cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9vy9wc
title: Occurrence Download

description: A dataset containing 4827 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carpinus japonica Blume"
 ]
}

 The dataset includes 4827 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001014-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13889593
title: MSnLib Mass spectral libraries (.mgf and .json)

description: Flow injection method to acquire MSn data on an Orbitrap ID-X instrument for different compound libraries in positive and negative ionization mode. MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. .mgf and .json data formats are available with V3. 

7 Compound Libraries:



Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)

MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds

MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds

NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds

OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds

ENAMDISC: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds

ENAMMOL: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds

MCEDRUG: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds


Information regarding the SPECTYPE



no SPECTYPE or SINGLE_BEST_SCAN: Best spectrum for each precursor and energy (highest TIC)

'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).

'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).

'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.
DOI: 10.5281/zenodo.11163381
title: MSnLib Mass spectral libraries (.mgf)

description: Flow injection method to acquire MSn data on an Orbitrap ID-X instrument for four different compound libraries in positive and negative ionization mode. MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. 

4 Compound Libraries:



Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)

MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds

MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds

NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds

OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds


Information regarding the SPECTYPE



no SPECTYPE: Best spectrum for each precursor and energy (highest TIC)

'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).

'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).

'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.
DOI: 10.5281/zenodo.13889494
title: MSnLib Mass spectral libraries (.mgf)

description: Flow injection method to acquire MSn data on an Orbitrap ID-X instrument for different compound libraries in positive and negative ionization mode. MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. 

7 Compound Libraries:



Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)

MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds

MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds

NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds

OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds

ENAMDISC: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds

ENAMMOL: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds

MCEDRUG: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds


Information regarding the SPECTYPE



no SPECTYPE or SINGLE_BEST_SCAN: Best spectrum for each precursor and energy (highest TIC)

'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).

'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).

'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.
DOI: 10.5281/zenodo.13898009
title: MSnLib Mass spectral libraries (.mgf and .json)

description: Flow injection method to acquire MSn data on an Orbitrap ID-X instrument for different compound libraries in positive and negative ionization mode. MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. .mgf and .json data formats are available with V3. 

7 Compound Libraries:



Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)

MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds

MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds

NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds

OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds

ENAMDISC: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds

ENAMMOL: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds

MCEDRUG: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds


Information regarding the SPECTYPE



no SPECTYPE or SINGLE_BEST_SCAN: Best spectrum for each precursor and energy (highest TIC)

'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).

'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).

'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.
DOI: 10.5281/zenodo.13911806
title: MSnLib Mass spectral libraries (.mgf and .json)

description: The data for MSnLib are divided into several Zenodo records due to size constraints. 

raw positive: 10966404raw negative: 10967081mzml positive and negative: 10966280spectral libraries: 11163380

This record includes the automatically generated spectral libraries (MSnLib) within mzmine, acquired using a flow injection method on an Orbitrap ID-X instrument, for all compound libraries. There are multiple files for each compound library containing MS2 only or MSn in two data formats (.mgf or .json) for both polarities. 

MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. The first number for each file highlights the library building date.

7 Compound Libraries:



Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)

MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds

MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds

NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds

OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds

ENAMDISC: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds

ENAMMOL: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds

MCEDRUG: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds


Information regarding the SPECTYPE



no SPECTYPE or SINGLE_BEST_SCAN: Best spectrum for each precursor and energy (highest TIC)

'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).

'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).

'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.


 

V5 fixed USIs
DOI: 10.15468/dl.6wspuq
title: Occurrence Download

description: A dataset containing 25015 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carpinus caroliniana Walter"
 ]
}

 The dataset includes 25015 records from 323 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001013-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yk7hu8
title: Occurrence Download

description: A dataset containing 13867 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carya cordiformis (Wangenh.) K.Koch"
 ]
}

 The dataset includes 13867 records from 240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001015-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/4244
title: longCOVID_CaseReports_SDOH
DOI: 10.5281/zenodo.11204408
title: Supplementary data (excel tables) for manuscritpt under revision (more details when the manuscript will be accepted for publication)
DOI: 10.5281/zenodo.11204407
title: Supplementary data (excel tables) for manuscritpt under revision (more details when the manuscript will be accepted for publication)
DOI: 10.5281/zenodo.14502990
title: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Additional Data

description: This repository is intended to accompany the final report to the US Fish and Wildlife Service, entitled: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly

The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new microsatellite markers for use in population structure and kinship analyses.  We also used DNA from natural mortalities to determine whether non-invasively collected samples could be used to generate enough single nucleotide polymorphisms (SNPs) to perform fine-scale genomic analyses. Whole mitochondrial genomes were assembled, annotated, and used to infer a phylogeny with museum specimens of insulanus collected ~100 years ago from Vancouver Island and other members of the E. ausonides species complex. The results indicated that insulanus suffers from low heterozygosity, a small effective population size (Ne), and low allelic diversity. There was evidence of high levels of inbreeding in some individuals, but inbreeding was uneven across the population. There was no population structure or partitioning by host plant detected. The mitogenomes of extant insulanus were all identical and there was a loss of allelic diversity in modern samples compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management decisions and genetic monitoring.

