cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.j4sy8q
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011071-250914085247600/datasets/export for details.
DOI: 10.15468/dl.mf5fek
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iberis pinnata",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011068-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.3552873
title: Supplementary Table S5

description: Rywal biological evidence filtering results.


Output of 1st filtering step by biological evidence for cv. Rywal.


Layer _p_stRT/_I_STRT/_S_03_stCuSTr/ _A_03.1_filtering, DOI: 10.15490/fairdomhub.1.datafile.3112.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.5281/zenodo.3552874
title: Supplementary Table S5

description: Rywal biological evidence filtering results.


Output of 1st filtering step by biological evidence for cv. Rywal.


Layer _p_stRT/_I_STRT/_S_03_stCuSTr/ _A_03.1_filtering, DOI: 10.15490/fairdomhub.1.datafile.3112.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.5281/zenodo.3552905
title: Supplementary File 1

description: merged GFF.


The GFF file with merged ITAG and PGSC gene models for S. tuberosum group Phureja DM genome v4.04.


Layer _p_stRT/_I_STRT/_S_04_stPanTr/ _A_01_evigene_1_3cvs-gffmerged, DOI: 10.15490/fairdomhub.1.datafile.3114.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.5281/zenodo.3552906
title: Supplementary File 1

description: merged GFF.


The GFF file with merged ITAG and PGSC gene models for S. tuberosum group Phureja DM genome v4.04.


Layer _p_stRT/_I_STRT/_S_04_stPanTr/ _A_01_evigene_1_3cvs-gffmerged, DOI: 10.15490/fairdomhub.1.datafile.3114.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.5281/zenodo.16356976
title: Long-read metagenomics of Shanghai pet dogs

description: Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort by Anna Cuscó, Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and Luis Pedro Coelho (bioRxiv PREPRINT 2025)


We used deep long-read sequencing (ONT), polished with short reads (Illumina), on stool samples from 51 pet dogs in Shanghai. Raw data (Nanopore, and Illumina), and MAG catalog (fasta files) are available on ENA under Bioproject ID PRJEB85799.In this repository, we make available MAG annotations and other derived datasets to be further explored and used:



Metagenome-assembled genomes (MAG) catalog annotations: Shanghai Dog MAG catalog contains 2,676 MAGs that belong to 320 different bacterial species. Here, we provide:



Extracted rRNA genes (SHD1_rRNAs_fasta_barrnap.tar.gz), 

MAGs annotations using eggnog-mapper (SHD1_eggNOG_MAG_annotations.tar.gz)

MAGs annotations using RGI (SHD1_ARGs_MAGs.csv.gz), and contig-level annotations using RGI (SHD1_ARGs_contigs.csv.gz)



Extrachromosomal elements (ECEs) catalog (SHD1_EC.fna.gz): includes 185 single-contig circular elements (non-redundant). We identified 58 plasmids, 30 viruses, and 97 uncategorized elements (SHD1_EC_props.tsv.gz)

Gene catalog: includes 1,470,802 non-redundant genes (95% nucleotide identity, representing species-level unigenes). Of these, 98.7% are complete genes, and 73.5% are contained in MAGs or ECEs. Conceptually, there are three levels: (1) ORFs, the original open read frames (in the file SHD1_GC.ORF.fna.xz with associated metadata in SHD1_GC.ORF.orig.tsv.xz), (2) clustered ORFs at 100% nucleotide identity (in SHD1_GC.100NT.fna.xz), and (3) clustered ORFs at 95% nucleotide identity (in SHD1_GC.95NT.fna.xz and SHD1_GC.95NT.faa.xz, for nucleotide and amino acid sequences, respectively). The 100% clustered ORFs are a subset of the original ORFs, and the 95% clustered ORFs are a subset of the 100% clustered ORFs (these relationships are in the file SHD1_GC.clusters.tsv.xz. Eggnog-mapper annotations (in SHD1_GC.95NT.emapper.annotations.gz) are provided for the 95% clustered ORFs.

Small ORFs catalog: includes 403,491 non-redundant smORFs, which produce 273,065 clusters at 90% identity. The extracted smORFs, clustered at 100% amino acid identity are available in provided (SHD1_SM.100AA.faa.gz with associated metadata in SHD1_SM.100AA_origins.tsv.gz, note that same sequence identifier may be listed multiple times as identical sequences may be present in multiple samples). We also provide 90% amino acid clusterings (FASTA in SHD1_SM.90AA.faa.gz, with clustering in SHD1_SM.clusters.tsv.gz).).
DOI: 10.5281/zenodo.16356977
title: Long-read metagenomics of Shanghai pet dogs

description: Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort by Anna Cuscó, Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and Luis Pedro Coelho (bioRxiv PREPRINT 2025)


We used deep long-read sequencing (ONT), polished with short reads (Illumina), on stool samples from 51 pet dogs in Shanghai. Raw data (Nanopore, and Illumina), and MAG catalog (fasta files) are available on ENA under Bioproject ID PRJEB85799.In this repository, we make available MAG annotations and other derived datasets to be further explored and used:



