cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16982807
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sourcesThis dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).
Sequencing data QC and metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB38174 (cohort used in catalogue assembly) and PRJEB29033, PRJEB33338, PRJEB53667 (independent cohort not used in assembly).
DOI: 10.15468/dl.netxnb
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Psectrogaster curviventris)",
 "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 109 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012967-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2fvnk
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012970-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6yz2m2
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 138 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012968-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97q6kq
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 94 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012969-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16982752
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB4391, PRJEB9357, PRJNA758898, PRJNA906124, PRJNA908260, PRJNA923753 and PRJNA944553 used in catalogue assembly.
DOI: 10.15468/dl.a5k9gh
title: Occurrence Download

description: A dataset containing 5802 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus decapetalus"
 ]
}

 The dataset includes 5802 records from 215 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012971-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16982647
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sourcesThis dataset was constructed using metagenomic sequencing data from the bioproject PRJEB20308 from Coelho et al. 2018 (129 samples)
Metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (ROS_Cfam_1.0 GCF_014441545.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryReads were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,0M genes quantified in 129 samples). Then, co-abundant genes were binned in 234 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r220. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB20308 (cohort used in catalogue assembly) and PRNJNA714112 (independent cohort not used in assembly).
DOI: 10.15468/dl.mdyfq4
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis tef",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 21 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012972-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gv72qd
title: Occurrence Download

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

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012973-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8tpgzm
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012975-250827131500795/datasets/export for details.
DOI: 10.15468/dl.yabczv
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithocarpus shinsuiensis"
 ]
}

 The dataset includes 105 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012974-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ychhph
title: Occurrence Download

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

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012976-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awg48b
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012978-250827131500795/datasets/export for details.
DOI: 10.15468/dl.j3b8wk
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa meyeriana",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012977-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zegcd6
title: Occurrence Download

description: A dataset containing 3243987491 species occurrences available in GBIF matching the query:
{
 "BasisOfRecord" : [
 "is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Occurrence evidence, Specimen, Living Specimen)"
 ]
}

 The dataset includes 3243987491 records from 75182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012747-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17011232
title: Test Dataset for Pipeline for gene tree calculation from annotated long read MAGs and their visualization
DOI: 10.5281/zenodo.17011233
title: Test Dataset for Pipeline for gene tree calculation from annotated long read MAGs and their visualization
DOI: 10.15468/dl.e45hn6
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Spain",
 "PublishingOrg is def87a70-0837-11d9-acb2-b8a03c50a862",
 "TaxonKey is one of (Eucalyptus, Wisteria)"
 ]
}

 The dataset includes 50 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012980-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h56rzm
title: Occurrence Download

description: A dataset containing 384 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heuchera americana hispida"
 ]
}

 The dataset includes 384 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012979-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9pyt8u
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012981-250827131500795/datasets/export for details.
DOI: 10.15468/dl.s8gpz5
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa polystachya",
 "Country is Brazil",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012982-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yp47bf
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa polystachya",
 "Country is Costa Rica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 31 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012983-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfs74n
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithocarpus tubulosus"
 ]
}

 The dataset includes 50 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012984-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17011364
title: QO'QON XONLIGINI ROSSIYA BILAN DIPLOMATIK ALOQALARI MANBASHUNOSLIGI
DOI: 10.5281/zenodo.17011365
title: QO'QON XONLIGINI ROSSIYA BILAN DIPLOMATIK ALOQALARI MANBASHUNOSLIGI
DOI: 10.15468/dl.gpw4vf
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Phoenicurus alaschanicus",
 "Year 2015-2025"
 ]
}

 The dataset includes 149 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012985-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pn53gn
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heuchera pilosissima"
 ]
}

 The dataset includes 392 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012986-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.62hemg
title: Occurrence Download

description: A dataset containing 2265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "TaxonKey is Albizia kalkora"
 ]
}

 The dataset includes 2265 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012987-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhs887
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa polystachya",
 "Country is Honduras",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012988-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpazm9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa polystachya",
 "Country is Viet Nam",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012989-250827131500795/datasets/export for details.
DOI: 10.15468/dl.mm5k4y
title: Occurrence Download

description: A dataset containing 3604 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hibiscus moscheutos lasiocarpos"
 ]
}

 The dataset includes 3604 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012990-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hf5wc5
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012992-250827131500795/datasets/export for details.
DOI: 10.15468/dl.8eu6gh
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eustachys distichophylla",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012993-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8gusn
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eustachys distichophylla",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 39 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012991-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17011387
title: MARJONBULOQ OLTIN AJRATISH SEXI TEXNOGEN CHIQINDILARINI VA BOYITISH MAHSULOTLARINI PIROMETALLURGIK HAMDA GIDROMETALLURGIK ISHLOV BERISH
DOI: 10.5281/zenodo.17011388
title: MARJONBULOQ OLTIN AJRATISH SEXI TEXNOGEN CHIQINDILARINI VA BOYITISH MAHSULOTLARINI PIROMETALLURGIK HAMDA GIDROMETALLURGIK ISHLOV BERISH
DOI: 10.15468/dl.ug4gdc
title: Occurrence Download

description: A dataset containing 2791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hybanthus concolor"
 ]
}

 The dataset includes 2791 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012994-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.urfb2r
title: Occurrence Download

description: A dataset containing 81001 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Bryophyta"
 ]
}

 The dataset includes 81001 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012962-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.