cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14644030
title: Data and scripts for the "Genomic architecture of the clownfish hybrid Amphiprion leucokranos"

description: Data and scripts used for the analysis of the publication Genomic architecture of the clownfish hybrid Amphiprion leucokranos

Pictures

The "leucokranos_pictures" directory contains the picture of the hybrid (Amphiprion leucokranos) individuals used for the colour pattern analysis. Names of the files match the name of the individual. 

VCF files

filtered_snps_no_outgroup.vcf.gz

Filtered VCF file of 64 individuals, including only A. chrysopterus, A. sandaracinos and A. leucokranos. We hard-filtered the VCF  following the GATK recommendations, since no well-curated training resources are available for base recalibration  (QD < 2.0, MQ < 40.0, FS > 60.0, SOR > 3.0, MQRankSum < -12.5, ReadPosRankSum < -8.0). We performed additional filtering using VCFtools V0.1.16 (Danecek et al. 2011) and kept only biallelic SNPs with a quality above 30 (--minQ 30), which were informative for at least 85% of the individuals (--max-missing 0.85), with a minimum depth of 7 (--minDP 7), a maximum depth of 40 (--maxDP 40) and a minor allele count greater than or equal to 3 (--mac 3). More info about individuals present in the VCF file are available in the vcf_individuals_info.csv file.

filtered_snps_outgroup.vcf.gz

Filtered VCF file of 74 individuals, which includes the outgroup A. clarkii used for the ABBA-BABA analysis. We hard-filtered the VCF  following the GATK recommendations, since no well-curated training resources are available for base recalibration  (QD < 2.0, MQ < 40.0, FS > 60.0, SOR > 3.0, MQRankSum < -12.5, ReadPosRankSum < -8.0). We performed additional filtering using VCFtools V0.1.16 (Danecek et al. 2011) and kept only biallelic SNPs with a quality above 30 (--minQ 30), which were informative for at least 85% of the individuals (--max-missing 0.85), with a minimum depth of 7 (--minDP 7), a maximum depth of 40 (--maxDP 40) and a minor allele count greater than or equal to 3 (--mac 3). More info about individuals present in the VCF file are available in the vcf_individuals_info.csv file.

Scripts

The directory "scripts.zip" contains all the scripts to generate the VCF files as well as the scripts used for the analysis in the paper. All the information about the pipelines and the scripts are in the README in the scripts directory. Content of the directory:

1_filtering_reads/- 1_run_qc_trimming.sh- TruSeq3-PE-2.fa

2_mapping/- 2_1_run_bwa_ref_indexing.sh- 2_2_run_bwa_mapping.sh

3_variant_calling/- 3_1_gatk_preprocessing.py- 3_1_run_gatk_preprocessing.sh- 3_2_index_ref_genome.sh- 3_3_gatk_haplotype_call.sh- 3_4_merge_vcfs.sh- 3_5_genomics_db_import.sh- 3_6_joint_genotyping.sh- 3_7_gather_vcfs.sh

4_variants_filtering:- 4_1_variant_stats.sh- 4_2_individuals_filtering.sh- 4_2_variant_filtering.sh

5_analysis:- 5_1_pca- 5_2_admix- 5_3_mitogenomes- 5_4_elai- 5_5_pop_gen_stats

README.md
DOI: 10.15468/dl.dvhh5h
title: Occurrence Download

description: A dataset containing 1839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ceiba speciosa (A.St.-Hil., A.Juss. & Cambess.) Ravenna)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1839 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007188-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ha966q
title: Occurrence Download

description: A dataset containing 2638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Country is one of (Mexico, United States of America)",
 "DatasetKey is one of (Agrobiodiversidad de tres regiones de importancia biocultural en el centro-occidente de México, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (Plantas vasculares), Colecta y registro de la agrobiodiversidad en la Mixteca Alta, Oaxaca (recolectas recientes), Agrobiodiversidad de géneros selectos, parientes silvestres y quelites en un área de importancia biocultural en Durango, Pl@ntNet automatically identified occurrences, Desert Botanical Garden Herbarium, Computarización de colecciones y adquisición de infraestructura (mobiliario) para el herbario CIIDIR-Durango, University of Florida Herbarium (FLAS), UCR - University of California, Riverside Herbarium - Vascular Plants, iNaturalist Research-grade Observations)",
 "TaxonKey is Agave americana L.",
 "Year 2000-2025"
 ]
}

