cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.crmyzd
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tricyrtis ishiiana (Kitag. & T.Koyama) Ohwi & Okuyama"
 ]
}

 The dataset includes 84 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0131980-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eu64zf
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "SpeciesKey" : [
 "is Xerocomellus truncatus (Singer, Snell & E.A.Dick) Klofac"
 ]
}

 The dataset includes 306 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0134346-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mk7mys
title: Occurrence Download

description: A dataset containing 35 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 Coturnicops notatus (Gould, 1841)"
 ]
}

 The dataset includes 35 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031524-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yz95ib
title: Occurrence Download

description: A dataset containing 3606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Colaptes punctigula (Boddaert, 1783)"
 ]
}

 The dataset includes 3606 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009119-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tchre6
title: Occurrence Download

description: A dataset containing 21473 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 Citharichthys sordidus (Girard, 1854)"
 ]
}

 The dataset includes 21473 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088512-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cje83j
title: Occurrence Download

description: A dataset containing 1473 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eriophora ravilla (C.L.Koch, 1844)"
 ]
}

 The dataset includes 1473 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0245813-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eejhw5
title: Occurrence Download

description: A dataset containing 1392 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Iberis sempervirens L."
 ]
}

 The dataset includes 1392 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088532-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c9fvpn
title: Occurrence Download

description: A dataset containing 335536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Lathyrus pratensis L."
 ]
}

 The dataset includes 335536 records from 849 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088526-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7f9va
title: Occurrence Download

description: A dataset containing 193308 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is MVZ Bird Collection (Arctos)"
 ]
}

 The dataset includes 193308 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0432322-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9rsv4
title: Occurrence Download

description: A dataset containing 2061 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Rumex rupestris Le Gall"
 ]
}

 The dataset includes 2061 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088514-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxhucc
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scina rattrayi Stebbing, 1895"
 ]
}

 The dataset includes 99 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0132219-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dz6yjf
title: Occurrence Download

description: A dataset containing 11809 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 Tympanuchus phasianellus (Linnaeus, 1758)"
 ]
}

 The dataset includes 11809 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088542-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sr2h57
title: Occurrence Download

description: A dataset containing 460059 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanellus indicus (Boddaert, 1783)"
 ]
}

 The dataset includes 460059 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0388926-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4k85xj
title: Occurrence Download

description: A dataset containing 414231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Milvus migrans (Boddaert, 1783))",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 414231 records from 871 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0245775-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98ypuj
title: Occurrence Download

description: A dataset containing 575676 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is one of (Acer platanoides L., Adelges tsugae Annand, 1924, Agrilus planipennis Fairmaire, 1888, Alliaria petiolata (M.Bieb.) Cavara & Grande, Channa argus (Cantor, 1842), Crocodylus niloticus Laurenti, 1768, Dreissena polymorpha (Pallas, 1771), Faxonius rusticus (Girard, 1852), Frangula alnus Mill., Heracleum mantegazzianum Sommier & Levier, Heracleum sphondylium L., Hydrocharis morsus-ranae L., Impatiens glandulifera Royle, Kali tragus (L.) Scop., Lissachatina fulica (Bowdich, 1822), Lycorma delicatula (White, 1845), Myriophyllum spicatum L., Phragmites australis subsp. australis, Potamogeton crispus L., Pterois volitans (Linnaeus, 1758), Pueraria lobata (Willd.) Ohwi, Python bivittatus Kuhl, 1820, Reynoutria japonica Houtt., Reynoutria sachalinensis (F.Schmidt) Nakai, Reynoutria ×bohemica Chrtek & Chrtková, Rhamnus cathartica L., Rhinella marina (Linnaeus, 1758), Stratiotes aloides L., Trapa natans L., Vincetoxicum nigrum (L.) Moench, Vincetoxicum rossicum (Kleopow) Barbar.)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 575676 records from 567 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022541-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11218077
title: Metadata information for the events used in Ni et al. (2023)
DOI: 10.5281/zenodo.11218078
title: Metadata information for the events used in Ni et al. (2023)
DOI: 10.15468/dl.a6x6nm
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepadella triptera (Ehrenberg, 1832))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 74 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022547-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j386qj
title: Occurrence Download

description: A dataset containing 394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Pinus oocarpa Schiede ex Schltdl."
 ]
}

 The dataset includes 394 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022548-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cs5c94
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trichocerca simoneae De Smet, 1990)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022549-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82ztsw
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lecane bifurca (Bryce, 1892))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022550-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwvcym
title: Occurrence Download

description: A dataset containing 42511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "OccurrenceStatus is Present",
 "TaxonKey is Megaptera novaeangliae (Borowski, 1781)"
 ]
}

