cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1099223.10fu
title: SH1099223.10FU

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/sh1099224.10fu
title: SH1099224.10FU

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/sh1099226.10fu
title: SH1099226.10FU

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/sh1099227.10fu
title: SH1099227.10FU

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/sh1099228.10fu
title: SH1099228.10FU

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/sh1099230.10fu
title: SH1099230.10FU

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/sh1099231.10fu
title: SH1099231.10FU

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/sh1099234.10fu
title: SH1099234.10FU

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/sh1099236.10fu
title: SH1099236.10FU

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/sh1099238.10fu
title: SH1099238.10FU

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: 10.15468/dl.sy1n0u
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Costa Rica",
 "Country is Panama"
 ]
 },
 "TaxonKey is Achillea millefolium L."
 ]
}

 The dataset includes 43 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033140-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jvggz9
title: Occurrence Download

description: A dataset containing 2337 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 Rhynchocyclus fulvipectus (P.L.Sclater, 1860)"
 ]
}

 The dataset includes 2337 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004772-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vtbxvf
title: Occurrence Download

description: A dataset containing 11426664 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada"
 ]
 },
 {
 "or" : [
 "Issue is Coordinate rounded",
 "Issue is Geodetic datum assumed WGS84",
 "Issue is Coordinate reprojected",
 "Issue is Country derived from coordinates",
 "Issue is Taxon match fuzzy",
 "Issue is Elevation min max swapped",
 "Issue is Identified date unlikely"
 ]
 },
 "Year 1990-2011",
 "Geometry POLYGON((-120.94849 50.59204,-122.53052 48.79028,-122.7063 41.20972,-121.47583 37.67212,-116.1145 33.73901,-100.12939 33.37646,-98.71216 39.0564,-98.40454 48.87817,-102.32666 51.70166,-111.17065 52.3938,-119.4104 51.86646,-120.94849 50.59204))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11426664 records from 417 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033141-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/lohi5m
title: A-25.0219: Toldijk, Toldijk Kabelverzwaring Ring Toldijk, gemeente Bronckhorst. Opgraving (variant Archeologische begeleiding)

description: &lt;p&gt;In maart 2025 is een archeologische begeleiding uitgevoerd aan de Broekstraat, Moatweg, Elderinkweg, Olde Kaste, Steenderenseweg en de N316 in de gemeente Bronckhorst. De begeleiding vond plaats in kabelsleuven en proefputten ten behoeve van gestuurde boringen. Tijdens het veldwerk kon geconstateerd worden dat de bodems aan de Broekstraat, Moatweg, Elderinkweg, Olde Kaste en de Steenderenseweg reeds verstoord zijn tot minimaal één meter beneden maaiveld door de aanleg van kabels en leidingen in subrecente perioden. Ter hoogte van de N316 en in het meest noordelijke deel van het begeleide tracé aan de Broekstraat is het bodemprofiel intact. Tijdens het onderzoek zijn twee vondsten verzameld uit een (sub)recente akkerlaag.&lt;/p&gt;
DOI: 10.6084/m9.figshare.30010978
title: <b>Contrasting</b><b> genomic trajectories of </b><b><i>Bartonellaceae</i></b><b> symbionts of planthoppers</b>

description: This repository currently contains the following files, associated with the study:<br><b>Ma M., Michalik A., Deng J., Hu Y., Łukasik P. (preprint-2025). </b><b><i>Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers.</i></b><b> bioRxiv.</b> https://doi.org/10.1101/2025.08.24.672000<br><b>00_Supplementary_Tables.xlsx: </b>eight supplementary tables including sample metadata, bacterial composition, genome characteristics, genetic distances among <i>Tokpelaia</i> strains, and details of annotation and gene pathway reconstruction.Supplementary Table S1. Characteristics of the processed planthopper samples where Bartonellaceae were detected, and sample processing details.Supplementary Table S2. 16S rRNA sequences reconstructed using PhyloFlash from metagenomic data for Bartonellaceae-hosting planthopper samples.Supplementary Table S3. Binning information of metagenomic data.Supplementary Table S4. Summary of scaffolds assigned to different bins in planthopper metagenomes.Supplementary Table S5. 16S rRNA identities for Tokpelaia symbionts of planthoppers and ants.Supplementary Table S6. Average amino acid identity for phylogentically informative genes from genomes of Tokpelaia symbionts of planthoppers and ants.Supplementary Table S7. KEGG Orthologs (KOs) found in symbiont draft genomes.Supplementary Table S8. The list of genes identified in Tokpelaia-OECLID genome.<b>16S_rRNA_align.phy, draft_genome.phy, 16S_RAxML_bipartitions.all.tre</b><b>, </b><b>draft_genome_RAxML_bipartitions.all.tre</b>: alignment and raw tree files based on 16S rRNA and whole-genome data.<b>*_Tokpelaia.fasta, </b><b>*_Tokpelaia.gbk</b>: genome sequences and annotation files generated by Prokka for <i>Tokpelaia</i> from six planthopper species.
DOI: 10.6084/m9.figshare.30010978.v5
title: <b>Contrasting</b><b> genomic trajectories of </b><b><i>Bartonellaceae</i></b><b> symbionts of planthoppers</b>

