cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28000349
title: Pruning the tree: comparing OTUs and ASVs for processing High-Throughput Sequencing 5S-IGS nuclear ribosomal DNA in phylogenetic studies – online supplementary data repository

description: We perfomed HTS Illumina Sequencing of the nuclear 5S rDNA intergenic spacers to address taxonomy, diversity and evolution in <i>Fagus </i>(Fagaceae). We compared Operational Taxonomic Units (OTUs) and Amplicon Sequence Variants (ASVs) of seven species-samples (<i>F. caspica </i>Denk & G.W.Grimm<i>, </i><i>F. crenata </i>Blume<i>, F. hayatae </i>Palib.<i>, </i><i>F. hohenackeriana </i>Palib.<i>, F. japonica </i>Maxim.<i>, F. orientalis </i>Lipsky<i>, F. sylvatica </i>L.) obtained with MOTHUR (two different workflows) and DADA2 (three different pooling options). We assessed the capacity of the derived phylogenetic inferences to enclose pivotal 5S-IGS variant types across methods. Over 70% of processed reads were shared between OTUs (100% identity; cutoff abundance &gt;4) and ASVs. Despite a strong reduction (&gt;80%) of the representative sequences, DADA2-ASVs identified all main 5S-IGS variants known for <i>Fagus</i>, fully reflecting the overall genetic diversity patterns within each sample. In contrast, large proportions of low-abundant representative amplicons appeared in MOTHUR-OTUs and -ASVs profiles and were inference-wise redundant. The higher convenience and reliability of DADA2 datasets were confirmed by further comparison with MOTHUR-datasets generated with cutoff abundance &gt;25.This fileset includes basic information on the produced data, the used alignments and resultant inference files.<b>Supplementary Data Archive (SDA)</b>—zipped analysis files, see _content.txt for archive's content and naming conventions<b>File S1</b>—multiple spread-sheet (XLSX) file listing the abundance of detected OTU and ASV representative sequence sets<b>File S2</b>—multiple spread-sheet (XLSX) file summarising the inference difficulty scores and non-parametric bootstrap supports for (alternative) topological aspects seen in all inferred ML trees<b>File S3</b>–PDF with graphically enhanced versions of the inferred per-sample ML trees (subtrees representing known (Cardoni et al. 2022, <i>The Plant Journal</i> <b>109</b>:909–926; Denk et al. 2024, <i>Willdenowia </i><b>54</b>:151–181), and new 5S-IGS main types (<i>F. hayatae </i>sample) collapsed<br>
DOI: 10.6084/m9.figshare.28000349.v2
title: Pruning the tree: comparing OTUs and ASVs for processing High-Throughput Sequencing 5S-IGS nuclear ribosomal DNA in phylogenetic studies – online supplementary data repository

description: We perfomed HTS Illumina Sequencing of the nuclear 5S rDNA intergenic spacers to address taxonomy, diversity and evolution in <i>Fagus </i>(Fagaceae). We compared Operational Taxonomic Units (OTUs) and Amplicon Sequence Variants (ASVs) of seven species-samples (<i>F. caspica </i>Denk & G.W.Grimm<i>, </i><i>F. crenata </i>Blume<i>, F. hayatae </i>Palib.<i>, </i><i>F. hohenackeriana </i>Palib.<i>, F. japonica </i>Maxim.<i>, F. orientalis </i>Lipsky<i>, F. sylvatica </i>L.) obtained with MOTHUR (two different workflows) and DADA2 (three different pooling options). We assessed the capacity of the derived phylogenetic inferences to enclose pivotal 5S-IGS variant types across methods. Over 70% of processed reads were shared between OTUs (100% identity; cutoff abundance &gt;4) and ASVs. Despite a strong reduction (&gt;80%) of the representative sequences, DADA2-ASVs identified all main 5S-IGS variants known for <i>Fagus</i>, fully reflecting the overall genetic diversity patterns within each sample. In contrast, large proportions of low-abundant representative amplicons appeared in MOTHUR-OTUs and -ASVs profiles and were inference-wise redundant. The higher convenience and reliability of DADA2 datasets were confirmed by further comparison with MOTHUR-datasets generated with cutoff abundance &gt;25.This fileset includes basic information on the produced data, the used alignments and resultant inference files.<b>Supplementary Data Archive (SDA)</b>—zipped analysis files, see _content.txt for archive's content and naming conventions<b>File S1</b>—multiple spread-sheet (XLSX) file listing the abundance of detected OTU and ASV representative sequence sets<b>File S2</b>—multiple spread-sheet (XLSX) file summarising the inference difficulty scores and non-parametric bootstrap supports for (alternative) topological aspects seen in all inferred ML trees<b>File S3</b>–PDF with graphically enhanced versions of the inferred per-sample ML trees (subtrees representing known (Cardoni et al. 2022, <i>The Plant Journal</i> <b>109</b>:909–926; Denk et al. 2024, <i>Willdenowia </i><b>54</b>:151–181), and new 5S-IGS main types (<i>F. hayatae </i>sample) collapsed<br>
DOI: 10.15468/dl.rc44fb
title: Occurrence Download