 The dataset includes 2638 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007146-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00011164
title: Anaerobe agar dilution data

description: The data will be used, in combination with other available data, to create MIC distributions for anaerobic bacteria based on reference agar dilution. The MIC data will be used in the process for establishing EUCAST breakpoints for these species. 
We have MIC data from other collaborators (mainly from the anaerobe reference unit in Cardiff, UK) and would like to add MIC data from other studies/contributors to have a more robust dataset. In most publications, data are presented in the form om MIC50 and MIC90 and that is not useful for us in the breakpoint setting process. We are therefore actively looking for additional MIC distributions.
DOI: 10.15468/dl.9fud3v
title: Occurrence Download

description: A dataset containing 4220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Megalopta Smith, 1853",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4220 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007147-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2nuzj
title: Occurrence Download

description: A dataset containing 507 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is one of (Argentina, Falkland Islands (Malvinas), South Georgia and the South Sandwich Islands)",
 {
 "and" : [
 "Country is one of (Argentina, Falkland Islands (Malvinas), South Georgia and the South Sandwich Islands)",
 "HasGeospatialIssue is false"
 ]
 },
 "Geometry POLYGON((-74 -60, -25 -60, -25 -90, -74 -90, -74 -60))"
 ]
 },
 "TaxonKey is one of (Butia (Becc.) Becc.)"
 ]
}

 The dataset includes 507 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007189-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.56z92n
title: Occurrence Download

description: A dataset listing the 80 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Israel",
 "DatasetKey is Reptiles & Amphibians - The National Natural History Collections"
 ]
}

 The dataset's 80 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007142-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wy6xht
title: Occurrence Download

description: A dataset containing 9105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Celosia argentea L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 9105 records from 337 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007190-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sjswtm
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-87.89098 21.41824,-90.21382 20.97234,-90.26567 20.03906,-90.52491 19.76944,-90.64935 19.31317,-91.10562 18.67024,-91.85225 18.21397,-92.42259 17.48808,-91.8004 17.29106,-91.1471 17.30142,-91.1471 17.88213,-90.99155 17.8925,-90.5975 17.8925,-89.23906 17.91324,-89.08351 18.11027,-88.86574 17.98583,-87.36212 20.31904,-86.854 20.85827,-86.82289 21.38713,-86.90585 21.3975,-87.89098 21.41824))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ateles É.Geoffroy Saint-Hilaire, 1806",
 "Year 2025-2025"
 ]
}

 The dataset includes 48 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007191-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f295y5
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-12.45917 33.25424,-2.96083 33.25424,-2.96083 42.35265,-12.45917 42.35265,-12.45917 33.25424))",
 "TaxonKey is Orcinus orca (Linnaeus, 1758)",
 "Year 1975-2025"
 ]
}

 The dataset includes 111 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007148-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmptsf
title: Occurrence Download

description: A dataset containing 4220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Megalopta Smith, 1853",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4220 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007193-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6udbzc
title: Occurrence Download

description: A dataset containing 5831 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Albizia niopoides (Spruce ex Benth.) Burkart, Pithecellobium niopoides Spruce ex Benth.)"
 ]
}

 The dataset includes 5831 records from 286 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007192-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pt2v68
title: Occurrence Download

description: A dataset listing the 33 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-99.77529 19.2567,-99.77573 19.26035,-99.77931 19.26041,-99.78549 19.25571,-99.78821 19.25009,-99.78856 19.24307,-99.80481 19.24105,-99.80963 19.23749,-99.81366 19.23936,-99.82751 19.23775,-99.83497 19.23355,-99.83982 19.22842,-99.84648 19.22964,-99.84989 19.22494,-99.86399 19.22264,-99.86744 19.22466,-99.86914 19.23013,-99.87402 19.23132,-99.87461 19.23389,-99.87936 19.23486,-99.89348 19.22759,-99.89549 19.22082,-99.9013 19.21524,-99.90368 19.2155,-99.90658 19.21305,-99.90999 19.20789,-99.9063 19.20036,-99.90717 19.18973,-99.91707 19.16586,-99.91598 19.15928,-99.91778 19.15048,-99.91548 19.14546,-99.91335 19.14453,-99.91161 19.14926,-99.90895 19.15149,-99.90728 19.15146,-99.90566 19.1485,-99.90163 19.14753,-99.89398 19.15309,-99.89186 19.15148,-99.88809 19.15202,-99.88321 19.15612,-99.87363 19.15507,-99.87186 19.15074,-99.86851 19.15137,-99.86373 19.14791,-99.85972 19.13963,-99.85106 19.13015,-99.83947 19.13013,-99.84188 19.12836,-99.84098 19.12007,-99.8288 19.11707,-99.82632 19.11842,-99.81283 19.11775,-99.80828 19.11428,-99.80855 19.11205,-99.80472 19.11358,-99.79972 19.11325,-99.78815 19.10674,-99.77979 19.1082,-99.76891 19.10351,-99.76936 19.10899,-99.76703 19.1162,-99.77721 19.12866,-99.78335 19.13257,-99.7877 19.13821,-99.79137 19.1471,-99.79392 19.16639,-99.79837 19.17143,-99.79898 19.17778,-99.80268 19.18463,-99.80354 19.19076,-99.80271 19.19777,-99.80029 19.19977,-99.79878 19.20473,-99.7947 19.20648,-99.77752 19.22208,-99.77598 19.22908,-99.77743 19.24246,-99.77573 19.24402,-99.77529 19.2567))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset's 33 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007186-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e113622
title: Replication data for: Race, Ethnicity, and Discriminatory Zoning

