cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7th3wj
title: Occurrence Download

description: A dataset containing 97895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.80653 5.79923,-75.2541 5.79923,-75.2541 6.59252,-75.80653 6.59252,-75.80653 5.79923))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 97895 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020259-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4kts2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardamine sciaphila"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020295-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qvfp4
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cynometra cauliflora, Cynometra cauliflora)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 70 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020294-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.23rmc2
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Passerella arborea)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 57 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020296-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gmcy2
title: Occurrence Download

description: A dataset containing 6107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corbicula fluminea",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6107 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020298-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3zabd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Passerella arborea)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020297-250711103210423/datasets/export for details.
DOI: 10.15468/dl.h5whq5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Passerella arborea)",
 "Country is one of (Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize, Bolivia (Plurinational State of), Bonaire, Sint Eustatius and Saba, Bouvet Island, Brazil, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador, Falkland Islands (Malvinas), French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica, Martinique, Mexico, Montserrat, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Barthélemy, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Vincent and the Grenadines, Sint Maarten (Dutch part), South Georgia and the South Sandwich Islands, Suriname, Trinidad and Tobago, Turks and Caicos Islands, Uruguay, Venezuela (Bolivarian Republic of), Virgin Islands (British), Virgin Islands (U.S.))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020299-250711103210423/datasets/export for details.
DOI: 10.15468/dl.mvgw8h
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020300-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hnagzb
title: Occurrence Download

description: A dataset containing 3090 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Moenkhausia collettii"
 ]
}

 The dataset includes 3090 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020302-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2354y6
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa diplotricha",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 67 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020301-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ax4bt4
title: Occurrence Download

description: A dataset containing 1059 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Agropyron caninum, Agropyron caninum coloratum, Agropyron caninum muticum, Agropyron caninum subglaucum, Agropyron caninum submuticum, Agropyron caninum biflorum, Agropyron caninum muticum, Agropyron caninum subtriflorum, Agropyron caninum alpestre, Agropyron caninum alpinum)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 1059 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020304-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jg7n4d
title: Occurrence Download

description: A dataset containing 2669 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalaris ovata, Phalaris coerulescens, Phalaris aquatica macrostachya, Phalaris aquatica macrostachys, Phalaris bulbosa, Phalaris bulbosa caerulescens, Phalaris bulbosa coerulescens, Phalaris bulbosa nervosa, Phalaris caerulescens, Phalaris caerulescens lusitanica)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 2669 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020303-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15943315
title: Processed data in support of manuscript "Uncertainty quantification in 3D static modeling: Improving reserve estimation accuracy with adaptive physics-informed Monte Carlo simulation in Y-Field, Niger Delta Basin, Nigeria"

description: A supplement material containing the data used in the manuscript "Uncertainty quantification in 3D static modeling: Improving reserve estimation accuracy with adaptive physics-informed Monte Carlo simulation in Y-Field, Niger Delta Basin, Nigeria". The supplementary material is a text file that contains the numpy array of the uncertainty score, complexity score, predicted hydrocarbon initially in place, loss history, and the Python notebook.
DOI: 10.15468/dl.ncp5xn
title: Occurrence Download

description: A dataset containing 942 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sphaerophorus globosus",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 942 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020305-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25374/mcri.29565800
title: Data related to: The DNA methylation landscape of CD4 T cells in oligoarticular juvenile idiopathic arthritis

