cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5607185
title: ISDB: In Silico Spectral Database (of Natural Products)

description: ISDB: In Silico DataBase (of Natural Products)

Background

The ISDB repository contains in silico fragmented spectra of natural products, generated using cfm-predict 4 (DOI: 10.1021/acs.analchem.1c01465).

The initial database preparation and its application for dereplication were first described in:Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication (DOI: 10.1021/acs.analchem.5b04804).

Content

Previous versions of ISDB contained predicted spectra for compounds aggregated within the LOTUS Initiative (DOI: 10.7554/eLife.70780) and included only "merged" spectra.

This version expands beyond taxon-restricted compounds and includes:



Individual in silico spectra predictions (~1 million)

Substructure annotations

Data for compounds from Wikidata and LOTUS


File Structure

.zip Files

Each .zip file contains:



All original outputs from cfm-predict 4

Substructure annotations


Wikidata vs LOTUS Files



Wikidata files: Contain spectra for nearly all compounds found in Wikidata, obtained using this query: https://w.wiki/Cvdo.

LOTUS files: Contain spectra only for compounds with a "found in taxon" (P703) statement, obtained using this query: https://w.wiki/D35x.


Energy Levels: energyAll vs energySum



energyAll files: Include spectra for three individual energy levels plus a summed spectrum (4 spectra per polarity per compound).

energySum files: Contain only the summed spectrum (1 spectrum per polarity per compound).


Related Resources



Building scripts: https://github.com/mandelbrot-project/spectral_lib_builder

Matching scripts: https://github.com/mandelbrot-project/spectral_lib_matcher
DOI: 10.5281/zenodo.5607186
title: ISDB: In Silico Spectral Databases of Natural Products

description: An In Silico spectral DataBase (ISDB) of natural products initially calculated from the Universal Natural Products Database (UNPD). This spectral file is in positive ionisation mode only. Fragmented using cfm-predict 2.0 https://sourceforge.net/projects/cfm-id/ Originally described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> https://doi.org/10.1021/ACS.ANALCHEM.5B04804 See http://oolonek.github.io/ISDB/ for associated scripts
DOI: 10.5281/zenodo.5607264
title: ISDB: In Silico Spectral Databases of Natural Products

description: An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative. This spectral file is in positive ionisation mode only. Fragmented using cfm-predict 3.0 https://cfmid.wishartlab.com/ Intensities at the low, medium and high energy level have been meaned. In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> https://doi.org/10.1021/ACS.ANALCHEM.5B04804 See http://oolonek.github.io/ISDB/ for associated spectral matching scripts LOTUS Initiative initially described in https://doi.org/10.7554/eLife.70780
DOI: 10.5281/zenodo.6939173
title: ISDB: In Silico Spectral Databases of Natural Products

description: An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (https://doi.org/10.7554/eLife.70780).<br> Fragmented using cfm-predict 4 (https://doi.org/10.1021/acs.analchem.1c01465) . In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> https://doi.org/10.1021/ACS.ANALCHEM.5B04804 See https://github.com/mandelbrot-project/spectral_lib_builder for associated building scripts. See https://github.com/mandelbrot-project/spectral_lib_matcher for associated matching scripts.
DOI: 10.5281/zenodo.7534250
title: ISDB: In Silico Spectral Databases of Natural Products

description: An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (https://doi.org/10.7554/eLife.70780).<br> Fragmented using cfm-predict 4 (https://doi.org/10.1021/acs.analchem.1c01465) . In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> https://doi.org/10.1021/ACS.ANALCHEM.5B04804 See https://github.com/mandelbrot-project/spectral_lib_builder for associated building scripts. See https://github.com/mandelbrot-project/spectral_lib_matcher for associated matching scripts.
DOI: 10.5281/zenodo.8287341
title: ISDB: In Silico Spectral Databases of Natural Products

description: An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (https://doi.org/10.7554/eLife.70780).<br> Fragmented using cfm-predict 4 (https://doi.org/10.1021/acs.analchem.1c01465) . In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> https://doi.org/10.1021/ACS.ANALCHEM.5B04804 See https://github.com/mandelbrot-project/spectral_lib_builder for associated building scripts. See https://github.com/mandelbrot-project/spectral_lib_matcher for associated matching scripts. The pickle formated ISDBs are build for quicker loading via matchms.
DOI: 10.5258/soton/d3388
title: SargSnap 2023 Qualitative Dataset Ghana

description: Qualitative interview, focus group and workshop data collected in the Western Region of Ghana in January 2023, as part of the SargSnap project.
DOI: 10.15468/dl.8dp6g5
title: Occurrence Download

description: A dataset listing the 5182 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Denmark",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2015-2025"
 ]
}

