cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0161960.10fu
title: SH0161960.10FU

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/sh0161961.10fu
title: SH0161961.10FU

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/sh0161962.10fu
title: SH0161962.10FU

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/sh0161963.10fu
title: SH0161963.10FU

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/sh0161964.10fu
title: SH0161964.10FU

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/sh0161965.10fu
title: SH0161965.10FU

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/sh0161966.10fu
title: SH0161966.10FU

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.mzbgqq
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kimberleyeleotris notata Hoese & Allen, 1987"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343197-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112042534
title: Cuneiform Tablet 1913.14.1728, Spurlock 1913.14.1728

description: [Text Description:] Administrative tablet ❧ [Text or Publication Number Note:] Spurlock 1913.14.1728; CDLI P421579 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Light Brown (5YR 6.5/4) Yellowish White (10YR 9/2) Dark Gray (N 3.25/ 7.7% R) ❧ [Physical Object Note:] 5 x 3.4 x 1.6 cm (25 g)
DOI: 10.15468/dl.6myrxg
title: Occurrence Download

description: A dataset containing 10814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Laminaria hyperborea (Gunnerus) Foslie",
 "Year 2000-2023"
 ]
}

 The dataset includes 10814 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0290243-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yq5py6
title: Occurrence Download

description: A dataset containing 792342 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brachypodium P.Beauv."
 ]
}

 The dataset includes 792342 records from 2173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015822-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hq7f97
title: Occurrence Download

description: A dataset containing 341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Pakistan",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aquila nipalensis Hodgson, 1833",
 "Year 1000-2022"
 ]
}

 The dataset includes 341 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240217-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eaeq2u
title: Occurrence Download

description: A dataset containing 553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Fossil)",
 "Country is one of (Chile, Panama, Uruguay, Nicaragua)",
 "Geometry POLYGON((-108.81474 -60.68627,-23.6217 -60.68627,-23.6217 12.88673,-108.81474 12.88673,-108.81474 -60.68627))",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "MediaType is Image",
 "TaxonKey is Caracara plancus (J.F.Miller, 1777)"
 ]
}

 The dataset includes 553 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122959-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vdy2a2
title: Occurrence Download

description: A dataset containing 953610 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ondatra zibethicus (Linnaeus, 1766)"
 ]
}

 The dataset includes 953610 records from 516 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139575-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/cbgyyf
title: 0219_cerisier.3mf

description: :unav
DOI: 10.15468/dl.jjxzgz
title: Occurrence Download

description: A dataset listing the 14535 species recorded in GBIF matching the query:
{
 "Country" : [
 "is Benin"
 ]
}

 The dataset's 14535 records were derived from 493 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240713-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.66gseq
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucothoe hipposideros White & Thomas, 2009"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122965-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x3wg88
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Codium intricatum Okamura, 1902"
 ]
}

 The dataset includes 169 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139574-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ftwnuf
title: Occurrence Download

description: A dataset containing 1644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Country is one of (United States of America, Mexico, Canada)",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Coryphaenoides cinereus (Gilbert, 1896)"
 ]
}

 The dataset includes 1644 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048001-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esnget
title: Occurrence Download

description: A dataset listing the 41211 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-34.08417 29.57049,1.93084 29.57049,1.93084 43.98280,-34.08417 43.98280,-34.08417 29.57049))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 41211 records were derived from 723 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138897-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17114540
title: GapView Experiment

description: This repository accompanies the paper “Mind the Gap: Measuring Knowledge Gaps in RAG Pipelines” and provides all data, embeddings, and analysis scripts used in the study.

The project introduces GapView, a preretrieval diagnostic method that uses cosine similarity between question and document embeddings to evaluate whether a knowledge base contains the information needed to answer user questions before invoking a RAG pipeline.