 The dataset includes 42511 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022551-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qbwr94
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Specimen, Human Observation, Occurrence evidence, Living Specimen)",
 "Country is Brazil",
 "TaxonKey is Spinus yarrellii (Audubon, 1839)",
 "Year 2013-2021"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022552-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abkjd9
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepadella triptera (Ehrenberg, 1832))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 74 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022553-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10107359
title: Salmonella enterica serovar Derby isolated from eggs show genomic and phenotypic traits that may be linked to inability to produce human infection.

description: Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. Enteritidis from contaminated poultry, we conducted a large survey of commercially available eggs, where we isolated many S. Enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. At that time, reporting of suspected Salmonella-related human infection was mandatory in the country but no single case of S. Derby infection was detected in that period suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates as well as fifteen isolates from pork or human infection, that were isolated in Uruguay before and after that period. All sequenced strains had the same sequence type ST40, but phylogenomic analysis showed that they clustered in three different groups. All egg isolates clustered together as a monophyletic group and showed marked differences in gene content with the strains in the other two clusters. Differences included absence of genes involved in acid tolerance, heme-uptake, and type VI secretion system, as well as the absence of a C terminal fragment of SpeF protein. We also identified differences in the mobile genetic element contents, the composition of plasmids, insertion sequences, transposons, and phages between egg isolates and human/pork isolates. Mice challenge experiments showed that while mice infected with human/pork isolates died between 1-7 days p.i., all animals infected with the egg strains survived the challenge. Altogether our results suggest that loss of gene functions, and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being the main serovar recovered from eggs countrywide.
DOI: 10.5281/zenodo.10403151
title: Salmonella enterica serovar Derby isolated from eggs show genomic and phenotypic traits that may be linked to inability to produce human infection.

description: Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. Enteritidis from contaminated poultry, we conducted a large survey of commercially available eggs, where we isolated many S. Enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. At that time, reporting of suspected Salmonella-related human infection was mandatory in the country but no single case of S. Derby infection was detected in that period suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates as well as fifteen isolates from pork or human infection, that were isolated in Uruguay before and after that period. All sequenced strains had the same sequence type ST40, but phylogenomic analysis showed that they clustered in three different groups. All egg isolates clustered together as a monophyletic group and showed marked differences in gene content with the strains in the other two clusters. Differences included absence of genes involved in acid tolerance, heme-uptake, and type VI secretion system, as well as the absence of a C terminal fragment of SpeF protein. We also identified differences in the mobile genetic element contents, the composition of plasmids, insertion sequences, transposons, and phages between egg isolates and human/pork isolates. Mice challenge experiments showed that while mice infected with human/pork isolates died between 1-7 days p.i., all animals infected with the egg strains survived the challenge. Altogether our results suggest that loss of gene functions, and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being the main serovar recovered from eggs countrywide.
DOI: 10.15468/dl.bkq5rc
title: Occurrence Download

description: A dataset containing 7766 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Fringilla montifringilla Linnaeus, 1758"
 ]
}

 The dataset includes 7766 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022554-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8qeks9
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "Geometry POLYGON((-98.19335 -16.05501,-48.77487 -16.05501,-48.77487 3.70392,-98.19335 3.70392,-98.19335 -16.05501))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ophidiiformes"
 ]
}

 The dataset includes 132 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022555-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfrq25
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Specimen, Human Observation, Occurrence evidence, Living Specimen)",
 "Country is Brazil",
 "TaxonKey is Spinus yarrellii (Audubon, 1839)",
 "Year 2013-2022"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022556-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvmv75
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trichocerca simoneae De Smet, 1990)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022558-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqzts5
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lecane bifurca (Bryce, 1892))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022560-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11183043
title: ICTVdump (VMR_MSL38_v3)

description: The user interested in quickly accessing the pre-computed data should download the following two files:

Exemplar_sorts.fa.gz Viral genomes (DNA) grouped by 'sort', filtered according to the paper's criteria [TBD] and with concatenated segmented sequences. FASTA headers are formatted as '>sort_{sort}_{number of concatenated segments}_{genome length}'Exemplar_sorts.tsv.gz ICTV taxonomy for the above. The column 'header' links the FASTA headers for easy access.

 

For convenience, we also included the full dataset, which is unfiltered and contains the raw GenBank DNA sequences (exemplars.tsv.gz). The precalculated LLRs for taxonomic prediction (see paper) are stored in the compressed folder LLR.zip.
DOI: 10.15468/dl.3ckkks
title: Occurrence Download

description: A dataset containing 42511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "OccurrenceStatus is Present",
 "TaxonKey is Megaptera novaeangliae (Borowski, 1781)"
 ]
}

 The dataset includes 42511 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022559-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qybgsp
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Kellicottia bostoniensis (Rousselet, 1908))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 431 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022561-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rd4ctu
title: Occurrence Download

description: A dataset containing 2065 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Keratella tropica (Apstein, 1907))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2065 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022562-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.