cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15263700
title: Whole genome re-sequencing workshop data: filtered vcf file, bed file, edited fam file and bim file for population genomics workshop

description: Whole genome re-sequencing data analysis workshop datasets. The files are necessary inputs for the workshop in https://github.com/PoODL-CES/Genomics_learning_workshop

Tools and scripts listed in the https://github.com/PoODL-CES/Genomics_learning_workshop repository.

The files contain filtered variants from the "raw" variants in https://zenodo.org/records/15173226

filters used are:

minimum Q 30

minimum GQ 30

no Indels

variants flagged as "PASS"

Hardy Weinberg chi square p value of 0.05

Individuals with more than 60% missing data removed

loci with more than 60% missing data removed

mean depth was mid 95 percentile of depths across loci

and all zoo born individuals removed from the dataset

This a part of the vcf file with data of chromosome E2 from:Khan, A., Patel, K., Shukla, H., Viswanathan, A., van der Valk, T., Borthakur, U., Nigam, P., Zachariah, A., Jhala, Y.V., Kardos, M. and Ramakrishnan, U., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proceedings of the National Academy of Sciences, 118(49), p.e2023018118.

The reference genome is from :

Shukla, H., Suryamohan, K., Khan, A., Mohan, K., Perumal, R.C., Mathew, O.K., Menon, R., Dixon, M.D., Muraleedharan, M., Kuriakose, B. and Michael, S., 2023. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. GigaScience, 12, p.giac112.
DOI: 10.15468/dl.u7h64j
title: Occurrence Download

description: A dataset containing 4963 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Aliger gigas (Linnaeus, 1758)"
 ]
}

 The dataset includes 4963 records from 128 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010079-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a3quch
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum microphyllum (Oerst.) Hemsl.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 82 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010080-250415084134356/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.28736903
title: Dataset: EEG-Controlled Exoskeleton for Walking and Standing - A Longitudinal Study of Healthy Individuals

description: <b>1.</b><b> </b><b>BMI Experiment Sessions</b>The <b>“ExperimentSessions”</b> folder contains data derived from a multi-session brain-machine interface (BMI) training study involving seven healthy participants, focusing on both open-loop and closed-loop lower-limb exoskeleton control. It includes raw EEG data, IMU data, and control signals and feedback from the exoskeleton, collected during training and testing sessions.<b>2.</b><b> </b><b>MRI and EEG Data for Kinesthetic Motor Imagery (KI) Study</b>The “<b>MRI_Data”</b> folder includes structural MRI, fMRI, and EEG data from five participants, recorded while they watched a 10-minute video of themselves walking in an exoskeleton for 11 Stop-Walk-Stop (SWS) cycles. During the video, participants were instructed to evoke kinesthetic motor imagery (KI) in sync with the exoskeleton’s movements. Baseline data, including both fMRI and EEG, were collected during a resting condition for comparison.<b>3.</b><b> </b><b>Data Validation</b>The <b>“ValidationTables”</b> folder contains files used to track and record validation results. The status and availability of each data/file are summarized in various Excel (.xls) files. The validation process focuses on key aspects, including data synchronization, electrode location validation, and the validation of both EEG and MRI data.<br><br><b>4. MIQ-RS Responses</b>The completed Motor Imagery Questionnaire-Revised 2nd version (MIQ-RS) from participants S1 to S5 and S7 are provided as PDF files in the folder 'MIQ-RS'. The completed MIQ-RS files are saved as MIQ-RS-Sx.pdf, where x indicates the participant number.<b>Note:</b> All the datasets provided are raw, with no filtering or artifact removal algorithms applied.
DOI: 10.6084/m9.figshare.28736903.v1
title: Dataset: EEG-Controlled Exoskeleton for Walking and Standing - A Longitudinal Study of Healthy Individuals

description: <b>1.</b><b> </b><b>BMI Experiment Sessions</b>The <b>“ExperimentSessions”</b> folder contains data derived from a multi-session brain-machine interface (BMI) training study involving seven healthy participants, focusing on both open-loop and closed-loop lower-limb exoskeleton control. It includes raw EEG data, IMU data, and control signals and feedback from the exoskeleton, collected during training and testing sessions.<b>2.</b><b> </b><b>MRI and EEG Data for Kinesthetic Motor Imagery (KI) Study</b>The “<b>MRI_Data”</b> folder includes structural MRI, fMRI, and EEG data from five participants, recorded while they watched a 10-minute video of themselves walking in an exoskeleton for 11 Stop-Walk-Stop (SWS) cycles. During the video, participants were instructed to evoke kinesthetic motor imagery (KI) in sync with the exoskeleton’s movements. Baseline data, including both fMRI and EEG, were collected during a resting condition for comparison.<b>3.</b><b> </b><b>Data Validation</b>The <b>“ValidationTables”</b> folder contains files used to track and record validation results. The status and availability of each data/file are summarized in various Excel (.xls) files. The validation process focuses on key aspects, including data synchronization, electrode location validation, and the validation of both EEG and MRI data.<b>Note:</b> All the datasets provided are raw, with no filtering or artifact removal algorithms applied.
DOI: 10.15468/dl.n2xu5d
title: Occurrence Download

description: A dataset containing 73009 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rangifer tarandus (Linnaeus, 1758)"
 ]
}