description: This is a table of DNA methylation Beta values for individual participants in the study. The values range from 0 to 1, representing 0% methylation to 100% methylation. Raw data (idat files) were analysed in R using Bioconductor software packages [36]. The Minfi package [37] was used to preprocess raw signal intensities to methylation measurements, and also to detect any low-quality samples by inspecting the median of the methylated and unmethylated signal intensities. The SWAN (Subset-quantile Within Array Normalization) package [38] was used for probe type normalization by correcting for technical differences between type I and type II probes (which measure methylated and unmethylated signals using two paired probes, or use a single probe, respectively).Juvenile idiopathic arthritis (JIA) is presumed to be driven by an adverse combination of genes and environment. Epigenetic processes, including DNA methylation, act as a conduit through which the environment can regulate gene activity. Altered DNA methylation has been associated with adult autoimmune rheumatic diseases such as rheumatoid arthritis, but studies are lacking for paediatric autoimmune rheumatic diseases including JIA. Here, we performed a genome-scale case-control analysis of CD4 T cell DNA methylation from 56 oligoarticular JIA (oJIA) cases and 57 age and sex matched controls using Illumina HumanMethylation450 arrays. DNA methylation at each array probe was tested for association with oJIA using RUV (Remove Unwanted Variation) together with a moderated t-test. Further to this ‘all-inclusive’ analysis, we stratified by age at diagnosis (?6yrs, &gt;6yrs) and by sex as potential sources of heterogeneity. Following False Discovery Rate (FDR) adjustment, no probes were associated with oJIA in the all-inclusive, &gt;6yrs-diagnosed, or sex-stratified analyses, and only one probe was associated with oJIA in the ?6yrs-diagnosed analysis. We attempted technical validation and replication of 14 probes (punadj&lt;0.01) at genes of known/potential relevance to disease. At VPS53, we demonstrated a regional shift towards higher methylation in oJIA (all-inclusive) compared to controls. At REEP3, where polymorphism has been previously associated with JIA, we demonstrated higher DNA methylation in male oJIA compared to male controls. This is the most comprehensive JIA case-control analysis of DNA methylation to date. While we have generated some evidence of altered methylation in oJIA, substantial differences are not apparent in CD4þ T cells. This may indicate a lesser relevance of DNA methylation levels in childhood, compared to adult, rheumatic disease.
DOI: 10.25374/mcri.29565800.v1
title: Data related to: The DNA methylation landscape of CD4 T cells in oligoarticular juvenile idiopathic arthritis

description: This is a table of DNA methylation Beta values for individual participants in the study. The values range from 0 to 1, representing 0% methylation to 100% methylation. Raw data (idat files) were analysed in R using Bioconductor software packages [36]. The Minfi package [37] was used to preprocess raw signal intensities to methylation measurements, and also to detect any low-quality samples by inspecting the median of the methylated and unmethylated signal intensities. The SWAN (Subset-quantile Within Array Normalization) package [38] was used for probe type normalization by correcting for technical differences between type I and type II probes (which measure methylated and unmethylated signals using two paired probes, or use a single probe, respectively).Juvenile idiopathic arthritis (JIA) is presumed to be driven by an adverse combination of genes and environment. Epigenetic processes, including DNA methylation, act as a conduit through which the environment can regulate gene activity. Altered DNA methylation has been associated with adult autoimmune rheumatic diseases such as rheumatoid arthritis, but studies are lacking for paediatric autoimmune rheumatic diseases including JIA. Here, we performed a genome-scale case-control analysis of CD4 T cell DNA methylation from 56 oligoarticular JIA (oJIA) cases and 57 age and sex matched controls using Illumina HumanMethylation450 arrays. DNA methylation at each array probe was tested for association with oJIA using RUV (Remove Unwanted Variation) together with a moderated t-test. Further to this ‘all-inclusive’ analysis, we stratified by age at diagnosis (?6yrs, &gt;6yrs) and by sex as potential sources of heterogeneity. Following False Discovery Rate (FDR) adjustment, no probes were associated with oJIA in the all-inclusive, &gt;6yrs-diagnosed, or sex-stratified analyses, and only one probe was associated with oJIA in the ?6yrs-diagnosed analysis. We attempted technical validation and replication of 14 probes (punadj&lt;0.01) at genes of known/potential relevance to disease. At VPS53, we demonstrated a regional shift towards higher methylation in oJIA (all-inclusive) compared to controls. At REEP3, where polymorphism has been previously associated with JIA, we demonstrated higher DNA methylation in male oJIA compared to male controls. This is the most comprehensive JIA case-control analysis of DNA methylation to date. While we have generated some evidence of altered methylation in oJIA, substantial differences are not apparent in CD4þ T cells. This may indicate a lesser relevance of DNA methylation levels in childhood, compared to adult, rheumatic disease.
DOI: 10.15468/dl.az97kz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Passerella arborea)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020306-250711103210423/datasets/export for details.
DOI: 10.15468/dl.3bvxzn
title: Occurrence Download

description: A dataset containing 222 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Populus purdomii)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 222 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020307-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgm34j
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliophila ephemera"
 ]
}

