cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5739611
title: Default SingleM reference "metapackage" data

description: SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.

The data here is the singlem "metapackage" which is the reference package to be used with SingleM in e.g. "pipe" mode.

SingleM is available at https://github.com/wwood/singlem.

The newest version is built from Genome Taxonomy Database (GTDB) version 10-RS226, but older versions available in the history of this record should still work with the newest SingleM software.

 

Changelog

version 5.4.0



Updated to GTDB 10-RS226.

The 5.x version number indicates the metapackage format. Old 4.x versions still work with the current software version.


version 4.3.0



Updated to GTDB 09-RS220.


version 4.2.2



Fixed name of .zb folder to be correct version


version 4.2.1



Changed name of .zb folder to be standard


version 4.2.0



Updated GTDB 08-RS214 package to metapackage version 5, and smafa database version 2.


version 4.1.0



Updated GTDB 07-RS207 package to metapackage version 5, and smafa database version 2 (this is the same as version 3.1.2, but with an updated version number).


version 3.2.1



Updated genome sizes for GTDB genomes (for use with `read_fraction`) corrected based on CheckM v2 estimates of completeness and contamination.


version 3.2.0



Updated to GTDB 08-RS214.


version 3.1.2



Updated GTDB 07-RS207 package to metapackage version 5, and smafa database version 2.
DOI: 10.5281/zenodo.5739612
title: SingleM pipe search database

description: Data to be used with SingleM in "pipe" mode. https://github.com/wwood/singlem
DOI: 10.5281/zenodo.6469357
title: SingleM pipe search database

description: Data to be used with SingleM in "pipe" mode. https://github.com/wwood/singlem
DOI: 10.5281/zenodo.7955518
title: Default SingleM reference "metapackage" data

description: SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery. The data here is the singlem "metapackage" which is the reference package to be used with SingleM in e.g. "pipe" mode. https://github.com/wwood/singlem. Built from Genome Taxonomy Database (GTDB) version 08-RS214.
DOI: 10.5281/zenodo.15233385
title: 호지추측 2(1) (1)
DOI: 10.5281/zenodo.15233386
title: 호지추측 2(1) (1)
DOI: 10.6084/m9.figshare.28812275
title: Huang, et al.Supplementary Figures and Tables

description: Metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are major health burdens. Appropriate in vitro models are necessary to study these diseases and to understand the molecules and mechanisms involved. Most in vitro models are based on tumour cells. In this research we have used CRISPR/Cas9 prime editing to introduce the <i>PNPLA3</i> p.I148M gene variant into a healthy-derived immortalised human hepatocyte (IHH) cell line to generate a new <i>in vitro</i> model of MASLD to help understand stetatotic liver disease.
DOI: 10.15468/dl.ftzk93
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dontostemon pinnatifidus subsp. pinnatifidus)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 211 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014690-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fkxrkc
title: Occurrence Download

description: A dataset containing 2910 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amphibalanus improvisus (Darwin, 1854)"
 ]
}

 The dataset includes 2910 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030487-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pkhnwc
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Machaonia haitiensis Urb. & Ekman"
 ]
}

 The dataset includes 13 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019306-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unb6qj
title: Occurrence Download

description: A dataset containing 13069 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Year 1000-2020",
 "TaxonKey is Phytolacca americana L."
 ]
}

 The dataset includes 13069 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061410-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3ri4d
title: Occurrence Download

description: A dataset containing 233456 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "HasCoordinate is true",
 "TaxonKey is Tracheophyta",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 233456 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002999-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k4budn
title: Occurrence Download

description: A dataset containing 533629 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Corvus splendens Vieillot, 1817",
 "Year 1950-2021"
 ]
}

 The dataset includes 533629 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047625-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2dt38k
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Material sample"
 ]
 },
 "Country is Brazil",
 "Year 2011-2015",
 "TaxonKey is Nannostomus beckfordi Günther, 1872"
 ]
}

 The dataset's 2 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054154-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syvfu0
title: Occurrence Download

description: A dataset containing 598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "DatasetKey is University of British Columbia Herbarium (UBC) - Vascular Plant Collection",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 598 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002999-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vk7faw
title: Occurrence Download

description: A dataset containing 211740 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Myanmar"
 ]
}

 The dataset includes 211740 records from 622 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032935-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wv99yb
title: Occurrence Download

description: A dataset containing 1480 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Metachirus nudicaudatus (É.Geoffroy Saint-Hilaire, 1803)"
 ]
}

 The dataset includes 1480 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013381-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r8htba
title: Occurrence Download

description: A dataset containing 276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Country is Brazil",
 "Country is Peru",
 "Country is Colombia",
 "Country is Ecuador",
 "Country is Chile",
 "Country is Suriname",
 "Country is Argentina",
 "Country is Uruguay",
 "Country is Bolivia (Plurinational State of)",
 "Country is Guyana",
 "Country is Venezuela (Bolivarian Republic of)"
 ]
 },
 "TaxonKey is Cyanoliseus patagonus (Vieillot, 1818)"
 ]
}