 The dataset includes 73009 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010069-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2aj7z
title: Occurrence Download

description: A dataset containing 36175 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Quaid-i-Azam University Herbarium"
 ]
}

 The dataset includes 36175 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010082-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mh37a2
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum stenocalyx (Oerst.) Hemsl.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 126 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010086-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxea9a
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (CHN.2_1, CHN.2.1_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Pieridae",
 "Year 2016-2025"
 ]
}

 The dataset includes 309 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010085-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15263829
title: Galaxy Training Material for the 'Use Jupyter notebooks in Galaxy' tutorial

description: This dataset was originally curated by Software Carpentry, a branch of The Carpentries non-profit organization, and is based on data from the Gapminder Foundation. It consists of six tabular CSV files containing GDP data for various countries across different years. The dataset was initially prepared for the Software Carpentry tutorial "Plotting and Programming in Python" and is also reused in the Galaxy Training Network (GTN) tutorial "Use Jupyter Notebooks in Galaxy."

This GTN tutorial provides an introduction to launching a Jupyter Notebook in Galaxy, installing dependencies, and importing and exporting data. It serves as a setup guide for a Jupyter Notebook environment that can be used to follow the Software Carpentry tutorial "Plotting and Programming in Python."
DOI: 10.5281/zenodo.15263830
title: Galaxy Training Material for the 'Use Jupyter notebooks in Galaxy' tutorial

description: This dataset was originally curated by Software Carpentry, a branch of The Carpentries non-profit organization, and is based on data from the Gapminder Foundation. It consists of six tabular CSV files containing GDP data for various countries across different years. The dataset was initially prepared for the Software Carpentry tutorial "Plotting and Programming in Python" and is also reused in the Galaxy Training Network (GTN) tutorial "Use Jupyter Notebooks in Galaxy."

This GTN tutorial provides an introduction to launching a Jupyter Notebook in Galaxy, installing dependencies, and importing and exporting data. It serves as a setup guide for a Jupyter Notebook environment that can be used to follow the Software Carpentry tutorial "Plotting and Programming in Python."
DOI: 10.15468/dl.4u38kf
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum caudatum Greenm.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 89 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010089-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c6dhj2
title: Occurrence Download

description: A dataset containing 3847 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-72.89623 -41.50152,-72.8717 -41.50152,-72.8717 -41.48925,-72.89623 -41.48925,-72.89623 -41.50152))"
 ]
}

 The dataset includes 3847 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010091-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.meugga
title: Occurrence Download

description: A dataset containing 562566 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungi (S)"
 ]
}

 The dataset includes 562566 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010081-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cfa5qq
title: Occurrence Download

description: A dataset containing 26698 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lactarius deterrimus Gröger"
 ]
}

 The dataset includes 26698 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010090-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7924/r4zs30t4h
title: Data from: High-speed 4D fluorescence light field tomography of whole freely moving organisms

description: Volumetric fluorescence imaging techniques, such as confocal, multiphoton, light sheet, and light field microscopy, have become indispensable tools across a wide range of cellular, developmental, and neurobiological applications. However, it is difficult to scale such techniques to the large 3D fields of view (FOV), volume rates, and synchronicity requirements for high-resolution 4D imaging of freely behaving organisms. Here, we present reflective Fourier light field computed tomography (ReFLeCT), a new high-speed volumetric fluorescence computational imaging technique. ReFLeCT synchronously captures entire tomograms of multiple unrestrained, unanesthetized model organisms over multi-millimeter 3D FOVs at 120 volumes per second. In particular, we applied ReFLeCT to reconstruct 4D videos of fluorescently labeled zebrafish and Drosophila larvae, enabling us to study their heartbeat, fin and tail motion, gaze, jaw motion, and muscle contractions with nearly isotropic 3D resolution while they are freely moving. As a novel approach for snapshot tomographic capture, ReFLeCT is a major advance towards bridging the gap between current volumetric fluorescence microscopy techniques and macroscopic behavioral imaging. 