 

The included .zip file contains six synthetic datasets spanning clinical and programming domains, along with Python scripts and result files that reproduce the experiments for this work.
DOI: 10.5281/zenodo.17299908
title: GapView Experiment

description: This repository accompanies the paper “Mind the Gap: Measuring Knowledge Gaps in RAG Pipelines” and provides all data, embeddings, and analysis scripts used in the study.

The project introduces GapView, a preretrieval diagnostic method that uses cosine similarity between question and document embeddings to evaluate whether a knowledge base contains the information needed to answer user questions before invoking a RAG pipeline.

 

The included .zip file contains six synthetic datasets spanning clinical and programming domains, along with Python scripts and result files that reproduce the experiments for this work.
DOI: 10.5281/zenodo.18514308
title: Citrus_segregation_landscapes

description: Datasets for haplotype reshuffling shatters the Mendelian equilibrium of asexual lineages

This data repository stores datasets generated in the study of segregation distortion uncovered during the evolutionary transition from apomixis to sexual reproduction in Citrus hindsii. These files are provided to support full reproducibility of all analyses in the corresponding manuscript.The deposited data include key intermediate results across three major research components:



Genome assembly and pangenome construction: haplotype-resolved genome assemblies of PN and DB, genome annotation files (gene models, repeat annotation, TE annotation, LTR annotation), variation calls (inversions, presence/absence variants), pangenome graphs, and supporting alignment files.

Haplotype-specific marker development and progeny haplotype reconstruction: haplotype-diagnostic markers, high-density genotype calls of the mapping population, recombination breakpoint coordinates, haplotype origin assignments along chromosomes, and genome-wide haplotype shuffling landscapes.


Tree for these datasets:├── breakpoints_bins_haplotype│   ├── Shuffle_interval_DB_PN_chr1.txt│   ├── Shuffle_interval_DB_PN_chr2.txt│   ├── Shuffle_interval_DB_PN_chr3.txt│   ├── Shuffle_interval_DB_PN_chr4.txt│   ├── Shuffle_interval_DB_PN_chr5.txt│   ├── Shuffle_interval_DB_PN_chr6.txt│   ├── Shuffle_interval_DB_PN_chr7.txt│   ├── Shuffle_interval_DB_PN_chr8.txt│   └── Shuffle_interval_DB_PN_chr9.txt├── genome_and_annotations│   ├── DB.hap1.EDTA.TEanno.gff3│   ├── DB.hap1.fa│   ├── DB.Hap1.Final.gff3│   ├── DB.hap2.EDTA.TEanno.gff3│   ├── DB.hap2.fa│   ├── DB.Hap2.Final.gff3│   ├── PN.hap1.EDTA.TEanno.gff3│   ├── PN.hap1.fa│   ├── PN.Hap1.Final.gff3│   ├── PN.hap2.EDTA.TEanno.gff3│   ├── PN.hap2.fa│   └── PN.Hap2.Final.gff3├── pangenome_and_variation│   ├── DBhap1.specific.0.vcf│   ├── DBhap1.specific.1.vcf│   ├── DBhap2.specific.0.vcf│   ├── DBhap2.specific.1.vcf│   ├── KumquatPG.gfa.gz│   ├── KumquatPG.vcf.gz│   ├── PNhap1.specific.0.vcf│   ├── PNhap1.specific.1.vcf│   ├── PNhap2.specific.0.vcf│   └── PNhap2.specific.1.vcf└── progeny_and_variation    ├── DB.male.markers.map    ├── merged_queries.raw.vcf.gz    └── PN.female.markers.map
DOI: 10.5281/zenodo.18514307
title: Citrus_segregation_landscapes

description: Datasets for haplotype reshuffling shatters the Mendelian equilibrium of asexual lineages

This data repository stores datasets generated in the study of segregation distortion uncovered during the evolutionary transition from apomixis to sexual reproduction in Citrus hindsii. These files are provided to support full reproducibility of all analyses in the corresponding manuscript.The deposited data include key intermediate results across three major research components:



Genome assembly and pangenome construction: haplotype-resolved genome assemblies of PN and DB, genome annotation files (gene models, repeat annotation, TE annotation, LTR annotation), variation calls (inversions, presence/absence variants), pangenome graphs, and supporting alignment files.

