cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/5rm-wze-3b1
title: Clibadium peruvianum Poepp. ex DC.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/837-8h1-qrr
title: Stenoptera peruviana C.Presl

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/jz0-cwh-exr
title: Gwilymia paniculata (Poepp.) A.G.Lima, Paula-Souza & Scalon

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/x2z-9ft-954
title: Senecio scopulorum Poepp.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/xbh-hvm-4xx
title: Oreopolus glacialis (Poepp.) Ricardi

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/fsq-es8-1f0
title: Sicyos montanus Poepp. & Endl.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/k65-1km-fww
title: Stevia cathartica Poepp. & Endl.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.25954/fk7v-7125
title: Lipoceramic Technologies: a Solution to Low and Variable Bioavailability of Poorly Soluble Anti-Inflammatory Drugs [IWEMC-251]
DOI: 10.3535/qsd-q6d-9b5
title: Dichaea calyculata Poepp. & Endl.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/8gw-q9t-k52
title: Pseudoconnarus subtriplinervis (Radlk.) G. Schellenb.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/bhh-ddf-t1s
title: Lantana trifolia L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/a9p-1dl-0ma
title: Carpotroche longifolia (Poepp.) Benth.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/ncg-k4h-vqb
title: Maxillaria affinis (Poepp. & Endl.) Garay

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.gb8uke
title: Occurrence Download

description: A dataset containing 29440 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Progne elegans)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 29440 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065789-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/0g0-88d-ra7
title: Manettia hispida Poepp.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/wax-amb-fkh
title: Clusia octandra (Poepp. & Endl.) Pipoly

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/6y2-czn-vxh
title: Cyclopogon inaequilaterus (Poepp. & Endl.) Schltr.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.gyay2c
title: Occurrence Download

description: A dataset containing 15688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "GadmGid is one of (BRA.21_1, BRA.21.244_2, BRA.21.461_2, BRA.21.215_2)",
 "OccurrenceStatus is Present",
 "TaxonKey is Asteraceae"
 ]
}

 The dataset includes 15688 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016133-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rdnemv
title: Occurrence Download

description: A dataset containing 11235 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tremarctos ornatus"
 ]
}

 The dataset includes 11235 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016135-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4u47v4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Beroe constricta",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016136-251025141854904/datasets/export for details.
DOI: 10.15468/dl.zvnnvk
title: Occurrence Download

description: A dataset containing 1838 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vincetoxicum hirsutum"
 ]
}

 The dataset includes 1838 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016137-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t8g3gw
title: Occurrence Download

description: A dataset containing 66293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cantharellus cibarius"
 ]
}

 The dataset includes 66293 records from 442 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016114-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zvmww
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Beroe flemingii",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016138-251025141854904/datasets/export for details.
DOI: 10.34740/kaggle/dsv/13616584
title: Berita UII
DOI: 10.15468/dl.tjfrwa
title: Occurrence Download

description: A dataset containing 3828 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sylvilagus brasiliensis"
 ]
}

 The dataset includes 3828 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016139-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a63k9b
title: Occurrence Download