This data repository contains the raw data for performing 4D reconstructions for four of the samples featured in the accompanying publication (link TBD). The code that processes this data can be found here: https://github.com/kevinczhou/ReFLeCT.
DOI: 10.15468/dl.7c6fv8
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum microcarpum Cham. & Schltdl.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 209 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010093-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytmk6z
title: Occurrence Download

description: A dataset containing 52765 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is a41250f0-7c3e-11d8-a19c-b8a03c50a862",
 "DatasetName ~*Hudson Bay Lowlands Project"
 ]
}

 The dataset includes 52765 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010084-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/6dd464ad0dfd5ad64d5f9e2dad24d0cb
title: Tree-ring measurements from permanent study plot in old-growth hemlock-hardwood forest, Dukes RNA, Hiawatha NF, Marquetee Co., MI

description: This package includes tree growth-ring widths for increment cores collected from a long-term 'macroplot' established in old-growth hemlock-northern hardwoods forest at the Dukes Research Natural Area/Dukes Experimental Forest in the Hiawatha National Forest in Marquette Co., MI. Tree demographic monitoring data for the entire ca. 3.0 ha macroplot, from 1992 to 2019, are available in the EDI package edi.1526.1. In 1993, 1994 and 1995, increment cores were taken for all 'core-able' trees greater than ~ 10 cm diameter for a subsection of the macroplot about 1 ha in area. Trees that were obviously badly rotten and hollow or steeply leaning were not cored. Cores are not cross-dated. See Methods for more details. This data-package may be cross-referenced to the demographic data in edi.1526.1 using stem numbers.
DOI: 10.15468/dl.24tvu3
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Synthyris lanuginosa (Piper) Pennell & J.W.Thomps.)"
 ]
}

 The dataset includes 127 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010095-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3j7trz
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum loeseneri Graebn.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 49 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010097-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxtf2d
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (CHN.2_1, CHN.2.1_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Papilionidae",
 "Year 2016-2025"
 ]
}

 The dataset includes 284 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010096-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d92kw6
title: Occurrence Download

description: A dataset containing 562566 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungi (S)"
 ]
}

 The dataset includes 562566 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010088-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nkqud4
title: Occurrence Download

description: A dataset containing 47297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Lantana camara L.",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 47297 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010098-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8a5z4p
title: Occurrence Download

description: A dataset containing 52765 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is a41250f0-7c3e-11d8-a19c-b8a03c50a862",
 "DatasetName ~*Hudson Bay Lowlands Project"
 ]
}

 The dataset includes 52765 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010087-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qx7uuu
title: Occurrence Download

description: A dataset containing 4737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Canis lupus Linnaeus, 1758"
 ]
}

 The dataset includes 4737 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010100-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hs2e6q
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.071 42.288,-6.166 42.288,-6.166 42.939,-7.071 42.939,-7.071 42.288))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trollius europaeus L."
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010101-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkyqkq
title: Occurrence Download

description: A dataset containing 276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Annona muricata L."
 ]
}

 The dataset includes 276 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010105-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cgce7u
title: Occurrence Download

description: A dataset containing 4257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Viburnum dentatum L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4257 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010103-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9kyfn
title: Occurrence Download

description: A dataset containing 32588 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-43.92101 -20.05478,-43.76355 -20.05478,-43.76355 -19.94197,-43.92101 -19.94197,-43.92101 -20.05478))",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Aves, Mammalia)"
 ]
}

 The dataset includes 32588 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010104-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60520/ieda/113778
title: Bulk major and trace element and isotopic composition of volcanic and intrusive rocks from the Macusani Volcanic Field, SE Peru

description: This dataset provides geochemical analyses of strongly peraluminous volcanic and intrusive rocks from the Neogene Macusani Volcanic Field in southeastern Peru, focusing on the lithium-rich Falchani deposit. Samples were analyzed for major elements using X-ray fluorescence (XRF) after loss on ignition (LOI) determination, and trace elements were quantified using inductively coupled plasma mass spectrometry (ICP-MS). Whole rock isotope ratios were obtained using MC-TIMS (Rb-Sr, Sm-Nd) and MC-ICPMS (Pb). The data characterizes the Falchani deposit's distinctive geochemistry, where lithium ore occurs primarily in tuffaceous mudstone (LIthium-rich Tuff) between two Li-rich volcaniclastic units (Upper and Lower Breccia). The chemical composition of Li-ore units resembles highly evolved peraluminous obsidian glasses and shows characteristics typical of rare-metal granites and Li-Cs-Ta pegmatites. Isotope ratios provide constraints on magma sources and petrogenetic processes in this economically significant lithium province.
description: Ramirez-Briones, J.S., Torró, L., Chiaradia, M., Laurent, O., Mandrou, S., Tavazzani, L., Chelle-Michou, C., Vallance, J., & Baby, P. (submitted). Petrogenesis of Volcanogenic Sedimentary Lithium Ore in the Neogene Macusani Volcanic Field, Puno, Peru. Journal of Petrology.
DOI: 10.15468/dl.hdrh3z
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-60.58 -30.45,-59.42 -30.45,-59.42 -29.55,-60.58 -29.55,-60.58 -30.45))",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 83 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010106-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.