description: This repository currently contains the following files, associated with the study:<br><b>Ma M., Michalik A., Deng J., Hu Y., Łukasik P. (preprint-2025). </b><b><i>Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers.</i></b><b> bioRxiv.</b> https://doi.org/10.1101/2025.08.24.672000<br><b>00_Supplementary_Tables.xlsx: </b>eight supplementary tables including sample metadata, bacterial composition, genome characteristics, genetic distances among <i>Tokpelaia</i> strains, and details of annotation and gene pathway reconstruction.Supplementary Table S1. Characteristics of the processed planthopper samples where Bartonellaceae were detected, and sample processing details.Supplementary Table S2. 16S rRNA sequences reconstructed using PhyloFlash from metagenomic data for Bartonellaceae-hosting planthopper samples.Supplementary Table S3. Binning information of metagenomic data.Supplementary Table S4. Summary of scaffolds assigned to different bins in planthopper metagenomes.Supplementary Table S5. 16S rRNA identities for Tokpelaia symbionts of planthoppers and ants.Supplementary Table S6. Average amino acid identity for phylogentically informative genes from genomes of Tokpelaia symbionts of planthoppers and ants.Supplementary Table S7. KEGG Orthologs (KOs) found in symbiont draft genomes.Supplementary Table S8. The list of genes identified in Tokpelaia-OECLID genome.<b>16S_rRNA_align.phy, draft_genome.phy, 16S_RAxML_bipartitions.all.tre</b><b>, </b><b>draft_genome_RAxML_bipartitions.all.tre</b>: alignment and raw tree files based on 16S rRNA and whole-genome data.<b>*_Tokpelaia.fasta, </b><b>*_Tokpelaia.gbk</b>: genome sequences and annotation files generated by Prokka for <i>Tokpelaia</i> from six planthopper species.
DOI: 10.6084/m9.figshare.30010978.v4
title: <b>Contrasting</b><b> genomic trajectories of </b><b><i>Bartonellaceae</i></b><b> symbionts of planthoppers</b>

description: Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in the family <i>Bartonellaceae</i> (Hyphomicrobiales), notorious for also including virulent vertebrate pathogens. Here we show that <i>Bartonellaceae</i> phylogenetically placed within the clade that has only encompassed ant symbionts to date – <i>Candidatus</i> genus Tokpelaia – have established as symbionts in four different clades of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Genome size and contents indicate different levels of integration of these strains into the planthopper host biology and their diverse roles. Symbionts infecting one of the clades have some of the largest genomes among <i>Bartonellaceae</i>, at ca. 2 Mb, two others are under 700 kb, and the fourth is reduced to barely 158 kb. The planthopper-associated <i>Tokpelaia </i>strains with larger genomes, similarly to ant symbionts, encode multiple amino acid and vitamin biosynthesis genes, complementing the degraded nutritional capabilities of their hosts’ ancient heritable endosymbionts. Strikingly, the smallest <i>Tokpelaia </i>genome lacks any genes linked to essential amino acid biosynthesis, in contrast to all other known insect-associated bacteria with genomes of comparable size. We identified a single vitamin biosynthesis gene and iron-sulfur cluster assembly genes as its only putative contributions to the host biology. Our results broaden the host spectrum of non-pathogenic <i>Bartonellaceae</i>, indicating that they have contributed to nutrition and symbiotic consortium function in diverse diet-restricted host clades. They also highlight an unexpectedly broad range of evolutionary outcomes for this important bacterial group.
DOI: 10.5281/zenodo.14900505
title: Unprocessed data from the Jungle Rhythms citizen science project

description: The Jungle Rhythms project aimed to transcribe phenology observations recorded between ~1940 and 1960 in the tropical rainforest of the Democratic Republic of the Congo. This is the raw data provided by Zooniverse after the completion of the project, and linked to the Jungle Rhythms workflow (see related projects) for converting the data to usable phenology observations.

Summary

Both input and output of the citizen science transcriptions are provided in this data set. This includes the original cut-outs as used in the Zoonivese project, and the output as generated by the Zooniverse data export routines. The data export routines provided CSV output with JSON subfields on the content of each classification made. In addition, we provided the exported subject list and the details of each workflow.

In total the project output constitutes of four files:



jungle-rhythms-classifications.csv (annotations of the tables)

jungle-rhythms-workflows.csv (description of the citsci workflow)

jungle-rhythms-subjects.csv (list of all images transcribed, and their online location for validation / referencing)

project-153-tags_2017-05-15.json (forum tags)

project-153-comments_2017-05-15.json (forum comments)


and roughly ~700MB in data volume.
DOI: 10.5281/zenodo.14900504
title: Unprocessed data from the Jungle Rhythms citizen science project

description: The Jungle Rhythms project aimed to transcribe phenology observations recorded between ~1940 and 1960 in the tropical rainforest of the Democratic Republic of the Congo. This is the raw data provided by Zooniverse after the completion of the project, and linked to the Jungle Rhythms workflow (see related projects) for converting the data to usable phenology observations.

Summary

Both input and output of the citizen science transcriptions are provided in this data set. This includes the original cut-outs as used in the Zoonivese project, and the output as generated by the Zooniverse data export routines. The data export routines provided CSV output with JSON subfields on the content of each classification made. In addition, we provided the exported subject list and the details of each workflow.

In total the project output constitutes of four files:



jungle-rhythms-classifications.csv (annotations of the tables)

jungle-rhythms-workflows.csv (description of the citsci workflow)

jungle-rhythms-subjects.csv (list of all images transcribed, and their online location for validation / referencing)

project-153-tags_2017-05-15.json (forum tags)

project-153-comments_2017-05-15.json (forum comments)


and roughly ~700MB in data volume.
DOI: 10.15468/dl.6kab43
title: Occurrence Download

description: A dataset containing 123499 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Corbicula fluminea, Dreissena bugensis, Dreissena polymorpha, Hydrocotyle ranunculoides, Lagarosiphon major)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2024",
 "HasCoordinate is true"
 ]
}

 The dataset includes 123499 records from 913 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002693-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.