cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rtxy58
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.17616 54.59594,-3.1808 54.56857,-3.17431 54.52821,-3.19518 54.5194,-3.20585 54.49319,-3.18706 54.48391,-3.11795 54.49829,-3.10751 54.53146,-3.12212 54.56068,-3.10913 54.58388,-3.12027 54.60289,-3.14903 54.60916,-3.17616 54.59594))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Muscicapa striata (Pallas, 1764)"
 ]
}

 The dataset includes 55 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001509-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/1rmuxd
title: imbert_inprep_tableS03.tab

description: Supplementary Table 3: Orthologous genes of V. faba genes hosting marker-trait associations from the GWAS of the current study. These relationships were retrieved from OrthoLegKB.
Supplementary Table 3 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/7xdxti
title: imbert_inprep_tableS01.tab

description: Supplementary Table 1: General table of the GWAS performed for frost tolerance on Vicia faba. The position of the significant SNP marker and of the gene in which it is located are indicated. The functional annotation from MapMan, GO and InterPro (Pfam, PANTHER, SUPERFAMILY) for the candidate genes were also added.
Supplementary Table 1 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/b54inc
title: imbert_inprep_tableS09.tab

description: Supplementary Table 9: Overview of syntenic QTL for the multi-trait analysis (cold tolerance, flowering, morphology, sugar and fat content), with their position on their respective chromosomes.
Supplementary Table 9 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/c1xtzq
title: imbert_inprep_tableS06.tab

description: Supplementary Table 6: Genes found differentially expressed in low temperatures in Saral and ILC533 or between the two varieties of Cicer arietinum, in the reanalysis of the dataset from Akbari et al. 2023. Saral is the cold-tolerant variety while ILC533 is the cold-susceptible variety. C = control; LT = low temperature.
Supplementary Table 6 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/c5fckw
title: imbert_inprep_table2.xlsx

description: Table 2: List of candidate genes for frost tolerance in Vicia faba. For each gene, its position on the corresponding V. faba chromosome, and functional annotation is indicated. Information supporting the gene as a candidate, either genetic or expression are also provided.
Table 2 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/dr7q9l
title: imbert_inprep_table3.tab

description: Table 3: Overview of cold tolerance QTL integrated in OrthoLegKB along with the number of QTL found syntenic.
FT: frost tolerance,
FD: frost damage response trait,
SR: survival rate after freezing air temperature exposure,
CMS: cell membrane stability,
LA: leaf attitude,
LC: leaf chlorosis,
RQ: root quality trait.
Table 3 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/fb42cr
title: imbert_inprep_tableSM1.tab

description: Supplementary Material Table 1: Genes included in upset plots intersections of Supplementary Material Fig. 5, along with their MapMan annotation. The first column indicates the presence or absence of contrasts in the intersection. For example in the intra-variety figure with down-regulated genes (intra_down), 1111 indicates that the set of genes is downregulated in Champagne and Térèse at T1 and T2. 0001 indicates that the set of genes is downregulated in Térèse at T2.
Supplementary Material Table 1 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/fcoxjb
title: imbert_inprep_tableS11.tab

description: Supplementary Table 11: Log2 fold-change of genes differentially expressed in low temperature conditions, in Bahrman et al., 2019 and in Akbari et al., 2023, for which an ortholog in V. faba was found linked to a MTA. Genes were filtered with the columns “common_contrast” to compare conditions across studies and “same_FC_direction” to ensure the same fold change sign across studies. Te = Térèse (sensi); Ch = Champagne (tol); LT = low temperature; N/C = control ILC533 = ILC533 (sensi); Saral = Saral (tol).
Supplementary Table 11 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/g7te7p
title: imbert2023_tableS1.tab

description: Table S1: List of QTL and RNA-seq datasets currently integrated in OrthoLegKB.
Supplementary Table 1 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes".
DOI: 10.57745/iaeb16
title: imbert_inprep_tableS08.tab

description: Supplementary Table 8: Overview of cold tolerance, flowering, morphology, sugar and fat content integrated datasets with the trait and number of QTL/syntenic QTL for the trait associated. Note that some multi-annotated QTL may be called for several queried_trait, therefore the sum of QTL is slightly inflated.
Supplementary Table 8 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/jcqmpn
title: imbert2023_tableS5.tab

description: Table S5: QTL included in syntenic blocks encompassing the FT locus in V. faba, P. sativum, M. truncatula and L. culinaris.
Supplementary Table 5 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"
DOI: 10.57745/lxomb7
title: imbert2023_tableS4.tab

description: Table S4: List of nodes stored in OrthoLegKB along with their respective count.
Supplementary Table 4 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"
DOI: 10.57745/movsgy
title: imbert_inprep_tableS10.tab