description: A dataset containing 311453 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Clarkia amoena, Silene caryophylloides, Calandrinia nitida, Cylindropuntia bernardina, Rorippa curvisiliqua, Crusea longiflora, Muraltia heisteria, Cardamine pentaphyllos, Phagnalon pygmaeum, Acis tingitana, Restio ramosissimus, Calorezia nutans, Restio wittebergensis, Montiopsis parviflora, Chamaecytisus danubialis, Cynanchica bornmuelleri, Thelypteris nevadensis, Medicago tornata, Cynanchica pinifolia, Restio dodii, Phaseolus vulcanicus, Medicago monspeliaca, Euploca epacridea, Cicerbita plumieri, Sclerolaena patenticuspis, Sclerolaena obliquicuspis, Sclerolaena parallelicuspis, Dichoropetalum minutifolium, Dissocarpus paradoxus, Vachellia pennatula, Cajanus marmoratus, Grevillea dilatata, Vachellia gummifera, Hakea divaricata, Filago crocidion, Vachellia astringens, Canavalia rosea, Vachellia ditricha, Acmispon utahensis, Vachellia karroo, Grevillea ilicifolia, Hakea dactyloides, Pyracantha coccinea, Echinopepon rosei, Filago libyaca, Bernardia mexicana, Dillwynia divaricata, Glycosmis trifoliata, Crepis pantocsekii, Crepis sancta, Berberis amplectens, Austrostipa nullarborensis, Gesnouinia arborea, Austrostipa tuckeri, Mentha requienii, Crepis clausonis, Leucadendron conicum, Austrostipa scabra, Ochthodium aegyptiacum, Gazania linearis, Bakerolimon plumosum, Microdon nitidus, Caladenia catenata, Plumbago africana, Rhodanthe tietkensii, Caladenia stricta, Disa comosa, Cota tinctoria, Kewa salsoloides, Lysimachia wildpretii, Pelargonium luridum, Xylonagra arborea, Stipa subaristata, Pelargonium caffrum, Convolvulus despreauxii, Convolvulus namaquensis, Lomelosia stellata, Pelargonium aristatum, Dipcadi ciliare, Dipcadi viride, Pelargonium lanceolatum, Viola epirota, Cyphostemma quinatum, Boechera pendulocarpa, Sphaeralcea angustifolia, Puccinellia stricta, Sesamum eriocarpum, Tetraria fimbriolata, Psorothamnus spinosus, Boechera glaucovalvula, Psorothamnus emoryi, Jacquemontia tamnifolia, Miraglossum pilosum, Puccinellia festuciformis, Oncidium graminifolium, Boechera constancei, Paramollugo nudicaulis, Camassia quamash)",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 311453 records from 1861 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016125-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.exduqu
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.64723 -41.25579,-53.35277 -41.25579,-53.35277 -26.74421,-89.64723 -26.74421,-89.64723 -41.25579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pristidactylus valeriae (Donoso-Barros, 1966)"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008644-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.22gj32
title: Occurrence Download

description: A dataset containing 1179487 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Insecta",
 "Year is 2021",
 "Month is September"
 ]
}

 The dataset includes 1179487 records from 1350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008626-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygy4m3
title: Occurrence Download

description: A dataset containing 2201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Apamea anceps (Denis & Schiffermüller), 1775"
 ]
}

 The dataset includes 2201 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008645-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gaaqaf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-04-05",
 "EventDate is less than or equal to 2025-05-05",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008633-250426092105405/datasets/export for details.
DOI: 10.15468/dl.ave65j
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Drimys angustifolia Miers"
 ]
}

 The dataset includes 337 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000971-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15496744
title: New Zealand ICESat-2 Derived Beach Slopes

description: This dataset proposes a new method driven by the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) ATL03 product to estimate the coastal slope of beaches by considering the photon characteristics and beach morphology of ICESat-2. We calculated the coastal slopes of 1297 profiles from 212 beaches in New Zealand, and our results showed that our method has high accuracy in inverting beach slopes (root mean square error (RMSE)=0.06, coefficient of determination (R ²)=0.76). In the future, this method may be applied globally using ICESat-2 data and become a valuable tool for estimating global beach and coastal slopes.
DOI: 10.5281/zenodo.15496745
title: New Zealand ICESat-2 Derived Beach Slopes

description: This dataset proposes a new method driven by the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) ATL03 product to estimate the coastal slope of beaches by considering the photon characteristics and beach morphology of ICESat-2. We calculated the coastal slopes of 1297 profiles from 212 beaches in New Zealand, and our results showed that our method has high accuracy in inverting beach slopes (root mean square error (RMSE)=0.06, coefficient of determination (R ²)=0.76). In the future, this method may be applied globally using ICESat-2 data and become a valuable tool for estimating global beach and coastal slopes.
DOI: 10.5281/zenodo.15514723
title: New Zealand ICESat-2 Derived Beach Slopes

