cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id372625.1
title: StrainInfo SI-ID 372625.1

description: StrainInfo dataset 372625 about a strain of Leptospira interrogans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id372626.1
title: StrainInfo SI-ID 372626.1

description: StrainInfo dataset 372626 about a strain of Leptospira interrogans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id372627.1
title: StrainInfo SI-ID 372627.1

description: StrainInfo dataset 372627 about a strain of Leptospira interrogans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id372628.1
title: StrainInfo SI-ID 372628.1

description: StrainInfo dataset 372628 about a strain of Leptospira interrogans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id372716.1
title: StrainInfo SI-ID 372716.1

description: StrainInfo dataset 372716 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id372717.1
title: StrainInfo SI-ID 372717.1

description: StrainInfo dataset 372717 about a strain of Lysinibacillus sphaericus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.5281/zenodo.15482484
title: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

description: ABSTRACT

Generating high-quality variant callsets across diverse species remains challenging as most bioinformatics tools default to assumptions based on human genomes. DeepVariant (DV) excels without joint genotyping while offering fewer implementation barriers. However, the growing appeal of a “universal” algorithm has magnified the unknown impacts when used with non-human species. We use bovine genomes to assess the limits of using human-genome-trained variant callers, including the allele frequency channel (DV-AF) and joint-caller DeepTrio (DT). Our novel approach, TrioTrain, automates extending DV for diploid species lacking Genome-in-a-Bottle (GIAB) resources, using a region shuffling approach to mitigate barriers for SLURM-based clusters. Imperfect animal truth labels are curated to remove Mendelian discordant sites before training DV to genotype the offspring correctly. With TrioTrain, we use cattle, yak, and bison trios to create the first multi-species-trained DV-AF checkpoint. Although incomplete bovine truth sets constrain recall within challenging repetitive regions, we observe a mean SNV F1 score >0.990 across new checkpoints during GIAB benchmarking. With HG002, a bovine-trained checkpoint (28) decreased the Mendelian Inheritance Error (MIE) rate by a factor of two compared to the default (DV). Checkpoint 28 has a mean MIE rate of 0.03 percent in three bovine interspecies cross genomes. These results illustrate that a multi-species, trio-based training strategy reduces inheritance errors during single-sample variant calling. While exclusively training with human genomes deters transferring deep-learning-based variant calling to new species, we use the diverse ancestry within bovids to illustrate the need for advanced tools designed for comparative genomics.

 





TrioTrain_README.md

README file that describes the contents and purpose of these files in further detail.




TrioTrain_project_metadata.csv

Pedigree and breed labels for all bovine samples included in this study.




CallableRegions.tar.gz

Per-sample callable region files. After cohort QC, we generated truth sets based on the UMAG1 cohort using GATK-derived genotypes. The regions files produced by GATK (v3.8-1-0-gf15c1c3ef), followed by parsing per-sample CallableLoci to extract only PASS regions for downstream analyses.




UMAG1.POP.FREQ.vcf.gz

UMAGv1 cohort population allele frequency file.




ReferenceGenome.tar.gz 

Bovine reference genome files




ModelCheckpoint.tar.gz

Final selected TrioTrain checkpoint (28). This file is compatible with DeepVariant (v1.4) for short-read, whole-genome-sequencing (WGS) data. Using this alternative checkpoint requires a Population VCF compatible with the reference genome provided to DeepVariant.




DV-TrioTrain-0.8.tar.gz

The source code for the TrioTrain pipeline (v0.8) at the time of publication. Additional information, including installation instructions, are available on Github: https://github.com/jkalleberg/DV-TrioTrain/releases/tag/v0.8
DOI: 10.5281/zenodo.15482485
title: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

description: ABSTRACT

Generating high-quality variant callsets across diverse species remains challenging as most bioinformatics tools default to assumptions based on human genomes. DeepVariant (DV) excels without joint genotyping while offering fewer implementation barriers. However, the growing appeal of a “universal” algorithm has magnified the unknown impacts when used with non-human species. We use bovine genomes to assess the limits of using human-genome-trained variant callers, including the allele frequency channel (DV-AF) and joint-caller DeepTrio (DT). Our novel approach, TrioTrain, automates extending DV for diploid species lacking Genome-in-a-Bottle (GIAB) resources, using a region shuffling approach to mitigate barriers for SLURM-based clusters. Imperfect animal truth labels are curated to remove Mendelian discordant sites before training DV to genotype the offspring correctly. With TrioTrain, we use cattle, yak, and bison trios to create the first multi-species-trained DV-AF checkpoint. Although incomplete bovine truth sets constrain recall within challenging repetitive regions, we observe a mean SNV F1 score >0.990 across new checkpoints during GIAB benchmarking. With HG002, a bovine-trained checkpoint (28) decreased the Mendelian Inheritance Error (MIE) rate by a factor of two compared to the default (DV). Checkpoint 28 has a mean MIE rate of 0.03 percent in three bovine interspecies cross genomes. These results illustrate that a multi-species, trio-based training strategy reduces inheritance errors during single-sample variant calling. While exclusively training with human genomes deters transferring deep-learning-based variant calling to new species, we use the diverse ancestry within bovids to illustrate the need for advanced tools designed for comparative genomics.

 





TrioTrain_README.md

README file that describes the contents and purpose of these files in further detail.




TrioTrain_project_metadata.csv

Pedigree and breed labels for all bovine samples included in this study.




CallableRegions.tar.gz

Per-sample callable region files. After cohort QC, we generated truth sets based on the UMAG1 cohort using GATK-derived genotypes. The regions files produced by GATK (v3.8-1-0-gf15c1c3ef), followed by parsing per-sample CallableLoci to extract only PASS regions for downstream analyses.




