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

description: A dataset containing 644 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 (Deutzia setchuenensis)"
 ]
}

 The dataset includes 644 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020650-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkgrnt
title: Occurrence Download

description: A dataset containing 838 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-63.60479 48.76726, -63.86801 48.7966, -64.19413 48.77846, -64.13756 48.44325, -63.65606 48.44589, -63.60479 48.76726))",
 "InstitutionCode is one of (iNaturalist)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 838 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020654-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wssx7s
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Conradina glabra",
 "HasCoordinate is true"
 ]
}

 The dataset includes 66 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020655-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mthuu
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Catopsilia pyranthe",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 147 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020657-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zgtst2
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Drosophila melanogaster",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 95 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020660-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jytc5a
title: Occurrence Download

description: A dataset containing 945 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The results of synchronous surveys of birds in the wetlands of the Azov-Black Sea region of Ukraine in August 2012"
 ]
}

 The dataset includes 945 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020659-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a8n6s2
title: Occurrence Download

description: A dataset containing 50506 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ixodes"
 ]
}

 The dataset includes 50506 records from 492 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020591-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17203395
title: Simlation for META-DIFF benchmark

description: Most of the files necessary to replicate our work: simulation of benchmark datasets, scripts to build tables, and scripts to produce figures using the tables.

Simulated datasets for META-DIFF benchmark:



Contains abundances profiles

reference genomes

unique k-mers of targeted species

config files (which have a seed for reporoductibility)

scripts to produce replicates of abundances profiles.

results from the search of functions in unitigs for the functional recall


Figures:



contains scripts to produce tables 

scripts to apply univariate analysis methods (aldex2, ancombc, deseq2, limma, wilcoxon's test)

tables

script to generate figures from the tables


The bash and R scripts all have CLI arguments and take --help to display option (no argument also prints help for the bash scripts). Script Diff_Bif_metrics.sh executes Kmidff, Bifrost and the metrics script to make it easier. The colored DBG is too heavy for github and was uploaded here, it can be produced from the files on github.

NOTE: we chose to upload config files instead of the whole simulated dataset as it weights several hundred Gigabytes, and as CAMISIM is a published tool with replication in mind.
DOI: 10.15468/dl.uva2c2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Drosophila melanogaster",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020661-250920141307145/datasets/export for details.
DOI: 10.15468/dl.cpsrhw
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-99.66537 18.16767,-98.30577 18.19326,-98.17806 19.33539,-99.73721 19.33539,-99.66537 18.16767))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Canis latrans",
 "Year 1990-2025"
 ]
}

 The dataset includes 108 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020662-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dbpv6v
title: Occurrence Download

description: A dataset containing 529664 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calidris ferruginea)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 529664 records from 483 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020596-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xb6573
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnium cameronianum (Oliv.) Engl."
 ]
}

 The dataset includes 36 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155671-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.byfbxa
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnium breviflorum Ghaz."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155670-230224095556074/datasets/export for details.
DOI: 10.15468/dl.yxayhh
title: Occurrence Download

description: A dataset containing 193 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artocarpus chaplasha Roxb."
 ]
}

 The dataset includes 193 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023174-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jab4xq
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches aureum Lindl. & Paxton"
 ]
}

 The dataset includes 19 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155681-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evuyrv
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "or" : [
 "ScientificName is Alnus × peculiaris Hiyama",
 "ScientificName is Alnus × peculiaris",
 "ScientificName is Alnus x peculiaris",
 "ScientificName is Alnus x peculiaris Hiyama",
 "ScientificName is Alnus xpeculiaris Hiyama",
 "ScientificName is Alnus peculiaris Hiyama"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005672-160803222355964/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dn6y87
title: Occurrence Download

description: A dataset containing 12535813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 12535813 records from 711 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155757-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n2wlxi
title: Occurrence Download

description: A dataset containing 671 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Osmia texana Cresson, 1872",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 671 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005673-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygzquk
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Slovenia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ischyropsalis muellneri Hamann, 1898"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155679-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kaz2k5
title: Occurrence Download

description: A dataset containing 509 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-122.83379 25.27208,-59.16621 25.27208,-59.16621 50.72792,-122.83379 50.72792,-122.83379 25.27208))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cambarus diogenes Girard, 1852",
 "Year 1950-2018"
 ]
}