description: This dataset proposes a new method driven by the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) ATL03 product to estimate the coastal slope of beaches by considering the photon characteristics and beach morphology of ICESat-2. We calculated the coastal slopes of 1297 profiles from 212 beaches in New Zealand, and our results showed that our method has high accuracy in inverting beach slopes (root mean square error (RMSE)=0.06, coefficient of determination (R ²)=0.76). In the future, this method may be applied globally using ICESat-2 data and become a valuable tool for estimating global beach and coastal slopes.
DOI: 10.5281/zenodo.15514807
title: New Zealand ICESat-2 Derived Beach Slopes

description: This dataset proposes a new method driven by the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) ATL03 product to estimate the coastal slope of beaches by considering the photon characteristics and beach morphology of ICESat-2. We calculated the coastal slopes of 1297 profiles from 212 beaches in New Zealand, and our results showed that our method has high accuracy in inverting beach slopes (root mean square error (RMSE)=0.06, coefficient of determination (R ²)=0.76). In the future, this method may be applied globally using ICESat-2 data and become a valuable tool for estimating global beach and coastal slopes.
DOI: 10.15468/dl.4getfr
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhodiola himalensis (D.Don) S.H.Fu"
 ]
}

 The dataset includes 120 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000970-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15514815
title: New Zealand ICESat-2  Beach Slopes

description: This dataset proposes a new method driven by the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) ATL03 product to estimate the coastal slope of beaches by considering the photon characteristics and beach morphology of ICESat-2. We calculated the coastal slopes of 1297 profiles from 212 beaches in New Zealand, and our results showed that our method has high accuracy in inverting beach slopes (root mean square error (RMSE)=0.06, coefficient of determination (R ²)=0.76). In the future, this method may be applied globally using ICESat-2 data and become a valuable tool for estimating global beach and coastal slopes.
DOI: 10.5281/zenodo.12913342
title: Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".

description: Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species”.

BreakpointsData.tar.xz contains:



Pairwise genome alignment files for Oikopleura, Ciona, Caenorhabditis, insects and muntjaks in GFF format in `inst/extdata/`.

dN / dS computation results in `inst/extdata/dNdS/`.

Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.

OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,

N3 the tunicates and N20 the _Ciona_ clade.

`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.

The files needed to build the `BreakpointsData` package.


Oidioi_pairwise_v3.tar.gz contains:



The pairwise alignment files between genomes, in MAF format.

A copy of the Nextflow pipeline used to generate them.


oist-assembler.tar.gz contains:



A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.

A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.

A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.


Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.

Oidioi_genomes.tar.gz contains:



For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.

For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.


OrthoFinderRun.tar.xz contains:



A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.


Supplemental_Code.tar.gz contains:



A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.


AugustusAnnotation.tar.gz (added July 26th 2024) contains:



AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.
description: The authors listed here are responsible for the upload to Zenodo. Please refer to the manuscript for comprehensive information on the authors, their affiliations and their contributions.
DOI: 10.5281/zenodo.6601988
title: Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".

description: Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species”.

BreakpointsData.tar.xz contains:



Pairwise genome alignment files for Oikopleura, Ciona, Caenorhabditis, insects and muntjaks in GFF format in `inst/extdata/`.

dN / dS computation results in `inst/extdata/dNdS/`.

Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.

OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,

N3 the tunicates and N20 the _Ciona_ clade.

`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.

The files needed to build the `BreakpointsData` package.


Oidioi_pairwise_v3.tar.gz contains:



The pairwise alignment files between genomes, in MAF format.

A copy of the Nextflow pipeline used to generate them.


oist-assembler.tar.gz contains:



A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.

A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.

A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.


Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.

Oidioi_genomes.tar.gz contains:



For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.

For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.


OrthoFinderRun.tar.xz contains:



A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.


Supplemental_Code.tar.gz contains:



A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.


AugustusAnnotation.tar.gz (added July 26th 2024) contains:



AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.
description: The authors listed here are responsible for the upload to Zenodo. Please refer to the manuscript for comprehensive information on the authors, their affiliations and their contributions.