description: Supplementary Table 10: Syntenologs groups identified bearing at least one cold tolerance QTL and with all genes bearing a QTL with a trait from the multi-trait analysis. See the Materials and Methods section for the identification of cliques. Whether the P. sativum gene was found differentially expressed in the reanalysis of Bahrman et al. 2019 is indicated in the is_DE column.
Supplementary Table 10 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/nknluu
title: imbert_inprep_tableS04.tab

description: Supplementary Table 4: Overview of syntenic cold tolerance related QTL, with their position on their respective chromosomes.
Supplementary Table 4 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/o3o4qg
title: imbert_inprep_tableS07.tab

description: Supplementary Table 7: Groups of syntenologs identified all bearing a cold tolerance QTL. See the Materials and Methods section for the identification of cliques. Whether the P. sativum gene was found differentially expressed in the reanalysis of Bahrman et al. 2019 is indicated in the is_DE column.
Supplementary Table 7 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/qotjrr
title: imbert_inprep_tableS05.tab

description: Supplementary Table 5: Genes found differentially expressed in low temperatures in Champagne and Térèse or between the two varieties of Pisum sativum, in the reanalysis of the dataset from Bahrman et al. 2019. Orthologous Vicia faba genes are indicated if bearing a MTA. Te = Térèse; Ch = Champagne; LT = low temperature; N = control; T1 = sampling point 1; T2 = sampling point 2.
Supplementary Table 5 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/qptxct
title: imbert_inprep_tableS02.tab

description: Supplementary Table 2: Description of chromosomal regions rich in marker-trait associations along with their underlying genes. A threshold of 675,000 bp was used on each side of MTA to create non-overlapping clusters. Only clusters of at least five MTAs are represented.
Supplementary Table 2 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/tgpr8p
title: imbert2023_tableS6.tab

description: Table S6: Expression of FT genes for the integrated RNA-seq datasets. The “tpm_count” column indicates the expression of the gene in the sample (“sample_id“), in TPM.
Supplementary Table 6 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"
DOI: 10.57745/utqorc
title: imbert2023_tableS3.tab

description: Table S3: Description of relationships connecting nodes (from Table S1) with their associated properties. The “mandatory“ column indicates whether the property must be present for each imported relationship. Finally, the “is_indexed” indicates if an index was applied for this property. For these columns, “T” indicates True and “F” False.
Supplementary Table 3 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"
DOI: 10.57745/xirxqx
title: imbert_inprep_table1.tab

description: Table 1: Number of marker-trait associations and unique markers identified across environments. Note that the same loci can be assigned to both traits.
Table 1 from the paper "Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes"
DOI: 10.57745/yc2mxc
title: imbert2023_tableS2.tab

description: Table S2: Description of node properties included in the Ortho_KB model. The “mandatory“ column indicates whether the property must be present for each imported node, the “is_import_id” whether the property is the one used for the import and therefore should be unique. Finally, the “is_indexed” indicates if an index was applied for this property. For these columns, “T” indicates True and “F” False.
Supplementary Table 3 from the paper "Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"
DOI: 10.5258/soton/d3383
title: Dataset in support of the thesis 'Model predictive valve control to assist in tracking a lung pressure profile'

description: Data presented in the thesis as well as corresponding journal/conference papers. Data includes all control datasets for this research as well as all identification datasets. These are in '.xlsx' format requiring Microsoft Excel software or similar. This data was collected using the equipment stated in the thesis.
DOI: 10.15468/dl.yun2nb
title: Occurrence Download

description: A dataset containing 644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Panthera onca (Linnaeus, 1758), Myrmecophaga tridactyla Linnaeus, 1758)"
 ]
}

 The dataset includes 644 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001511-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2e9a3r
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-2.12958 39.21453,0.20126 39.21453,0.20126 40.32978,-2.12958 40.32978,-2.12958 39.21453))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brenthis daphne (Denis & Schiffermüller), 1775"
 ]
}

 The dataset includes 27 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001512-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10622913
title: AMaze: fully discrete training with three regimes (direct, scaffolding, interactive) and two algorithms (A2C, PPO)

description: Dataset containing all training artifacts (final models, training curves, intermediate visualizations, ...) as well as the raw data used to assert generalization capabilities.

The associated archive final_behavior.tar.gz provides a visualization of every replicate's final behavior for easier navigation.

Distribution files contain a sampling across 1000 seeds, 5 probabilities for traps and lures, 4 sizes and 5 set sizes resulting in 486356 mazes. Descriptive graphs provide an overview of the accessible "maze space".