 The dataset's 5182 records were derived from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001514-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.11583/dtu.25896595
title: Upper Isar River, Germany

description: The Upper Isar River survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Upper Isar River survey in Munich Germany was conducted in February 2024. The primary purpose was to validate the new UAWOS hydrometry payloads against in-situ ground truth and legacy UAS hydrometry payloads. The dataset contains water surface elevation, bathymetry, land elevation, and water surface velocity datasets collected using different drone-borne and in-situ sensors. Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.11583/dtu.25896595.v1
title: Upper Isar River, Germany

description: The Upper Isar River survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Upper Isar River survey in Munich Germany was conducted in February 2024. The primary purpose was to validate the new UAWOS hydrometry payloads against in-situ ground truth and legacy UAS hydrometry payloads. The dataset contains water surface elevation, bathymetry, land elevation, and water surface velocity datasets collected using different drone-borne and in-situ sensors. Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.11583/dtu.26830696
title: Orco_Po Rivers, Italy

description: The Orco_Po Rivers survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Orco_Po Rivers survey in the Turin Province Italy was conducted in July 2024.<br>The survey's primary purpose was to measure WSE, river depth, and river surface velocity based on UAS hydrometry payloads. Throughout the survey, multiple payloads were utilized to separately collect water surface elevation (Geolux LX-80 Altimetry Radar), cross-sectional bathymetry (ZondAeroLF Water Penetrating Radar), and the water surface velocity (RSS 300 Doppler Radar). Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.11583/dtu.26830696.v2
title: Orco_Po Rivers, Italy

description: The Orco_Po Rivers survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Orco_Po Rivers survey in the Turin Province Italy was conducted in July 2024.<br>The survey's primary purpose was to measure WSE, river depth, and river surface velocity based on UAS hydrometry payloads. Throughout the survey, multiple payloads were utilized to separately collect water surface elevation (Geolux LX-80 Altimetry Radar), cross-sectional bathymetry (ZondAeroLF Water Penetrating Radar), and the water surface velocity (RSS 300 Doppler Radar). Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.11583/dtu.26830696.v1
title: Orco_Po Rivers, Italy

description: The Orco_Po Rivers survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Orco_Po Rivers survey in the Turin Province Italy was conducted in July 2024.<br>The survey's primary purpose was to measure WSE, river depth, and river surface velocity based on UAS hydrometry payloads. Throughout the survey, multiple payloads were utilized to separately collect water surface elevation (Geolux LX-80 Altimetry Radar), cross-sectional bathymetry (ZondAeroLF Water Penetrating Radar), and the water surface velocity (RSS 300 Doppler Radar). Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.11583/dtu.27169848.v1
title: Torne River, Sweden and Finland

description: The Torne Rivers survey is part of the EU Horizon project UAWOS. All datasets belonging to the UAWOS project can be accessed here. The Torne River flows along the border between Sweden and Finland from North to South and drains into the Gulf of Bothnia. The UAWOS focus area on the Torne was the river reach between Pello and Övertorneå and the survey was carried out from September 3<sup>rd</sup> to 9<sup>th</sup>, 2024.The survey primarily aimed to measure WSE, river depth, and river surface velocity based on UAS hydrometry payloads. Throughout the survey, multiple payloads were utilized to separately collect water surface elevation (Geolux LX-80 Altimetry Radar), cross-sectional bathymetry (ZondAeroLF Water Penetrating Radar), and the water surface velocity (RSS 300 Doppler Radar). Data is shared at three processing levels: The raw data (Level 1), processed point data (Level 2), and point data referenced to a reference river centerline/reference cross section lines (Level 3). Specialized software is required to process most Level 1 data, while Level 2/3 data comes in standard comma-separated ASCII files. More details about the different datasets and processing levels are included in the dataset readme file and the readme files belonging to the individual datasets.
DOI: 10.15468/dl.hjt6zv
title: Occurrence Download

description: A dataset containing 9983 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Baccharis halimifolia L.",
 "Country is France",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 9983 records from 274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001522-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cp37ae
title: Occurrence Download

description: A dataset containing 152420 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is one of (Thymus mastichina (L.) L., Cyatheaceae)"
 ]
}

 The dataset includes 152420 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001513-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wqpj7s
title: Occurrence Download

description: A dataset containing 5378101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Denmark",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2015-2025"
 ]
}

 The dataset includes 5378101 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001519-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28359555.v1
title: Table S2 from Proximal Partners of the Organellar N-terminal Acetyltransferase NAA60: Insights into Golgi Structure and Transmembrane Protein Topology

description: BioID Interaction Profiling: Comparing the Proxeomes of Golgi-Localized NAA60, SLC35A1, and SLC35C2
DOI: 10.6084/m9.figshare.28359558.v1
title: Supplementary Material from Proximal Partners of the Organellar N-terminal Acetyltransferase NAA60: Insights into Golgi Structure and Transmembrane Protein Topology

description: Table_S5.xlsx
DOI: 10.6084/m9.figshare.28359561.v1
title: Table S4 from Proximal Partners of the Organellar N-terminal Acetyltransferase NAA60: Insights into Golgi Structure and Transmembrane Protein Topology

