cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1382093.10fu
title: SH1382093.10FU

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/sh1382094.10fu
title: SH1382094.10FU

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/sh1382095.10fu
title: SH1382095.10FU

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.18229587
title: Mitochondrial genome sequences of Fireflies (Coleoptera: Lampyridae)

description: This dataset contains 82 published and 22 newly sequenced and assembled complete mitochondrial genomes of fireflies. From these complete mitochondrial genomes, we extracted 13 protein coding genes and 2 rRNA genes, which we aligned and curated. Finally, we built a time-calibrated phylogeny for these 104 firefly species.

Description of the data and file structure

We collected 22 firefly species from Europe and Central America. Bioluminiscent adults (Luciola, Photinus, Photuris and Bicellonycha) were collected using an insect net and dark adults were collected using light traps (Lamprohiza and Lampyris). High molecular weight DNA was extracted from single males using the MagAttract HMW DNA kit (Qiagen) following manufacturer’s guidelines. DNA fragment sizes and integrity were checked with a 1% agarose gel. Long DNA fragments were sequenced from a single male individual using Nanopore PromethION sequencer.

We additionally collected mitochondrial genomes from GenBank for 82 firefly species.### Files and variables

File: alignments.zip

Description: Multiple sequence alignments of all 104 firefly species used in this study (one file per locus). We extracted 13 protein coding genes and two rRNA genes from the complete mitochondrial genomes. We combined these published genomes with our 22 mitochondrial genomes. We aligned the 13 protein coding genes using MACSE v2, using the insect mitochondrial code. We also used MACSE to replace artificial stopcodons with ‘NNN’ if these occurred within a protein coding sequence. Furthermore, we trimmed the alignments using trimAl with the option automated1. For the two ribosomal RNA genes 12S and 16S, we used the alignment software MAFFT v7 and trimAl with the option automated1.

File: Lampyridae_Mito_final.tre

Description: Our final estimated time-calibrated phylogeny containing the 104 firefly species. The phylogeny was estimated using RevBayes.

File: mitochondrial_genomes.zip

Description: Full mitochondrial genomes of the 22 newly sequenced species and 82 published species (one file per species). We assmbled the genomes using MitoFinder and MitHifi. The mitochondrial genomes were annotated using Mitoz v3.6.

Code/software

We analyzed the multiple sequence alignment using the software RevBayes (https://github.com/revbayes/revbayes) to estimate the time-calibrated phylogeny.
DOI: 10.5281/zenodo.18229588
title: Mitochondrial genome sequences of Fireflies (Coleoptera: Lampyridae)

description: This dataset contains 82 published and 22 newly sequenced and assembled complete mitochondrial genomes of fireflies. From these complete mitochondrial genomes, we extracted 13 protein coding genes and 2 rRNA genes, which we aligned and curated. Finally, we built a time-calibrated phylogeny for these 104 firefly species.

Description of the data and file structure

We collected 22 firefly species from Europe and Central America. Bioluminiscent adults (Luciola, Photinus, Photuris and Bicellonycha) were collected using an insect net and dark adults were collected using light traps (Lamprohiza and Lampyris). High molecular weight DNA was extracted from single males using the MagAttract HMW DNA kit (Qiagen) following manufacturer’s guidelines. DNA fragment sizes and integrity were checked with a 1% agarose gel. Long DNA fragments were sequenced from a single male individual using Nanopore PromethION sequencer.

We additionally collected mitochondrial genomes from GenBank for 82 firefly species.### Files and variables

File: alignments.zip

Description: Multiple sequence alignments of all 104 firefly species used in this study (one file per locus). We extracted 13 protein coding genes and two rRNA genes from the complete mitochondrial genomes. We combined these published genomes with our 22 mitochondrial genomes. We aligned the 13 protein coding genes using MACSE v2, using the insect mitochondrial code. We also used MACSE to replace artificial stopcodons with ‘NNN’ if these occurred within a protein coding sequence. Furthermore, we trimmed the alignments using trimAl with the option automated1. For the two ribosomal RNA genes 12S and 16S, we used the alignment software MAFFT v7 and trimAl with the option automated1.

File: Lampyridae_Mito_final.tre

Description: Our final estimated time-calibrated phylogeny containing the 104 firefly species. The phylogeny was estimated using RevBayes.

File: mitochondrial_genomes.zip

Description: Full mitochondrial genomes of the 22 newly sequenced species and 82 published species (one file per species). We assmbled the genomes using MitoFinder and MitHifi. The mitochondrial genomes were annotated using Mitoz v3.6.