 

v2: Added script to aggregate run dynamics (mean reward, errors, maze lengths...) and resulting generated dataset (csv) and plots (pdf)
DOI: 10.5281/zenodo.10622914
title: AMaze: fully discrete training with three regimes (direct, scaffolding, interactive) and two algorithms (A2C, PPO)

description: Dataset containing all training artifacts (final models, training curves, intermediate visualizations, ...) as well as the raw data used to assert generalization capabilities.

The associated archive final_behavior.tar.gz provides a visualization of every replicate's final behavior for easier navigation.

Distribution files contain a sampling across 1000 seeds, 5 probabilities for traps and lures, 4 sizes and 5 set sizes resulting in 486356 mazes. Descriptive graphs provide an overview of the accessible "maze space".
DOI: 10.5281/zenodo.14892301
title: AMaze: fully discrete training with three regimes (direct, scaffolding, interactive) and two algorithms (A2C, PPO)

description: Dataset containing all training artifacts (final models, training curves, intermediate visualizations, ...) as well as the raw data used to assert generalization capabilities.

The associated archive final_behavior.tar.gz provides a visualization of every replicate's final behavior for easier navigation.

Distribution files contain a sampling across 1000 seeds, 5 probabilities for traps and lures, 4 sizes and 5 set sizes resulting in 486356 mazes. Descriptive graphs provide an overview of the accessible "maze space".

 

v2: Added script to aggregate run dynamics (mean reward, errors, maze lengths...) and resulting generated dataset (csv) and plots (pdf)
DOI: 10.5441/001/1.3nj3qj45_2
title: Data from: Study "African elephants in Etosha National Park (data from Tsalyuk et al. 2018)"

description: The relationship between resource availability and wildlife movement patterns is pivotal to understanding species behavior and ecology. Movement response to landscape variables occurs at multiple temporal scales, from sub-diurnal to multiannual. Additionally, individuals may respond to both current and past conditions of resource availability. In this paper, we examine the temporal scale and variation of current and past resource variables that affect movement patterns of African elephants (Loxodonta africana) using sub-hourly movement data from GPS-GSM collared elephants in Etosha National Park, Namibia. We created detailed satellite-based spatiotemporal maps of vegetation biomass, as well as distance from surface water, road and fence. We used step selection functions to measure the relative importance of these landscape variables in determining elephants’ local movement patterns. We also examined how elephants respond to information, in locations they have previously visited, on productivity integrated over different temporal scales: from current to historical conditions. Our results demonstrate that elephants choose patches with higher than average annual productivity and grass biomass, but lower tree biomass. Elephants also prefer to walk close to water, roads, and fences. These preferences vary with time of day and with season, thereby providing insights into diurnal and seasonal behavioral patterns and the ecological importance of the landscape variables examined. We also discovered that elephants respond more strongly to long-term patterns of productivity than to immediate forage conditions, in familiar locations. Our results illustrate how animals with high cognitive capacity and spatial memory integrate long-term information on landscape conditions. We illuminate the importance of long-term high temporal resolution satellite imagery to understanding the relationship between movement patterns and landscape structure.
DOI: 10.15468/dl.kh64py
title: Occurrence Download

description: A dataset containing 2799 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is PRT.3.11_1",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 2799 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001515-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bjcueu
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum vinosum Soest"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001516-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25824/redu/jrdydz
title: Electroendephalography data from study on neurorehabilitation after stroke

description: Electroencephalography data collected from a study investigating the neurophysiological aspects of a neurorehabilitation protocol combining neuromodulation with transcranial direct current stimulation (tDCS) and extreme reality for people with stroke. The generated data associated with the study are not publicly available due to ethical requirements, but are available from the corresponding author on reasonable request.
DOI: 10.15468/dl.9xvfhk
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lagerstroemia tomentosa C.Presl"
 ]
}

 The dataset includes 196 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001517-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qx39j
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.17616 54.59594,-3.1808 54.56857,-3.17431 54.52821,-3.19518 54.5194,-3.20585 54.49319,-3.18706 54.48391,-3.11795 54.49829,-3.10751 54.53146,-3.12212 54.56068,-3.10913 54.58388,-3.12027 54.60289,-3.14903 54.60916,-3.17616 54.59594))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Muscicapa striata (Pallas, 1764)"
 ]
}

 The dataset includes 55 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001518-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3w4ffk
title: Occurrence Download

description: A dataset containing 939 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 {
 "or" : [
 "InstitutionKey is not null",
 "CollectionKey is not null"
 ]
 },
 "BasisOfRecord is one of (Specimen, Fossil, Material sample, Living Specimen, Material citation)"
 ]
 },
 "TaxonKey is one of (Cairina J.Fleming, 1822)"
 ]
}

 The dataset includes 939 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001520-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14887271
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