 The dataset includes 276 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0335008-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zj8lab
title: Occurrence Download

description: A dataset containing 735891 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Accipiter striatus Vieillot, 1808"
 ]
}

 The dataset includes 735891 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002999-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.idkhku
title: Occurrence Download

description: A dataset containing 3120 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Inventaires naturalistes du Service du Patrimoine naturel / UMS PatriNat-Inventaire du legs Thénard (Bourgogne)"
 ]
}

 The dataset includes 3120 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032948-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cjnvoo
title: Occurrence Download

description: A dataset containing 660 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Catathelasma imperiale (P.Karst.) Singer"
 ]
}

 The dataset includes 660 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002999-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9z7szp
title: Occurrence Download

description: A dataset containing 376 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Country is Brazil",
 "Country is Peru",
 "Country is Colombia",
 "Country is Ecuador",
 "Country is Chile",
 "Country is Suriname",
 "Country is Argentina",
 "Country is Uruguay",
 "Country is Bolivia (Plurinational State of)",
 "Country is Guyana",
 "Country is Venezuela (Bolivarian Republic of)"
 ]
 },
 "TaxonKey is Prochilodus magdalenae Steindachner, 1879"
 ]
}

 The dataset includes 376 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0335014-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n2ym2d
title: Occurrence Download

description: A dataset containing 42992 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ephedra Tourn. ex L."
 ]
}

 The dataset includes 42992 records from 468 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061413-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cpddz
title: Occurrence Download

description: A dataset containing 1577 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus chrysanthus subsp. chrysanthus"
 ]
}

 The dataset includes 1577 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040046-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9krab6
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus chrysanthus subsp. meridionalis (A.H.Gentry) S.O.Grose"
 ]
}

 The dataset includes 107 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040047-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9t6zh
title: Occurrence Download

description: A dataset containing 193 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus chrysanthus subsp. pluvicola (A.H.Gentry) S.O.Grose"
 ]
}

 The dataset includes 193 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040048-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3xcz5c
title: Occurrence Download

description: A dataset containing 2278 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus chrysotrichus (Mart. ex DC.) Mattos"
 ]
}

 The dataset includes 2278 records from 206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040049-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unc7kq
title: Occurrence Download

description: A dataset containing 2997 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus coralibe (Standl.) S.O.Grose"
 ]
}

 The dataset includes 2997 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040050-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gfy7td
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus coronatus (Proença & Farias) Farias"
 ]
}

 The dataset includes 74 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040051-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dx3b4u
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus cristatus (A.H.Gentry) S.O.Grose"
 ]
}

 The dataset includes 49 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040053-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpdws8
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus diamantinensis F.Esp.Santo & M.M.Silva"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040054-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u3qdy6
title: Occurrence Download

description: A dataset containing 13954 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is one of (Todiramphus reichenbachii Hartlaub, 1852, Todiramphus cinnamominus (Swainson, 1821), Zenaida macroura (Linnaeus, 1758), Notiomystis cincta (Du Bus de Gisignies, 1839), Zenaida graysoni (Lawrence, 1871), Lophura nycthemera (Linnaeus, 1758), Lophura edwardsi (Oustalet, 1896))"
 ]
}

 The dataset includes 13954 records from 172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040052-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akptnf
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus grandiflorus F.Esp.Santo & M.M.Silva"
 ]
}

 The dataset includes 5 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040055-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a8t74y
title: Occurrence Download

description: A dataset containing 924 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus guayacan (Seem.) S.O.Grose"
 ]
}

 The dataset includes 924 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040056-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d2hhja
title: Occurrence Download

description: A dataset containing 2077 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus heptaphyllus (Vell.) Mattos"
 ]
}

 The dataset includes 2077 records from 158 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040057-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuecxu
title: Occurrence Download

description: A dataset containing 744 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nisaetus bartelsi (Stresemann, 1924)",
 "Year 2010-2024"
 ]
}

 The dataset includes 744 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040059-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2exuw
title: Occurrence Download

description: A dataset containing 5315 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Handroanthus impetiginosum (Mart. ex DC.) Mattos"
 ]
}

 The dataset includes 5315 records from 289 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040058-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzafhq
title: Occurrence Download

description: A dataset listing the 4016609 species recorded in GBIF matching the query:
{ }

 The dataset's 4016609 records were derived from 75237 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040038-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxbryu
title: Occurrence Download

description: A dataset containing 191982 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salix repens L.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 191982 records from 535 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040032-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bn8kg9
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa pigra",
 "Country is Sri Lanka",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020895-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17163271
title: BBP beta2 simulation data

description: Data simulation to generate all plots in BBP beta 2.0 paper.
DOI: 10.5281/zenodo.17163272
title: BBP beta2 simulation data

description: Data simulation to generate all plots in BBP beta 2.0 paper.
DOI: 10.15468/dl.qarugk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa pigra",
 "Country is Saint Kitts and Nevis",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020897-250914085247600/datasets/export for details.
DOI: 10.15468/dl.9dudaw
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa pigra",
 "Country is Sudan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020898-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfphas
title: Occurrence Download

description: A dataset containing 66198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Briza media",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 66198 records from 251 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020867-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.