Code/software

We analyzed the multiple sequence alignment using the software RevBayes (https://github.com/revbayes/revbayes) to estimate the time-calibrated phylogeny.
DOI: 10.15156/bio/sh1382096.10fu
title: SH1382096.10FU

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.53866x
title: Occurrence Download

description: A dataset containing 61386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vulpes vulpes (Linnaeus, 1758)",
 "Year is less than 2000",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 61386 records from 196 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052503-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c5w4hf
title: Occurrence Download

description: A dataset containing 966 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pachycephala sulfuriventer (Walden, 1872))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 966 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296280-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.achb3h
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Leiopicus auriceps (Vigors, 1831))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297480-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dnz6tx
title: Occurrence Download

description: A dataset containing 756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pachycephala meyeri Salvadori, 1890, Pachycephala homeyeri (W.Blasius, 1890))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 756 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296283-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9v46aq
title: Occurrence Download

description: A dataset containing 32925 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cypripedium acaule Aiton"
 ]
}

 The dataset includes 32925 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033636-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dzz626
title: Occurrence Download

description: A dataset containing 704380 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5.43_1",
 "Geometry POLYGON((-122.11435 37.469,-122.13182 37.42396,-122.14435 37.39251,-122.14415 37.38086,-122.13881 37.36533,-122.07086 37.32938,-122.02346 37.33567,-122.02465 37.44881,-122.11435 37.469))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 704380 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052491-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tm5qa5
title: Occurrence Download

description: A dataset containing 3907 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-21.39718 26.85786,49.39718 26.85786,49.39718 55.14214,-21.39718 55.14214,-21.39718 26.85786))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ophrys fusca Link",
 "Year 1969-2002"
 ]
}

 The dataset includes 3907 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297460-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3e6bg5
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pachycephala lorentzi Mayr, 1931)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 147 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296290-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eymcag
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abobra tenuifolia Naudin"
 ]
}

 The dataset includes 178 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0291718-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78xzy5
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis sphaciotica Greuter"
 ]
}

 The dataset includes 11 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052507-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.47dc65
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Penelopides mindorensis Steere, 1890)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 150 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296297-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.btuda7
title: Occurrence Download

description: A dataset containing 3381819 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is New South Wales Bird Atlassers"
 ]
}

 The dataset includes 3381819 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068012-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jnhbds
title: Occurrence Download

description: A dataset containing 716 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Medicago constricta Durieu"
 ]
}

 The dataset includes 716 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033651-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtqa6c
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis spinosissima Baker"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052508-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k76eua
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Boerhavia diffusa var. leiocarpa (Heimerl) C.D.Adams"
 ]
}

 The dataset includes 70 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297476-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzx2ag
title: Occurrence Download

description: A dataset containing 6075 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhyticeros plicatus (J.R.Forster, 1781), Rhyticeros plicatus (Pennant, 1781), Rhytideres plicatus (Olivier, 1790))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6075 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296284-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2au3b
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Medicago crassipes (Boiss.) E.Small"
 ]
}

 The dataset includes 96 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033659-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mxn7fz
title: Occurrence Download

description: A dataset containing 36515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 36515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052562-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pfw6bb
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pachycephala flavifrons (Peale, 1848))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 450 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0296298-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsj4c5
title: Occurrence Download

description: A dataset containing 886 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Broussonetia papyrifera (L.) L'Hér. ex Vent."
 ]
}

 The dataset includes 886 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297481-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j53nd3
title: Occurrence Download

description: A dataset containing 138407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Barbarea vulgaris (L.) W.T.Aiton)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 138407 records from 1163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067547-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc5ypd5
title: CCDC 177487: Experimental Crystal Structure Determination

description: Related Article: V.V.Zhdankin, O.Maydanovych, J.Herschbach, J.Bruno, E.D.Matveeva, N.S.Zefirov|2002|Tetrahedron Lett.|43|2359|doi:10.1016/S0040-4039(02)00275-7
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc5qrzl
title: CCDC 170840: Experimental Crystal Structure Determination

description: Related Article: Ren-Wang Jiang, P.Pui-Hay But, Shuang-Cheng Ma, Wen-Cai Ye, Siu-Pang Chan, T.C.W.Mak|2002|Tetrahedron Lett.|43|2415|doi:10.1016/S0040-4039(02)00232-0
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc5l462
title: CCDC 166383: Experimental Crystal Structure Determination

description: Related Article: R.Miyatake, S.Kuroda, T.Kajioka, A.Taketani, M.Oda|2002|Tetrahedron|58|3647|doi:10.1016/S0040-4020(02)00353-8
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc5x1z2
title: CCDC 175924: Experimental Crystal Structure Determination

description: Related Article: R.Miyatake, S.Kuroda, T.Kajioka, A.Taketani, M.Oda|2002|Tetrahedron|58|3647|doi:10.1016/S0040-4020(02)00353-8
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.