Included in this repository are:



Sample metadata for all samples used, including which analysis they were used in (microsatellite, mitogenome, and/or ddRAD), and the BioSample and SRA accessions for sequenced samples desposited with NCBI GenBank under BioProject PRJNA1156227 (IMB_metadata.csv)

The VCF file of SNPs produced from ddRAD NovaSeq sequencing (novaseq_IMB_20_depth_Q30_50_missing.vcf)

The microsatellite loci used for population genetic analyses (IMB_microsatellite_loci.csv)
DOI: 10.5281/zenodo.14502991
title: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Additional Data

description: This repository is intended to accompany the final report to the US Fish and Wildlife Service, entitled: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly

The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new microsatellite markers for use in population structure and kinship analyses.  We also used DNA from natural mortalities to determine whether non-invasively collected samples could be used to generate enough single nucleotide polymorphisms (SNPs) to perform fine-scale genomic analyses. Whole mitochondrial genomes were assembled, annotated, and used to infer a phylogeny with museum specimens of insulanus collected ~100 years ago from Vancouver Island and other members of the E. ausonides species complex. The results indicated that insulanus suffers from low heterozygosity, a small effective population size (Ne), and low allelic diversity. There was evidence of high levels of inbreeding in some individuals, but inbreeding was uneven across the population. There was no population structure or partitioning by host plant detected. The mitogenomes of extant insulanus were all identical and there was a loss of allelic diversity in modern samples compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management decisions and genetic monitoring.

Included in this repository are:



Sample metadata for all samples used, including which analysis they were used in (microsatellite, mitogenome, and/or ddRAD), and the BioSample and SRA accessions for sequenced samples desposited with NCBI GenBank under BioProject PRJNA1156227 (IMB_metadata.csv)

The VCF file of SNPs produced from ddRAD NovaSeq sequencing (novaseq_IMB_20_depth_Q30_50_missing.vcf)

The microsatellite loci used for population genetic analyses (IMB_microsatellite_loci.csv)
DOI: 10.15468/dl.jerurg
title: Occurrence Download

description: A dataset containing 415905 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (VU, EN, CR, EW, EX)",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 2000-2025"
 ]
}

 The dataset includes 415905 records from 876 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000996-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17160564
title: exchange interactions derived from fitting inelastic neutron scattering

description: The data contains details of exchange interactions derived from fitting inelastic neutron scattering (INS) data to spin-wave (SW) theory for over 70 magnetic compounds. Additionally, Monte Carlo simulation data for each compound, generated using ESpinS, is included.



The data is also available on GitHub: https://github.com/malaei/Magnetic_data/tree/main/INS_SW_MC


If you use this dataset, please cite:



Mojtaba Alaei, Zahra Mosleh, Nafise Rezaei, Artem R. Oganov,From Spin Waves to Monte Carlo Simulations: Compiling an Experimental Exchange Interaction Dataset for Magnetic Materials,arXiv:2504.15764
DOI: 10.15468/dl.8tjbd8
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amandava amandava",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 143 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018986-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvxwwu
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Myiopardalis pardalina"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018987-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnbrq6
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euplectes orix",
 "Country is Bahrain",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018989-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.psxyss
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euplectes orix",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018990-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h7d9nh
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euplectes orix",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018991-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17160493
title: Hard carbon structures from experiment-constrained simulations

description: These hard carbon atomic structures, in extended XYZ format, have been generated using a melt-graphitization-quench molecular augmented dynamics (MAD) [1] protocol using a Gaussian approximation potential (GAP) for carbon [2] from experimental X-ray diffraction patterns. HC_10648 and HC_1728 contain four hard carbon samples: bacterial cellulose, TEMPO-oxidized cellulose nanofibrils, Whatman filter paper, and a commercial hard carbon reference with a simulation box of 10648 and 1728 atoms respectively. Simulation details and characterization of structural properties will follow in a scientific paper.
DOI: 10.17863/cam.121372
title: Optical and magnetic response by design in GaAs quantum dots - Supplemental Data

description: Data sets and python scripts used to generate the data plots of the main manuscript and the supplemental material of the PRX Quantum publication "Optical and magnetic response by design in GaAs quantum dots". Please see the readme files for further information.
DOI: 10.15468/dl.muqda4
title: Occurrence Download

description: A dataset containing 27096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.50829 54.13587,6.79595 53.53839,7.12964 53.67493,8.13069 53.77705,8.42985 53.81782,8.13069 54.47156,7.14114 54.42473,6.50829 54.13587))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 27096 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018992-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mnjb3m
title: Occurrence Download

description: A dataset containing 27096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.50829 54.13587,6.79595 53.53839,7.12964 53.67493,8.13069 53.77705,8.42985 53.81782,8.13069 54.47156,7.14114 54.42473,6.50829 54.13587))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 27096 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018993-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.exbp89
title: Occurrence Download

description: A dataset listing the 7606 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is India Biodiversity Portal publication grade dataset"
 ]
}

 The dataset's 7606 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018983-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6j6f9q
title: Occurrence Download

description: A dataset containing 1059 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euplectes orix",
 "Country is United Arab Emirates",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1059 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018994-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7y6dz
title: Occurrence Download

description: A dataset containing 2102 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mammillaria magnimamma"
 ]
}

 The dataset includes 2102 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018996-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25420/britishmuseum.30148783
title: An Audio Interview with Mr. Mohammad Abdullah and Hasan Ali

description: An Audio Interview with Mr. Mohammad Abdullah and Hasan Ali
DOI: 10.25420/britishmuseum.30148783.v1
title: An Audio Interview with Mr. Mohammad Abdullah and Hasan Ali

description: An Audio Interview with Mr. Mohammad Abdullah and Hasan Ali
DOI: 10.25420/britishmuseum.30147235
title: An Audio Interview with Mr. Waddah and Hasan Ali

description: An Audio Interview with Mr. Waddah and Hasan Ali
DOI: 10.25420/britishmuseum.30147235.v1
title: An Audio Interview with Mr. Waddah and Hasan Ali

description: An Audio Interview with Mr. Waddah and Hasan Ali