 The dataset includes 509 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155676-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pdcng7
title: Occurrence Download

description: A dataset containing 663 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ateleopus Temminck & Schlegel, 1846"
 ]
}

 The dataset includes 663 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005673-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fgsizi
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium olympicum Boiss."
 ]
}

 The dataset includes 27 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005673-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7kksqr
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches chlorochilon Klotzsch"
 ]
}

 The dataset includes 75 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155688-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ulll4
title: Occurrence Download

description: A dataset containing 3892 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Incilius mazatlanensis (Taylor, 1940)"
 ]
}

 The dataset includes 3892 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005673-171002173027117/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.75kvs2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches bennettii Dodson"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155684-230224095556074/datasets/export for details.
DOI: 10.15468/dl.wvow7h
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dyckia reitzii L.B.Sm."
 ]
}

 The dataset includes 51 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005673-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gk5nhs
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches barthiorum G.F.Carr & Christenson"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155682-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3j9y6h
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches dianae Rchb.f."
 ]
}

 The dataset includes 12 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155694-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z72x3t
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Montiopsis capitata (Hook. & Arn.) D.I.Ford",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 29 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005674-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qsrxva
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Niphotrichum (Bedn.-Ochyra) Bedn.-Ochyra & Ochyra",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "DatasetKey is University of British Columbia Herbarium (UBC) - Bryophytes Collection"
 ]
}

 The dataset includes 135 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005675-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qhpdj
title: Occurrence Download

description: A dataset containing 4350 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spermophilus citellus (Linnaeus, 1766)"
 ]
}

 The dataset includes 4350 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155687-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9pyyt2
title: Occurrence Download

description: A dataset containing 1795229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DecimalLatitude is greater than 33.8161496245399",
 "DecimalLatitude is less than 34.4043905052934",
 "DecimalLongitude is greater than -119.317309531335",
 "DecimalLongitude is less than -118.122999773676"
 ]
}

 The dataset includes 1795229 records from 235 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005674-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgxmzz
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Balsamocitrus camerunensis Letouzey"
 ]
}

 The dataset includes 37 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036379-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3q42h
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches christensonii D.E.Benn."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155690-230224095556074/datasets/export for details.
DOI: 10.15468/dl.dmk23x
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches egertonianum Bateman"
 ]
}

 The dataset includes 155 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155693-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e0luf4
title: Occurrence Download

description: A dataset containing 1591 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ateleopodidae"
 ]
}

 The dataset includes 1591 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005674-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2dwui8
title: Occurrence Download

description: A dataset containing 109270 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ICN - Universidad Nacional de Colombia"
 ]
}

 The dataset includes 109270 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005674-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6hct6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches farnsworthianum D.E.Benn. & Christenson"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155696-230224095556074/datasets/export for details.
DOI: 10.15468/dl.2rk9c4
title: Occurrence Download

description: A dataset containing 2366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cremastosperma R.E.Fr.",
 {
 "or" : [
 "Country is Venezuela (Bolivarian Republic of)",
 "Country is Argentina",
 "Country is French Guiana",
 "Country is Brazil",
 "Country is Ecuador",
 "Country is Peru",
 "Country is Bolivia (Plurinational State of)",
 "Country is Colombia",
 "Country is Uruguay",
 "Country is Guyana",
 "Country is Paraguay",
 "Country is Suriname",
 "Country is Chile"
 ]
 }
 ]
}

 The dataset includes 2366 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005675-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcuexh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnoches glanduliferum Rolfe"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155697-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jo1qct
title: Occurrence Download

description: A dataset containing 36264 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium laevigatum Willd."
 ]
}

 The dataset includes 36264 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005675-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnk7xh
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnogeton microtuberosum (Aston) Mering & Kadereit"
 ]
}

 The dataset includes 354 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155740-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2jwfmg
title: Occurrence Download

description: A dataset containing 503 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycnogeton alcockiae (Aston) Mering & Kadereit"
 ]
}

 The dataset includes 503 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155732-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.49ws5q
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CatalogNumber is 259598800",
 "Country is New Zealand",
 "Month is January",
 "TaxonKey is Lonicera japonica Thunb.",
 "Year is 2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068413-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.