript "Role of Intersections in Fracture Connectivity"

description: Networks of intersecting fractures often provide the flow paths through subsurface reservoirs.  Assessing network connectivity is challenging because fracture intersections compose a vanishingly small fraction of the network void volume.  In the paper "Role of Intersections in Fracture Connectivity" by L.J. Pyrak-Nolte and D.D. Nolte, we perform a percolation and finite-size scaling analysis to study the connectivity provided by fracture intersections that was motivated by 3D X-ray imaging of the simplest element of fracture network, i.e., two orthogonal fractures.  This repository contains the laboratory data, Monte Carlo simulation data and computer codes associated with the analysis and results presented in the paper "Role of Intersections in Fracture Connectivity".
DOI: 10.5281/zenodo.17541739
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: 10.3334/cdiac/spruce.003
title: SPRUCE S1 Bog Vegetation Survey and Peat Depth Data: 2009

description: This data set reports the results of a field survey of the S1 Bog to characterize the vegetation and to determine peat depth. The survey was conducted on September 21 and 22, 2009. This initial survey of vegetation and peat depth characteristics of the target bog was conducted to evaluate the logical locations for installing replicated experimental blocks for SPRUCE. The goal was to identify multiple locations of uniform aboveground vegetation and belowground peat depth for positioning experimental units within the bog. The experimental work was conducted in a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).
DOI: 10.5281/zenodo.17541714
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: 10.15468/dl.eyfphu
title: Occurrence Download

description: A dataset containing 522728 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 one of (Nematolepis frondosa, Clarkia concinna, Galgera decurrens, Gomphrena tenella, Lophiolepis sorocephala, Lophiolepis spathulata, Arenaria capillipes, Isolepis montivaga, Isolepis prolifera, Lophiolepis dirmilensis, Silene multiflora, Crataegus germanica, Echinops acantholepis, Silene hampeana, Arctium ambiguum, Asynthema gracile, Bromus maritimus, Trigonella coerulescens, Gnidia squarrosa, Streptocarpus rexii, Cynanchica suberosa, Cynanchica rumelica, Chamaecytisus calcareus, Cynanchica affinis, Solenopsis annua, Solenopsis minuta, Ozothamnus ferrugineus, Cassinia storyi, Cynanchica litardierei, Gnidia ornata, Normeyera hostii, Soleirolia soleirolii, Euploca sessei, Kunzea juniperoides, Ozothamnus blackallii, Chamaecytisus supinus, Simethis mattiazzii, Cynanchica aristata, Tuberaria brevipes, Thelypteris gongylodes, Chamaecytisus spinescens, Polystichum lonchitis, Restio karooicus, Marrubium heterodon, Medicago intertexta, Vachellia seyal, Thymus citriodorus, Meiogyne cylindrocarpa, Dolichandra unguis-cati, Dasymalla glutinosa, Bungea trifida, Cirsium alatum, Collomia biflora, Rottboellia rottboellioides, Copiapoa humilis, Caesia capensis, Chloropyron maritimum, Protea nana, Ornithopus pinnatus, Minuartia recurva, Axonopus compressus, Blechnum attenuatum, Condea decipiens, Livistona australis, Berlandiera monocephala, Serapicamptis cytherea, Androcalva multiloba, Fimbristylis bisumbellata, Serapicamptis ligustica, Xylorhiza cognata, Cynodon dactylon, Aizoon sericeum, Aspalathus cordata, Xanthisma scabrellum, Aizoon glanduliferum, Cryptandra multispina, Moraea maximiliani, Vellereophyton vellereum, Justicia flava, Senecio ovatus, Senecio breviflorus, Petromarula pinnata, Aspalathus psoraleoides, Aspalathus monosperma, Thelymitra spiralis, Geochloa rufa, Moraea bulbillifera, Aruncus dioicus, Moraea namaquana, Adenostyles australis, Myriocephalus oldfieldii, Commersonia magniflora, Tephrosia villosa, Moraea sisyrinchium, Leptosiphon rattanii, Photinia arbutifolia, Dactylorhiza aschersoniana, Portulaca nitida, Roepera maculata, Helictochloa lusitanica)",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 522728 records from 2577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020253-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ns5zk8
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021688-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.63unxh
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.17806 1.9139,-69.645 1.9139,-69.645 6.5921,-76.17806 6.5921,-76.17806 1.9139))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "InstitutionCode is one of (pontificia universidad javeriana (puj), un, instituto de investigación de recursos biológicos alexander von humboldt (iavh), universidad del tolima (ut), uf, inciva)",
 "TaxonKey is Apistogramma macmasteri Kullander, 1979"
 ]
}

 The dataset includes 95 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006146-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.