 The dataset includes 10 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020308-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.436cn6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Passerella arborea)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020309-250711103210423/datasets/export for details.
DOI: 10.5281/zenodo.15944678
title: K-FluDB

description: K-FluDB: A Novel K-Mer Based Database for Enhanced Genomic Surveillance of Influenza A Viruses

K-FluDB is a compressed database composed of distinct sub-sequences specific to 50 influenza A subtypes. It includes unique sequences for all 18 hemagglutinin (HA) and 11 neuraminidase (NA) subtypes. The original influenza sequences were obtained from the NCBI database on May 8, 2022, comprising a total of 895,900 Influenza A sequences.

To generate this database, sequences were first subsampled based on genomic segment and variant group, resulting in 81,262 sequences. These sequences served as input for the PanGen-InfluenzaA tool (GitHub), which constructs pangenomes by identifying both unique subtype-specific sequences and sequences shared across multiple subtypes.

Repository Contents

This repository contains a ZIP archive with three folders, each corresponding to pangenome datasets designed for reads of 74, 150, and 300 nucleotides in length. Each folder includes the following files:





Dispensable data files (1_dispensable.fasta to 8_dispensable.fasta):These files contain the dispensable genomic fragments for each of the eight segments of the Influenza A virus.




Unique data files (1_unique.fasta to 8_unique.fasta):These files contain the unique genomic fragments for each segment. The recommended files for mapping against genomic reads are 4_unique.fasta and 6_unique.fasta, corresponding to segments 4 and 6, which are the targets commonly used for Influenza A subtyping.




pangenome.fasta:This file contains the combined set of unique and dispensable genomic fragments for all eight segments.




unique.fasta:This file includes only the unique genomic fragments for all eight segments.


4_6_unique.fasta:This file incudes unique pangenomic pieces only for segments 4 and 6, and contains all 18 Htypes and 11Ntypes, this is the recomended file to use for Influenza A subtyping purposes.


Compression Efficiency and Classification Accuracy

K-FluDB achieves a relative compression index of 96.54% when using the complete pangenome and 99.64% when considering only subtype-specific sequences. The average precision for correctly classifying Hx and Nx subtypes using the unique sequences is 99.2% and 99.71%, respectively.

This database provides a highly efficient and accurate resource for influenza A subtype classification while significantly reducing the storage and computational requirements associated with full-genome analyses.



Acknowledgements


This research was partially supported by grants by PAPIIT-DGAPA-IN230523 awarded to BT. The first author gratefully acknowledges the scholarship provided by CONAHCYT. We also extend our sincere appreciation to the National Autonomous University of Mexico (UNAM) for granting access to the MIZTLI supercomputer, supported by the General Directorate of Computing and Information and Communication Technologies (DGTIC) through project LANCAD-UNAM-DGTIC-350.
DOI: 10.15468/dl.xxmxx3
title: Occurrence Download

description: A dataset containing 991 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Cyanocorax violaceus"
 ]
}

 The dataset includes 991 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020310-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2h7ddk
title: CCDC 2301018: Experimental Crystal Structure Determination

description: Related Article: Kazuhiro Uemura, Momoka Oshika, Haruka Hasegawa, Atsushi Takamori, Masahiro Sato|2024|Angew.Chem.,Int.Ed.|63|e202407743|doi:10.1002/anie.202407743
description: Related Article: Kazuhiro Uemura|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.