cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10699186
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) 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.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) 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).
DOI: 10.5281/zenodo.10719613
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) 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.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) 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).
DOI: 10.5281/zenodo.10719092
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.11490010
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.13768924
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.10672306
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.10698657
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota
DOI: 10.5281/zenodo.10784569
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.12820719
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.5281/zenodo.14180833
title: A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota

description: Data sources
DOI: 10.6084/m9.figshare.27641784.v1
title: measurement value and part of the point cloud information

description: Conduct an experiment by operating the robot to dock with the charging port so as to verify the results of the algorithm.
DOI: 10.15468/dl.y8pfzq
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Utricularia fulva F.Muell."
 ]
}

 The dataset includes 306 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021569-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8k2mad
title: Occurrence Download

description: A dataset containing 61695 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Drosera anglica Huds."
 ]
}

 The dataset includes 61695 records from 493 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021568-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j64sc5
title: Occurrence Download

description: A dataset containing 791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Utricularia tenella R.Br."
 ]
}

 The dataset includes 791 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021571-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmygqx
title: Occurrence Download

description: A dataset containing 7044 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-6.89288 51.04879,12.31426 51.04879,12.31426 61.01868,-6.89288 61.01868,-6.89288 51.04879))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ostrea Linnaeus, 1758",
 "Year 1980-2024"
 ]
}

 The dataset includes 7044 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021570-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxrasy
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Equilabium acaule (Brummitt & Seyani) Mwany., Culham & A.J.Paton"
 ]
}

 The dataset includes 23 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043985-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rphesf
title: Occurrence Download

description: A dataset containing 5 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 Microcaecilia dermatophaga Wilkinson, Sherratt, Starace & Gower, 2013"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049625-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6raief
title: Occurrence Download

description: A dataset containing 10474 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor (Linnaeus, 1771)"
 ]
}

 The dataset includes 10474 records from 218 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003755-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5fcuy8
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia adenensis Deflers"
 ]
}

 The dataset includes 52 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043888-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7jedyj
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Donax fossor Say, 1822",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 345 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049606-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nchjcr
title: Occurrence Download

description: A dataset containing 3881 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Metriopelia ceciliae (R.Lesson, 1845)"
 ]
}

 The dataset includes 3881 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003741-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e62wdw
title: Occurrence Download

description: A dataset containing 20737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32496433333334 32.097476, 69.37031999999999 32.097476, 69.37031999999999 49.184106666666665, 35.32496433333334 49.184106666666665, 35.32496433333334 32.097476))",
 "EventDate is 2013-05-01,2013-05-31"
 ]
}

 The dataset includes 20737 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043880-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvx8s1
title: Occurrence Download

description: A dataset containing 2612 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chromis viridis (Cuvier, 1830)"
 ]
}

 The dataset includes 2612 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003764-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qcamz
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Pavo muticus Linnaeus, 1766",
 "Year 2013-2023"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049638-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zjjdab
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriophyton staintonii (Hedge) Ryding"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043972-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vwr7af
title: Occurrence Download

description: A dataset containing 365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolabrifera brazieri G.B.Sowerby II, 1870",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 365 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049583-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymmkzo
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Hirschfeldia incana (L.) Lagr.-Foss.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 42 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003759-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.djfrn8
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia alatavica Boiss."
 ]
}

 The dataset includes 65 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043984-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a45gs0
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Lepidium draba L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003762-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39ptab
title: Occurrence Download

description: A dataset containing 7448 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 Lissotriton boscai (Lataste, 1879)"
 ]
}

 The dataset includes 7448 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049586-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzbbkd
title: Occurrence Download

description: A dataset containing 5603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32496433333334 32.097476, 69.37031999999999 32.097476, 69.37031999999999 49.184106666666665, 35.32496433333334 49.184106666666665, 35.32496433333334 32.097476))",
 "EventDate is 2014-03-01,2014-03-31"
 ]
}

 The dataset includes 5603 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044006-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aitosx
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Carpobrotus edulis (L.) N.E.Br.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003771-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8acvbg
title: Occurrence Download

description: A dataset containing 351 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 Paramesotriton labiatus (Unterstein, 1930)"
 ]
}

 The dataset includes 351 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049629-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxhtsb
title: Occurrence Download

description: A dataset containing 912 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erioscirpus comosus (Wall.) Palla"
 ]
}

 The dataset includes 912 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044010-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxh339
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Garcinia engleriana A.C.Sm."
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000707-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wf8ker
title: Occurrence Download

description: A dataset containing 14913 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32496433333334 32.097476, 69.37031999999999 32.097476, 69.37031999999999 49.184106666666665, 35.32496433333334 49.184106666666665, 35.32496433333334 32.097476))",
 "EventDate is 2013-06-01,2013-06-30"
 ]
}

 The dataset includes 14913 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043890-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qqooi
title: Occurrence Download

description: A dataset containing 1427 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Evaluación del riesgo de extinción de setenta y tres especies de lagartijas (Sauria) incluidas en la Norma Oficial Mexicana-059-SEMARNAT-2001"
 ]
}

 The dataset includes 1427 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009516-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8k2sst
title: Occurrence Download

description: A dataset containing 1 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 Crotaphatrema bornmuelleri (Werner, 1899)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049593-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69hkgg
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriophyton oblongatum (Schrenk) Bendiksby"
 ]
}

 The dataset includes 125 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043957-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5zm94
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salicornia L.",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 244 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009516-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.