description: A dataset containing 10378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carassius auratus",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10378 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039308-250717081556266/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.28000349.v1
title: Pruning the tree: comparing OTUs and ASVs for processing High-Throughput Sequencing 5S-IGS nuclear ribosomal DNA in phylogenetic studies – online supplementary data repository

description: We perfomed HTS Illumina Sequencing of the nuclear 5S rDNA intergenic spacers to address taxonomy, diversity and evolution in <i>Fagus </i>(Fagaceae). We compared Operational Taxonomic Units (OTUs) and Amplicon Sequence Variants (ASVs) of seven species-samples (<i>F. caspica </i>Denk & G.W.Grimm<i>, </i><i>F. crenata </i>Blume<i>, F. hayatae </i>Palib.<i>, </i><i>F. hohenackeriana </i>Palib.<i>, F. japonica </i>Maxim.<i>, F. orientalis </i>Lipsky<i>, F. sylvatica </i>L.) obtained with MOTHUR (two different workflows) and DADA2 (three different pooling options). We assessed the capacity of the derived phylogenetic inferences to enclose pivotal 5S-IGS variant types across methods. Over 70% of processed reads were shared between OTUs and ASVs. Despite a strong reduction (&gt;80%) of the representative sequences, DADA2-ASVs identified all main 5S-IGS variants known for <i>Fagus</i>, fully reflecting the overall genetic diversity patterns within each sample. In contrast, large proportions of low-abundant representative amplicons appeared in MOTHUR-OTUs and -ASVs profiles and were inference-wise redundant.This fileset includes basic information on the produced data, the used alignments and resultant inference files.<b>Supplementary Data Archive</b>—zipped analysis files, see _content.txt for archive's content and naming conventions<b>File S1</b>—multiple spread-sheet (XLSX) file listing the abundance of detected OTU and ASV representative sequence sets<b>File S2</b>—multiple spread-sheet (XLSX) file summarising the inference difficulty scores and non-parametric bootstrap supports for (alternative) topological aspects seen in the inferred ML trees<b>File S3</b>–PDF with graphically enhanced versions of the inferred per-sample ML trees (subtrees representing known (Cardoni et al. 2022, <i>The Plant Journal</i> <b>109</b>:909–926; Denk et al. 2024, <i>Willdenowia </i><b>54</b>:151–181), and new 5S-IGS main types (<i>F. hayatae </i>sample) collapsed<br>
DOI: 10.15468/dl.3j3922
title: Occurrence Download

description: A dataset containing 1184 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sanicula laciniata"
 ]
}

 The dataset includes 1184 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039312-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vgwdxq
title: Occurrence Download

description: A dataset containing 16279 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sanicula crassicaulis"
 ]
}

 The dataset includes 16279 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039309-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8xn4p
title: Occurrence Download

description: A dataset containing 1701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "TaxonKey is Anoplolepis custodiens"
 ]
}

 The dataset includes 1701 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039311-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bgdty
title: Occurrence Download

description: A dataset containing 22292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chlidonias niger",
 "MediaType is Image"
 ]
}

 The dataset includes 22292 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039313-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ft3xh5
title: Occurrence Download

description: A dataset containing 2655 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Inula helenium",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2655 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039316-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ta9uph
title: Occurrence Download

description: A dataset containing 927 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styela clava",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 927 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039315-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xxnzxk
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carassius auratus",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039318-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pqjfqd
title: Occurrence Download

description: A dataset containing 2476 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Conyza"
 ]
}

 The dataset includes 2476 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039314-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.43q4jd
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Ficus barteri",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 212 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039319-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16410647
title: Data and code for the paper "Economic growth as a climate response strategy for low-income economies"

description: This repository stores data and code used in the above paper. The paper is currently under review. 

The active code repo can be found at: https://github.com/carnegie/clab_damage_function
DOI: 10.5284/1112528
title: Data from a Trial Trench Evaluation at Sparrow Lodge Farm, Wicken, Northamptonshire, 2021.

description: This collection comprises images, databases, site records, GIS files, and reports from the archaeological evaluation carried out by Oxford Archaeology at Sparrow Lodge Farm, Wicken, Northamptonshire from September to October 2021. The trial trench evaluation was commissioned by RPS Group on behalf of Elgin Energy and undertaken as a condition of planning permission in advance of a proposed solar farm. A series of archaeological features were revealed, conforming to anomalies previously identified via cropmark and geophysical survey of the area.
DOI: 10.15468/dl.p9fqvj
title: Occurrence Download

description: A dataset containing 3121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Xantho hydrophilus",
 "Year 2006-2025"
 ]
}