description: Differential 1D annotation Enrichment for the comparative NAA60, SLC35A1, and SLC35C2 BioID setups
DOI: 10.6084/m9.figshare.28443374.v1
title: 3D-PanoPACT_Data_Code

description: Supporting source data and codes for Wang et al. "Cross-regional real-time visualization of systemic physiology and dynamics with 3D panoramic photoacoustic computed tomography (3D-PanoPACT)"
DOI: 10.6084/m9.figshare.28359564.v1
title: Table S3 from Proximal Partners of the Organellar N-terminal Acetyltransferase NAA60: Insights into Golgi Structure and Transmembrane Protein Topology

description: Differential 1D Annotation Enrichment for the NAA60 versus the control BioID setups
DOI: 10.6084/m9.figshare.28359567.v1
title: Table S5 from Proximal Partners of the Organellar N-terminal Acetyltransferase NAA60: Insights into Golgi Structure and Transmembrane Protein Topology

description: Biotinylated Peptide and Corresponding Protein Identification of BioID Samples
DOI: 10.15468/dl.kmp6em
title: Occurrence Download

description: A dataset containing 7945 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ixodes ricinus Linnaeus, 1758"
 ]
}

 The dataset includes 7945 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018649-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fex5gs
title: Occurrence Download

description: A dataset containing 1030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((17.88275 46.38577,18.98648 42.83591,22.07692 41.65944,23.79873 43.35174,22.56256 45.49545,19.78116 46.44664,17.88275 46.38577))",
 "HasGeospatialIssue is false",
 "TaxonKey is Culicidae"
 ]
}

 The dataset includes 1030 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001524-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5287/bodleian:wvpobgjbd
title: Temperature dependence of lithium anode voiding in argyrodite solid-state batteries

description: Data was created in PGB labs during 2018-2021
DOI: 10.15468/dl.u4cpca
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((29.80062 70.17001,31.01277 70.17001,31.01277 70.65462,29.80062 70.65462,29.80062 70.17001))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polypodiales"
 ]
}

 The dataset includes 109 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001525-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14892359
title: The dataset used in the manuscript titled "Structure–Dopant Concentration Relations in Europium-Doped Yttrium Molybdate and Peak-Sharpening for Luminescence Temperature Sensing".

description: This dataset contains the experimental data used in the manuscript titled "Structure–Dopant Concentration Relations in Europium-Doped Yttrium Molybdate and Peak-Sharpening for Luminescence Temperature Sensing". The data includes the results used to generate the figures in the manuscript.
DOI: 10.5281/zenodo.14892360
title: The dataset used in the manuscript titled "Structure–Dopant Concentration Relations in Europium-Doped Yttrium Molybdate and Peak-Sharpening for Luminescence Temperature Sensing".

description: This dataset contains the experimental data used in the manuscript titled "Structure–Dopant Concentration Relations in Europium-Doped Yttrium Molybdate and Peak-Sharpening for Luminescence Temperature Sensing". The data includes the results used to generate the figures in the manuscript.
DOI: 10.5255/ukda-sn-857652
title: The Psychology of Interoperability: Critical Decision Method Interviews, 2023

description: This research aimed to explore the social psychological processes underpinning interoperability (i.e., multi-agency working) between the emergency services. Semi-structured interviews were conducted with a 16 participants (using the principle of data saturation) across the three emergency service groups (Police, Fire, Ambulance) to identify behaviours and attitudes that interfere with or promote interoperability. Interviews were designed using Cognitive Task Analysis (Crandall, Klein & Hoffman, 2006), where participants were interviewed using the Critical Decision Method; a narrative-based approach to understand how experts navigate their complex work domains and has been previously used successfully to understand complex choices in emergency response contexts (Power & Alison, 2017). Themes of interest included: (i) challenges to interoperability; (ii) indicators of effective interoperability; and (iii) the interplay between organisational identity, values, and intergroup attitudes.

There were several key findings. Firstly, participants were in favour of the concept of interoperability but in practice, this was more complex. Findings were grouped across 3 levels: i) macro-systemic, ii) meso-organisational and iii) micro-psychological. Macro-systemic included a frustration with a lack of funding), lack of training, and scope of JESIP. Meso-organisational factors highlighted incompatible command structures, differences in hierarchy/heterarchy, risk appetite. Finally, micro-psychological findings included struggles with stress/strain.
DOI: 10.15468/dl.p7gy86
title: Occurrence Download

description: A dataset containing 930 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal, Andorra)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ursus arctos Linnaeus, 1758"
 ]
}

 The dataset includes 930 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001526-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wm56yf
title: Occurrence Download

description: A dataset containing 19065 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anabaena Bory de Saint-Vincent ex Bornet & Flahault, 1886"
 ]
}

 The dataset includes 19065 records from 349 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001527-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c6tsa3
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",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Hemiboea olivifolia Souvann. & Tagane)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030945-241107131044228/datasets/export for details.
DOI: 10.15468/dl.67wucp
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Hemiboea omeiensis W.T.Wang)"
 ]
}

 The dataset includes 88 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030946-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.