Metagenome-assembled genomes (MAG) catalog annotations: Shanghai Dog MAG catalog contains 2,676 MAGs that belong to 320 different bacterial species. Here, we provide:



Extracted rRNA genes (SHD1_rRNAs_fasta_barrnap.tar.gz), 

MAGs annotations using eggnog-mapper (SHD1_eggNOG_MAG_annotations.tar.gz)

MAGs annotations using RGI (SHD1_ARGs_MAGs.csv.gz), and contig-level annotations using RGI (SHD1_ARGs_contigs.csv.gz)



Extrachromosomal elements (ECEs) catalog (SHD1_EC.fna.gz): includes 185 single-contig circular elements (non-redundant). We identified 58 plasmids, 30 viruses, and 97 uncategorized elements (SHD1_EC_props.tsv.gz)

Gene catalog: includes 1,470,802 non-redundant genes (95% nucleotide identity, representing species-level unigenes). Of these, 98.7% are complete genes, and 73.5% are contained in MAGs or ECEs. Conceptually, there are three levels: (1) ORFs, the original open read frames (in the file SHD1_GC.ORF.fna.xz with associated metadata in SHD1_GC.ORF.orig.tsv.xz), (2) clustered ORFs at 100% nucleotide identity (in SHD1_GC.100NT.fna.xz), and (3) clustered ORFs at 95% nucleotide identity (in SHD1_GC.95NT.fna.xz and SHD1_GC.95NT.faa.xz, for nucleotide and amino acid sequences, respectively). The 100% clustered ORFs are a subset of the original ORFs, and the 95% clustered ORFs are a subset of the 100% clustered ORFs (these relationships are in the file SHD1_GC.clusters.tsv.xz. Eggnog-mapper annotations (in SHD1_GC.95NT.emapper.annotations.gz) are provided for the 95% clustered ORFs.

Small ORFs catalog: includes 403,491 non-redundant smORFs, which produce 273,065 clusters at 90% identity. The extracted smORFs, clustered at 100% amino acid identity are available in provided (SHD1_SM.100AA.faa.gz with associated metadata in SHD1_SM.100AA_origins.tsv.gz, note that same sequence identifier may be listed multiple times as identical sequences may be present in multiple samples). We also provide 90% amino acid clusterings (FASTA in SHD1_SM.90AA.faa.gz, with clustering in SHD1_SM.clusters.tsv.gz).).
DOI: 10.7929/issda/dhx2lj
title: Irish Health Survey (IHS), 2015

description: The Irish Health Survey (IHS) was collected under Regulation (EC) No 1338/2008 of the European Parliament and of the Council of 16 December 2008 on Community statistics on public health and health and safety at work. This survey fulfils the need for public health policies to obtain reliable data on health status, health care usage and health determinants. Questionnaire The Irish Health Survey was designed in line with the third wave of the European Health Interview Survey (EHIS)2. The collection of the data under the aforementioned European Regulation implies that harmonised data can be obtained across the European continent. The Irish Health Survey can be divided into three fundamental components. These are the European Health Status Module (EHSM), the European Health Care Module (EHCM), and the European Health Determinants Module (EHDM). The European Health Status Module: The module on health status is a central element of the survey. It allows measurement of the health status of the population in general, and not only in relation to specific health problems. It covers different aspects and dimensions of health: physical and mental health, chronic and temporary problems and specific conditions. It covers the general impact on the functional status and the limitations in activities of daily living of the respondents. The first three general questions on self-perceived health, long standing illnesses or health problems, and activity limitations constitute the Minimum European Health Module (MEHM). The European Health Care Module: The ECHM module collects data on the use of health care services and the unmet needs for health care. Information on health care consumption is an essential part of the health information system in order to assign necessary resources to the population. This allows analysis of the relationships between health consumption and several determinants such as health status, lifestyles or socio-demographic characteristics as well as the relationships between different types of health care use. The European Health Determinants Module: The general focus of this module is to measure aspects in lifestyles or health-related behaviours. These may have a positive or negative impact on an individual’s health status. Along with the above data, additional variables collected included were; NUTS3 region, sex, age, nationality, and level of deprivation
DOI: 10.5281/zenodo.3552837
title: Supplementary Table S1

description: Detailed sample information table used to generate the de novo transcriptome assemblies.


Raw and processed reads summary.


Layer _p_stRT/_I_STRT/_S_01_sequences, DOI: 10.15490/fairdomhub.1.datafile.3090.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.5281/zenodo.3552838
title: Supplementary Table S1

description: Detailed sample information table used to generate the de novo transcriptome assemblies.


Raw and processed reads summary.