UMAG1.POP.FREQ.vcf.gz

UMAGv1 cohort population allele frequency file.




ReferenceGenome.tar.gz 

Bovine reference genome files




ModelCheckpoint.tar.gz

Final selected TrioTrain checkpoint (28). This file is compatible with DeepVariant (v1.4) for short-read, whole-genome-sequencing (WGS) data. Using this alternative checkpoint requires a Population VCF compatible with the reference genome provided to DeepVariant.




DV-TrioTrain-0.8.tar.gz

The source code for the TrioTrain pipeline (v0.8) at the time of publication. Additional information, including installation instructions, are available on Github: https://github.com/jkalleberg/DV-TrioTrain/releases/tag/v0.8
DOI: 10.15468/dl.6hmvur
title: Occurrence Download

description: A dataset containing 479883 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bacerial and archaeal diversity in Central Park"
 ]
}

 The dataset includes 479883 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265714-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kp7nv4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lobelia siphilitica L.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198734-220831081235567/datasets/export for details.
DOI: 10.15468/dl.55uthp
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diclidophlebia irvingiae Burckhardt, Aléné & Ouvrard, 2006"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244924-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8sq6p2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leonotis nepetaefolia (R.Br.) W.T.Aiton",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198735-220831081235567/datasets/export for details.
DOI: 10.15468/dl.gd9yzr
title: Occurrence Download

description: A dataset containing 315 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paraplotosus albilabris (Valenciennes, 1840)"
 ]
}

 The dataset includes 315 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242305-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9kz87
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor tabasarae (Savage, Hollingsworth, Lips & Jaslow, 2004)"
 ]
}

 The dataset includes 59 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198747-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gqws9c
title: Occurrence Download

description: A dataset containing 17308 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Enhydra lutris (Linnaeus, 1758)"
 ]
}

 The dataset includes 17308 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244927-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.husvsn
title: Occurrence Download

description: A dataset containing 789 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Spain",
 "Geometry POLYGON((0.61731 40.81129,2.0856 41.22521,2.77941 41.64857,3.0053 42.03323,2.81168 42.55835,2.00493 42.7956,0.89161 42.84294,0.21394 42.54647,-0.27011 41.93728,0.61731 40.81129))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio inaequidens DC."
 ]
}

 The dataset includes 789 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265720-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfqnvu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potentilla wrangelliana Fisch. & Avé-Lall.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198748-220831081235567/datasets/export for details.
DOI: 10.15468/dl.chanzr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrangea febrifuga (Lour.) Y.De Smet & C.Granados",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196472-220831081235567/datasets/export for details.
DOI: 10.15468/dl.u2nbzp
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crocodylia",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256564-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ek8yk
title: Occurrence Download

description: A dataset containing 2414 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "PublishingCountry is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Psittacula krameri (Scopoli, 1769)",
 "Year 2011-2013"
 ]
}

 The dataset includes 2414 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198753-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dysw2g
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteris insignis Mett. ex Kuhn"
 ]
}

 The dataset includes 194 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0248041-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9av2b
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amorphophallus oncophyllus Prain ex Hook.f.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198749-220831081235567/datasets/export for details.
DOI: 10.15468/dl.68dgb8
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichosanthes miyagii Hayata",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 33 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196478-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tu87ku
title: Occurrence Download

description: A dataset containing 135818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phalaropus fulicarius (Linnaeus, 1758)",
 "Year 2010-2022"
 ]
}

 The dataset includes 135818 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229846-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u84s8v
title: Occurrence Download

description: A dataset containing 558 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus americanus (L.) Morrone",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 558 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198770-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3q7nyc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllostachys dulcis McClure",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198761-220831081235567/datasets/export for details.
DOI: 10.15468/dl.fvcvsj
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Araeopteron kurokoi Inoue, 1958",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196473-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9c95w3
title: Occurrence Download

description: A dataset containing 912 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meconopsis horridula Hook.fil. & Thomson"
 ]
}

 The dataset includes 912 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0248042-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ggkgaz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ottelia ulvifolia (Planch.) Walp.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198754-220831081235567/datasets/export for details.
DOI: 10.15468/dl.duwqjy
title: Occurrence Download

description: A dataset containing 16865 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bambusa Schreb."
 ]
}

 The dataset includes 16865 records from 517 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242306-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ucrj5n
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cycas tansachana K.D.Hill & S.L.Yang",
 "Year 2000-2024"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066441-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxsak6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tibouchina heteromalla (D.Don) Cogn.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198756-220831081235567/datasets/export for details.
DOI: 10.15468/dl.f3yutj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coriaria napalensis Wall.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196474-220831081235567/datasets/export for details.
DOI: 10.15468/dl.wwpn5s
title: Occurrence Download

description: A dataset containing 628651 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tringa solitaria A.Wilson, 1813",
 "Year 2010-2022"
 ]
}

 The dataset includes 628651 records from 126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229856-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jwznf5
title: Occurrence Download

description: A dataset containing 604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pongo pygmaeus (Linnaeus, 1760)",
 "Year 1899-2022"
 ]
}

 The dataset includes 604 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198774-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46dsqt
title: Occurrence Download

description: A dataset containing 191 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dracocephalum integrifolium Bunge"
 ]
}

 The dataset includes 191 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0248043-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cbgh8m
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhododendron oldhamii Maxim.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196494-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.avqckv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer davidii Franch.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198762-220831081235567/datasets/export for details.