description: Zoning policies can have marked impacts on the spatial distribution of people and land use, yet there is little systematic evidence on their origin. Investigating the causes of these regulations is complicated by the fact that land use and zoning have been co-evolving for nearly a century. We employ a novel approach to overcome this challenge, studying the factors underpinning the introduction of comprehensive zoning in Chicago. We find evidence consistent with a precursor to exclusionary zoning as well as support for the hypothesis that industrial use zoning was disproportionately allocated to neighborhoods populated by ethnic and racial minorities.
DOI: 10.3886/e113622v1-169924
title: Replication data for: Race, Ethnicity, and Discriminatory Zoning

description: Zoning policies can have marked impacts on the spatial distribution of people and land use, yet there is little systematic evidence on their origin. Investigating the causes of these regulations is complicated by the fact that land use and zoning have been co-evolving for nearly a century. We employ a novel approach to overcome this challenge, studying the factors underpinning the introduction of comprehensive zoning in Chicago. We find evidence consistent with a precursor to exclusionary zoning as well as support for the hypothesis that industrial use zoning was disproportionately allocated to neighborhoods populated by ethnic and racial minorities.
DOI: 10.25934/00004138
title: A Phase 3 Randomized, Double-Blind, Placebo-Controlled Efficacy and Safety Comparison of Fixed-Dose Ranges (mg/kg/day) of Tomoxetine with Placebo in Child and Adolescent Outpatients with ADHD, Aged 8 to 18 Years

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.15468/dl.hs698q
title: Occurrence Download

description: A dataset containing 13895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salicornia L., Salicornia, Salicornia de Blainville, 1830, Salicorniaria Schinz, 1825)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13895 records from 399 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007195-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ngw5pk
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Stelis parvilabris Lindl."
 ]
}

 The dataset includes 32 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018370-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhqwpq
title: Occurrence Download

description: A dataset containing 957 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ukraine",
 "TaxonKey is Lacerta viridis (Laurenti, 1768)"
 ]
}

 The dataset includes 957 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018366-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbut3a
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.60824 -16.77931,-72.60824 -16.77931,-71.10906 -17.78115,-71.05801 -16.67738,-71.82384 -16.26891,-72.60824 -16.77931))",
 "HasGeospatialIssue is false",
 "TaxonKey is Metallura phoebe (R.Lesson & Delattre, 1839)"
 ]
}

 The dataset includes 78 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007166-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzfhqu
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scarthyla goinorum (Bokermann, 1962)"
 ]
}

 The dataset includes 299 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007167-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gp5rju
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arctoscopus japonicus (Steindachner, 1881)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 398 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007169-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t8uqks
title: Occurrence Download

description: A dataset containing 59664 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orchidaceae",
 "Country is Madagascar"
 ]
}

 The dataset includes 59664 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007168-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdjqg8
title: Occurrence Download

description: A dataset containing 11599 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Solidago altissima L.)"
 ]
}

 The dataset includes 11599 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007170-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8waf9t
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichodon japonicus Steindachner, 1881",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007172-241126133413365/datasets/export for details.
DOI: 10.15468/dl.9crq6s
title: Occurrence Download

description: A dataset containing 1092 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scinax boesemani (Goin, 1966)"
 ]
}

 The dataset includes 1092 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007171-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-1965506296
title: Swiss consortium in macromolecular X-ray crystallography structure determination for academic researchers: EPFL, UNIL, UNIGE, Zurich and SL

description: This proposal builds upon the foundation established in BAG MX 2521 and represents a collaborative effort among prominent Swiss academic institutions, including EPFL, UNIL, UNIGE and SLS. Under the leadership of Dr. Florence Pojer, the head of EPFL's Protein Production and Structure core facility, this initiative aims to streamline and enhance the process of determination of macromolecules structures by X-ray crystallography. Notably, the automated data collection established at ESRF has revolutionized our current pipeline, enabling the analysis of over 1000 crystals and the finalization at high-resolution of around 40 different structures in the past year alone. These achievements span diverse projects ranging from drug discovery to the design of novel protein folds. In addition, two PIs from University of Zurich, with expertise in structural biology, are joining this BAG.
DOI: 10.15468/dl.jxtgny
title: Occurrence Download

description: A dataset containing 2620112611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Year 1902-2024"
 ]
}

 The dataset includes 2620112611 records from 40583 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007109-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.