 The dataset includes 3121 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039317-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7a74gh
title: Occurrence Download

description: A dataset containing 89845 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Glycine max, Triticum aestivum, Oryza sativa, Hordeum vulgare, Vigna radiata, Ulmus pumila, Sorghum bicolor, Prunus persica, Cucumis melo, Castanea mollissima, Diospyros kaki, Phaseolus vulgaris, Vigna unguiculata, Zea mays, Prunus armeniaca, Sesamum indicum, Raphanus sativus, Vigna angularis, Setaria italica, Pisum sativum, Medicago sativa, Brassica rapa glabra, Citrullus lanatus, Pseudocydonia sinensis, Ziziphus jujuba, Juglans regia, Litchi chinensis, Cucurbita moschata, Avena sativa, Cucumis sativus, Cucurbita pepo, Helianthus annuus, Vigna unguiculata sesquipedalis, Panicum miliaceum, Vernicia montana, Prunus mume, Vicia faba, Cannabis sativa, Capsicum annuum, Citrus maxima, Elymus pseudocaninus, Solanum lycopersicum, Spinacia oleracea, Arachis hypogaea, Benincasa hispida, Lactuca sativa, Allium cepa, Solanum melongena, Agropyron cristatum, Lablab purpureus)",
 "Country is United States of America",
 "Year 1898-2024",
 "HasCoordinate is true"
 ]
}

 The dataset includes 89845 records from 312 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039301-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k74dzh
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Skagit Valley / Wrangel Island Snow Goose (aggregated per 1-degree cell)"
 ]
}

 The dataset includes 124 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039323-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gtrdmc
title: Occurrence Download

description: A dataset containing 1869 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aronia mitschurinii",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1869 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039324-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5udty
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Larus californicus)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039320-250717081556266/datasets/export for details.
DOI: 10.15468/dl.3eu49p
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styela clava",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039322-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5epfwg
title: Occurrence Download

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

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039325-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.chtcy3
title: Occurrence Download

description: A dataset containing 13282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chlidonias hybrida",
 "MediaType is Image"
 ]
}

 The dataset includes 13282 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039327-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fruuf
title: Occurrence Download

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

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039329-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48804/gk6lhh
title: Replication Data for: MATWI: A Multimodal Automatic Tool Wear Inspection dataset

description: MATWI, a new publicly available multimodal dataset for automatic tool wear inspection containing both images and captured sensor data during CNC milling processes. This dataset contains 17 tools ran to failure with 100 measurements over the lifespan, resulting in a large and unique dataset for tool wear estimation. It is also the first dataset that combines accelerometer, microphone and force measurements with image data captured along the tool life.
DOI: 10.15468/dl.86yzk6
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Styela clava",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039328-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82261/zwp2-qp19
title: Epigraphische Datenbank
title: EPIDAT
DOI: 10.15468/dl.ygaug7
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carassius auratus",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 710 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039330-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zr4hjz
title: Occurrence Download

description: A dataset containing 2132 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sanicula arguta"
 ]
}

 The dataset includes 2132 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039331-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25pdq7
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Ficus bivalvata",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039332-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/12nj6x
title: graph_info.zip

description: :unav
DOI: 10.57745/jgtopz
title: fasta_article.zip

description: :unav
DOI: 10.82261/0wrv-4788
title: Epigraphik-Datenbank  Clauss / Slaby
title: EDCS
DOI: 10.57745/uesd5v
title: Transposon_information.zip

description: :unav
DOI: 10.57745/tof86i
title: README – Apricot Pangenome Dataset Ove.md

description: :unav
DOI: 10.57745/wucadu
title: Genomic Resources for Apricot Pangenome Construction and TE Annotation

description: This dataset contains 25 assembled genome sequences from cultivated and wild apricot (Prunus armeniaca and relatives), used for pangenome graph construction. It also includes a curated library of transposable elements (TEs), with classification and non-redundant sequences across 11 reference assemblies. Graph files per chromosome and the phylogenetic guide tree used for the pangenome are provided.
DOI: 10.6084/m9.figshare.29635769
title: China Rice Terraces Dataset

description: This dataset contains the China rice terrace map at 1 km resolution (calculated from 30 m resolution map). The values shown on the map represent the proportion of rice terraces within each 1 km × 1 km grid cell.The dataset was generated based on three core data sources: a 30-meter resolution terraced farmland dataset for China from 2018 (https://zenodo.org/records/3895585); a 10-meter resolution double-season rice dataset covering the years 2016 to 2020 and nine provincial-level administrative regions, representing over 99% of China’s double-season rice cultivation area (https://doi.org/10.57760/sciencedb.IGA.00005); a 10-meter resolution single-season rice dataset spanning 2017 to 2022 and covering 21 provinces, accounting for approximately 98.91% of China’s single-season rice cultivation area (https://doi.org/10.57760/sciencedb.06963).<br>
DOI: 10.3535/4hc-agd-lln
title: Achillea santolina L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.