cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.zg4wax
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Hemerocallidaceae"
 ]
}

 The dataset includes 128 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045405-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xg3yxs
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lobelia acrochila (E.Wimm.) E.B.Knox"
 ]
}

 The dataset includes 44 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045402-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xerrx9
title: Occurrence Download

description: A dataset containing 4607 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Vultur gryphus Linnaeus, 1758"
 ]
}

 The dataset includes 4607 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045397-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.je8wzz
title: Occurrence Download

description: A dataset containing 4607 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Peru",
 "TaxonKey is Vultur gryphus Linnaeus, 1758"
 ]
}

 The dataset includes 4607 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045400-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3dk2ru
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Haloragidaceae"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045398-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nux6rb
title: Occurrence Download

description: A dataset containing 4607 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Vultur gryphus Linnaeus, 1758"
 ]
}

 The dataset includes 4607 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045399-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2tey6
title: Occurrence Download

description: A dataset containing 1897 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Hemidictyaceae"
 ]
}

 The dataset includes 1897 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045406-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10428452
title: Experimental characterisation of intact samples of Areolas da Estefania

description: Intact samples extracted from the Areolas da Estefania formation in Lisbon, Portugal, at depths of 8m, 18m and 21m were subjected to drained triaxial compression under constant mean effective stress levels. These files report the measured stress-strain response, as well as the variation of shear stiffness with deformation level. A complementary set of bender element tests were performed on two intact samples collected from depths of 8m and 18m to establish the shear stiffness of the material at very small strains.
DOI: 10.5281/zenodo.10522065
title: Experimental characterisation of intact samples of Areolas da Estefania

description: Intact samples extracted from the Areolas da Estefania formation in Lisbon, Portugal, at depths of 8m, 18m and 21m were subjected to drained triaxial compression under constant mean effective stress levels. These files report the measured stress-strain response, as well as the variation of shear stiffness with deformation level. A complementary set of bender element tests were performed on two intact samples collected from depths of 8m and 18m to establish the shear stiffness of the material at very small strains.
DOI: 10.5281/zenodo.10888728
title: Experimental characterisation of intact samples of Areolas da Estefania

description: Intact samples extracted from the Areolas da Estefania formation in Lisbon, Portugal, at depths of 8m, 18m and 21m were subjected to drained triaxial compression under constant mean effective stress levels. These files report the measured stress-strain response, as well as the variation of shear stiffness with deformation level. A complementary set of bender element tests were performed on two intact samples collected from depths of 8m and 18m to establish the shear stiffness of the material at very small strains.
DOI: 10.5281/zenodo.10428451
title: Experimental characterisation of intact samples of Areolas da Estefania

description: Intact samples extracted from the Areolas da Estefania formation in Lisbon, Portugal, at depths of 8m, 18m and 21m were subjected to drained triaxial compression under constant mean effective stress levels. These files report the measured stress-strain response, as well as the variation of shear stiffness with deformation level. A complementary set of bender element tests were performed on two intact samples collected from depths of 8m and 18m to establish the shear stiffness of the material at very small strains.
DOI: 10.5281/zenodo.10522406
title: Experimental characterisation of intact samples of Areolas da Estefania

description: Intact samples extracted from the Areolas da Estefania formation in Lisbon, Portugal, at depths of 8m, 18m and 21m were subjected to drained triaxial compression under constant mean effective stress levels. These files report the measured stress-strain response, as well as the variation of shear stiffness with deformation level. A complementary set of bender element tests were performed on two intact samples collected from depths of 8m and 18m to establish the shear stiffness of the material at very small strains.
DOI: 10.15468/dl.az5ufr
title: Occurrence Download

description: A dataset containing 1074292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "GadmGid is BEL.3_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2015-2024"
 ]
}

 The dataset includes 1074292 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045342-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8065112
title: individual gene knock outs in K562 cells-6

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065111
title: individual gene knock outs in K562 cells-6

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8068425
title: individual gene knock outs in K562 cells-6

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.15468/dl.7msvyx
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cebus Erxleben, 1777"
 ]
}

 The dataset includes 115 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045410-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8065370
title: individual gene knock outs in K562 cells-8

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065371
title: individual gene knock outs in K562 cells-8

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.15468/dl.bcnfaz
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((26.04041 44.3688,26.17413 44.3688,26.17413 44.51337,26.04041 44.51337,26.04041 44.3688))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fringilla montifringilla Linnaeus, 1758"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045417-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fgczw
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Hoplestigmataceae"
 ]
}

 The dataset includes 177 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045412-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r92jae
title: Occurrence Download

description: A dataset containing 5670 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora al interior del Área 2 del Banco de Hábitat del Meta de Terrasos"
 ]
}

 The dataset includes 5670 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045411-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5886s5
title: Occurrence Download

description: A dataset containing 1498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Observation)",
 "Geometry POLYGON((-90.55863 21.50705,-90.46182 20.58547,-87.26708 21.29072,-87.49943 21.777,-90.55863 21.50705))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gelochelidon nilotica (J.F.Gmelin, 1789)",
 "Year 2000-2024"
 ]
}

 The dataset includes 1498 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045413-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3p3tth
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Hippocastanaceae"
 ]
}