Layer _p_stRT/_I_STRT/_S_01_sequences, DOI: 10.15490/fairdomhub.1.datafile.3090.1
description: Project name: _p_stRT; 
Project home page: https://fairdomhub.org/projects/161; 
preprint article: doi: https://doi.org/10.1101/845818
DOI: 10.15468/dl.junrmb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tellinides timorensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011072-250914085247600/datasets/export for details.
DOI: 10.15468/dl.ebvm7a
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iberis sempervirens",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 80 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011073-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6hhqug
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iberis sempervirens",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 99 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011075-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tasjyd
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iberis sempervirens",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 55 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011077-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vr6ydf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malapterurus leonensis)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011076-250914085247600/datasets/export for details.
DOI: 10.15468/dl.emzqqu
title: Occurrence Download

description: A dataset containing 106309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Najadaceae, Nelumbonaceae, Nepenthaceae, Neuradaceae, Nyctaginaceae, Nymphaeaceae, Nyssaceae, Ochnaceae, Olacaceae, Oleaceae, Onagraceae, Opiliaceae, Orchidaceae, Orobanchaceae, Oxalidaceae, Paeoniaceae, Pandanaceae, Papaveraceae, Parnassiaceae, Passifloraceae, Pedaliaceae, Philadelphaceae, Philydraceae, Phrymaceae, Phytolaccaceae, Piperaceae, Pittosporaceae, Plagiopteraceae, Plantaginaceae, Platanaceae, Plumbaginaceae, Poaceae, Podophyllaceae, Podostemaceae, Polemoniaceae, Polygalaceae, Polygonaceae, Pontederiaceae, Portulacaceae, Potamogetonaceae, Primulaceae, Proteaceae, Punicaceae, Pyrolaceae)"
 ]
}

 The dataset includes 106309 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011034-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzavv2
title: Occurrence Download

description: A dataset containing 1310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Philippines",
 "MediaType is Image",
 "TaxonKey is Arecaceae"
 ]
}

 The dataset includes 1310 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055566-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ic3p9
title: Occurrence Download

description: A dataset containing 302852 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ploceus velatus Vieillot, 1819"
 ]
}

 The dataset includes 302852 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035214-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yk699y
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caryocar brasiliense subsp. intermedium (Wittm.) Prance & M.F.Silva"
 ]
}

 The dataset's 2 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005171-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnwpcz
title: Occurrence Download

description: A dataset containing 10324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ehrharta erecta Lam."
 ]
}

 The dataset includes 10324 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032791-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b0s22l
title: Occurrence Download

description: A dataset containing 4817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "Year 1960-2019",
 "TaxonKey is Copsychus malabaricus (Scopoli, 1786)"
 ]
}

 The dataset includes 4817 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035217-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vpjfdr
title: Occurrence Download

description: A dataset containing 3410 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stenandrium Nees"
 ]
}

 The dataset includes 3410 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043370-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dm3bwt
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-6.58683 36.83936,-5.19706 36.83936,-5.19706 37.45528,-6.58683 37.45528,-6.58683 36.83936))",
 "HasCoordinate is true",
 "TaxonKey is Jasminum fruticans L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 67 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075149-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hs5hp4
title: Occurrence Download

description: A dataset containing 15664 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyxicephalidae"
 ]
}

 The dataset includes 15664 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035216-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mejvrx
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Collection Bryozoa - ZMB"
 ]
}

 The dataset includes 94 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030392-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2jqq2a
title: Occurrence Download

description: A dataset containing 30428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1900-2020",
 "Geometry POLYGON((-6.271 41.50635,-6.78076 41.08447,-7.48389 39.71338,-6.92139 38.99268,-7.3081 38.55322,-7.00928 38.1665,-7.44873 37.63916,-7.396 37.16455,-7.7124 36.3208,-5.60303 36.00439,-1.47217 36.61963,4.32861 39.15088,4.69775 39.94189,3.48486 42.22705,3.5376 42.26221,-3.79248 43.49268,-5.42725 43.61572,-8.09912 43.82666,-9.29443 43.12354,-8.76709 42.05127,-8.08154 41.87549,-7.23779 41.92822,-6.79834 41.98096,-6.271 41.50635))",
 "HasCoordinate is true",
 "TaxonKey is Pinus halepensis Mill.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30428 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065021-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyv7ow
title: Occurrence Download

description: A dataset containing 29165 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corbicula fluminea (O.F.Müller, 1774)"
 ]
}

 The dataset includes 29165 records from 165 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017604-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9q82uw
title: Occurrence Download

description: A dataset containing 141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saimiri boliviensis (I.Geoffroy Saint-Hilaire & de Blainville, 1834)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 141 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043364-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcjt2h
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Registros de mamíferos de las Reservas Distritales de Humedal de Bogotá, D.C."
 ]
}

 The dataset includes 115 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051127-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z76z1b
title: Occurrence Download

description: A dataset containing 3512 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ploceus vitellinus (Lichtenstein, 1823)"
 ]
}

 The dataset includes 3512 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035220-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gcqx8n
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melicope wailauensis (H.St.John) T.G.Hartley & B.C.Stone"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051542-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.