Haplotype-specific marker development and progeny haplotype reconstruction: haplotype-diagnostic markers, high-density genotype calls of the mapping population, recombination breakpoint coordinates, haplotype origin assignments along chromosomes, and genome-wide haplotype shuffling landscapes.


Tree for these datasets:├── breakpoints_bins_haplotype│   ├── Shuffle_interval_DB_PN_chr1.txt│   ├── Shuffle_interval_DB_PN_chr2.txt│   ├── Shuffle_interval_DB_PN_chr3.txt│   ├── Shuffle_interval_DB_PN_chr4.txt│   ├── Shuffle_interval_DB_PN_chr5.txt│   ├── Shuffle_interval_DB_PN_chr6.txt│   ├── Shuffle_interval_DB_PN_chr7.txt│   ├── Shuffle_interval_DB_PN_chr8.txt│   └── Shuffle_interval_DB_PN_chr9.txt├── genome_and_annotations│   ├── DB.hap1.EDTA.TEanno.gff3│   ├── DB.hap1.fa│   ├── DB.Hap1.Final.gff3│   ├── DB.hap2.EDTA.TEanno.gff3│   ├── DB.hap2.fa│   ├── DB.Hap2.Final.gff3│   ├── PN.hap1.EDTA.TEanno.gff3│   ├── PN.hap1.fa│   ├── PN.Hap1.Final.gff3│   ├── PN.hap2.EDTA.TEanno.gff3│   ├── PN.hap2.fa│   └── PN.Hap2.Final.gff3├── pangenome_and_variation│   ├── DBhap1.specific.0.vcf│   ├── DBhap1.specific.1.vcf│   ├── DBhap2.specific.0.vcf│   ├── DBhap2.specific.1.vcf│   ├── KumquatPG.gfa.gz│   ├── KumquatPG.vcf.gz│   ├── PNhap1.specific.0.vcf│   ├── PNhap1.specific.1.vcf│   ├── PNhap2.specific.0.vcf│   └── PNhap2.specific.1.vcf└── progeny_and_variation    ├── DB.male.markers.map    ├── merged_queries.raw.vcf.gz    └── PN.female.markers.map
DOI: 10.15468/dl.5fkfay
title: Occurrence Download

description: A dataset containing 1432 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microchloa kunthii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1432 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019160-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8sjyab
title: Occurrence Download

description: A dataset containing 1604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microlaena stipoides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1604 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019161-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m7hsx8
title: Occurrence Download

description: A dataset containing 2406 records in GBIF matching the query:

 SELECT gbifid, datasetkey, specieskey, kingdom, phylum, class, "order", family, genus, species, scientificname, decimallatitude, decimallongitude, eventdate, institutioncode, "year" AS obs_year, basisofrecord, coordinateuncertaintyinmeters, issue
 FROM occurrence
 WHERE
 decimallatitude IS NOT NULL
 AND decimallongitude IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND coordinateuncertaintyinmeters IS NOT NULL
 AND coordinateuncertaintyinmeters &gt; 0
 AND coordinateuncertaintyinmeters &lt;= 200.0
 AND decimallatitude &gt;= 8.098015256935714
 AND decimallatitude &lt;= 12.166598047573723
 AND decimallongitude &gt;= 40.15865171642743
 AND decimallongitude &lt;= 45.534006342908626
 AND GBIF_Within('POLYGON ((45.534006 8.098015, 45.534006 12.166598, 40.158652 12.166598, 40.158652 8.098015, 45.534006 8.098015))', decimallatitude, decimallongitude) = TRUE
 

 The dataset's 2406 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019155-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2p3re9
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microstegium fasciculatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 549 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019162-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.