 The dataset includes 85 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045408-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qs25ay
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Phoeniconaias minor (É.Geoffroy Saint-Hilaire, 1798)"
 ]
}

 The dataset includes 89 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045409-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8065115
title: individual gene knock outs in K562 cells-7

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065116
title: individual gene knock outs in K562 cells-7

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065107
title: individual gene knock outs in K562 cells-5

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065108
title: individual gene knock outs in K562 cells-5

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065103
title: individual gene knock outs in K562 cells-4

description: This data includes (individual gene knock outs in K562 cells,1-8) bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065104
title: individual gene knock outs in K562 cells-4

description: This data includes (individual gene knock outs in K562 cells,1-8) bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8064683
title: individual gene knock outs in K562 cells-2

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8064684
title: individual gene knock outs in K562 cells-2

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8063669
title: individual gene knock outs in K562 cells-1

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8063670
title: individual gene knock outs in K562 cells-1

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8064008
title: GeCKO_v2_CRISPR_drug screens in K562 cells

description: The data contain raw DNA deep sequencing files for GeCKO-v2 genome scale transduced K562 screens with selected drugs (imatinib, dasatinib, asciminib, tivozanib, AZD1775, mepacrine). For all drug except mepacrine the drug, day 0 and day 17 control samples' files are provided. For mepacrine which was screened separately, a triplicate drug, D15 control sample files are provided. The dates are indicated in the file names.
DOI: 10.5281/zenodo.8064009
title: GeCKO_v2_CRISPR_drug screens in K562 cells

description: The data contain raw DNA deep sequencing files for GeCKO-v2 genome scale transduced K562 screens with selected drugs (imatinib, dasatinib, asciminib, tivozanib, AZD1775, mepacrine). For all drug except mepacrine the drug, day 0 and day 17 control samples' files are provided. For mepacrine which was screened separately, a triplicate drug, D15 control sample files are provided. The dates are indicated in the file names.
DOI: 10.5281/zenodo.8065099
title: individual gene knock outs in K562 cells-3

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.5281/zenodo.8065100
title: individual gene knock outs in K562 cells-3

description: This data (individual gene knock outs in K562 cells,1-8) includes bulk RNA sequencing data from individual gene knockouts K562 cells for 5 selected genes (KCTD5, EIF2AK1, APAF1, CCNC, IGF1R, triplicate samples for each) in addition to control guideRNA transduced K562 cells (n=5 samples)
DOI: 10.15468/dl.kashht
title: Occurrence Download

description: A dataset containing 29824 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083495-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ye4d4j
title: Occurrence Download

description: A dataset containing 28227 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Colias palaeno (Linnaeus, 1761)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 28227 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083496-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmtrqn
title: Occurrence Download

description: A dataset containing 29824 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083497-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13356510
title: Genome Sizes of Bacterial Species Detected in Cell-Free DNA of Patients with Acute Leukemia and Sepsis, Including Those Undergoing Bone Marrow Transplantation
title: Dataset of Bacterial Species along with their genome size, detected in Cell Free DNA of Acute Leukemia Patients diagnosed with Sepsis including those undergone bone marrow transplant

description: Next Generation Sequencing (NGS) analysis of Cell-Free DNA provides valuable insights into a spectrum of pathogenic species (particularly bacterial) in blood. Patients with Sepsis often face problems like delays in treatment regimens (combination or cocktail of antibiotics) due to the long turnaround time (TAT) of classical and standard blood culture procedures. NGS gives results with lower TAT along with high-depth coverage. The use of NGS may be a possible solution to deciding treatment regimens for patients without losing precious time and more accurately possibly saving lives.

Our curated dataset is of bacterial species or strains detected along with their genome size in 107 AML patients diagnosed with Sepsis clinically. Cell-free DNA profiles of patients were built and sequencing was done in Illumina (NovaSeq and NextSeq). Bioinformatic analysis was performed using two classification algorithms namely kraken2 and kaiju. For kraken2  based classification reference bacterial index developed by Carlo Ferravante et al (Zenodo 2020)  (link: https://zenodo.org/records/4055180) was used, while for kaiju-based classification reference database named "nr_euk" dated "2023-05-10" (link: https://bioinformatics-centre.github.io/kaiju/downloads.html) was used.

Genome size annotation is important in metagenomics since for the use of depth of coverage (abundance), genome size is required. In metagenomic classification algorithms like kraken/kraken2 and kaiju output computes reads assigned only and not abundance. In kaiju, the problem is more complicated since the reference database does not have a fasta file but only an index file from which alignment is done. 

To address the above challenges to compute "depth of coverage" or simply abundance, we build a Genome size annotator tool (https://github.com/patkarlab/Genome-Size-Annotation) which provides genome size for each species detected given its taxid is available. In this tool, the NCBI Datasets tool, NCBI Genome API check tool, and Data Mining from AI search engines like perplexity.ai are used. 

We have curated two datasets

Kraken2 dataset named "FINAL METAGENOMIC DATA MASTERSHEET - kraken_genome_annotation"Kaiju dataset named "FINAL METAGENOMIC DATA MASTERSHEET - kaiju_genome_annotation"

*Please note that for kraken2 curated dataset, we used data mining from the AI search engine perplexity.ai while for kaiju we did not use perplexity, ai, and any species whose genome size was not found was labeled "NA"