cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/bn46knt28h.1
title: TerraDactyl v1.0 software archive

description: TerraDactyl allows for the extraction of map layer data, currently curated by Google Earth Engine (GEE), at a set of point in space and time. It has been developed in tandem with eDNAExplorer.org as a means of automatically associated biodiversity data, derived from environmental DNA, with environmental conditions associated with each sample. However, these extracted environmental data can be associated with other types of data collected, not just biodiversity measurements.

Quick overview of this archive:
1. Example input file for TerraDactyl: TerraDactyl_ExampleInput.csv
2. Example output file from TerraDactyl: TerraDactyl_ExampleOutput.csv
3. Overview of environmental data sets utilized by TerraDactyl: TerraDactyl_Metadata.xlsx
4. Python requirements: requirements.txt
5. Script for processing environmental maps in raster format: RasterDataset.py
6. Script for processing environmental maps in vector format: VectorDataset.py
7. The TerraDactly script: terradactyl.py
8. Shell script for running terradactyl.py in parallel over input rows of metadata (These describe sample locations and dates).
DOI: 10.17632/7fr4wwrb45.1
title: Data and code for "Experimental test of the effects of prolonged flooding practices on animal communities in rice paddy fields"

description: This dataset contains data and R code associated with the following article:

Article Title: Experimental test of the effects of prolonged flooding practices on animal communities in rice paddy fields
Journal Name: Agriculture, Ecosystems and Environment
Author Names: Kosuke Nakanishi, Hiromi Akanuma, Raita Kobayashi, Hiroyuki Yokomizo, Takehiko I. Hayashi, Belinda Robson, Nisikawa Usio
DOI: https://doi.org/10.1016/j.agee.2024.109369

Data Description:
- Suppl_code.Rmd: R code for main and preliminary analyses.
- amphibia_data.csv: Raw data of amphibians.
- insect_data.csv: Raw data of freshwater insects.
- spider_data.csv: Raw data of spiders.
DOI: 10.17632/23vhgsjhmy.1
title: Analysis scripts and data for case studies of TerraDactyl software.

description: Research ranging from land use planning to ecology benefits from integrating spatial and temporal environmental data. Analyses on multiple environmental datasets are enhanced when there is a common set of variables, improving the ability of researchers to collaborate across a wide variety of projects. Addressing the need, we developed TerraDactyl, an online tool hosted on eDNA Explorer (ednaexplorer.org). TerraDactyl (Version 1 of TerraDactyl is available here: https://github.com/eDNA-Explorer/terradactyl/tree/v1.0 ) intakes user-provided geospatial coordinates and dates to extract environmental values from a series of datasets hosted on the Google Earth Engine (GEE). We demonstrate the utility of TerraDactyl with two case studies. The first study aims to classify protected areas in the US and Canada given only TerraDactyl data. In the second study we reanalyze published community compositional variation California environmental DNA (eDNA) samples to test whether variation is more strongly associated with environmental factor groups such as soil and topography when more variables are added by TerraDactyl. While some current limitations remain, such as the gaps in data available in polar and coastal regions, TerraDactyl offers a robust integrative tool to assist biodiversity and environmental research that has potential for expansion to include more datasets.

A detailed description of the files and scripts in this archive can be found in the README file. This README covers the structure of input files, and which scripts there are utilized by.
DOI: 10.17632/zfc679s9xn.1
title: Value Addition to Natural Resources and Minerals in Sri Lanka: A Science-for-Policy View

description: Sri Lanka, a nation rich in natural resources and minerals, has yet to fully exploit its minerals. There are enormous untapped opportunities for the mineral industry's contribution to boosting the economy. The objective of this paper is to examine the technical report (TR) recommendations proposed at the Ninth Biennial Conference on Science and Technology of Sri Lanka (BICOST) from the perspective of science for policy. TRs provide comprehensive analyses of the local mineral sector and propose a range of recommendations for value addition, high quality, and purity of minerals, as well as the need for scientific data from chemical analysis to take advantage of the industry on the island toward a more value-added, sustainable economy.
DOI: 10.17632/wgk3mxvv5c.1
title: Innovative low-cost, lightweight Follicular unit extraction micromotor device

description: Details of device and procedural video
DOI: 10.17632/pp23bxdr94.1
title: Remodeling of the Ventral Attention Network-Default Mode Network as Neural Markers of Anxiety in Lumbar Disc Herniation Patients Treated with Spinal Manipulative Therapy: A resting-state fMRI Study

description: The original data here include 3D imaging data and clinical questionnaire scales.
DOI: 10.17632/cvrrw88wry.1
title: Supplementary Material - Welk et al. 2024 - Effect of nonsteroidal anti-inflammatory drugs on neonatal calf diarrhea when administered at a disease alert generated by automated milk feeders

description: Supplementary Material (table outlining statistical models used) for manuscript: Welk et al., 2024 - Effect of nonsteroidal anti-inflammatory drugs on neonatal calf diarrhea when administered at a disease alert generated by automated milk feeders. Journal of Dairy Science.
DOI: 10.17632/47hzszw9hn.1
title: Workforce Analysis of Dermatology Residency Programs within the United States

description: Supplementary Figures 1-5 for "Workforce Analysis of Dermatology Residency Programs within the United States"
DOI: 10.17632/47hzszw9hn.2
title: Workforce Analysis of Dermatology Residency Programs within the United States

description: Supplementary Figures 1-5 for "Workforce Analysis of Dermatology Residency Programs within the United States"
DOI: 10.15468/dl.ufkxfp
title: Occurrence Download

description: A dataset containing 2226 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "TaxonKey is Meles meles (Linnaeus, 1758)"
 ]
}

 The dataset includes 2226 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014442-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/t6tr893z86.1
title: OpenSesame Task for Flanker and AXCPT Reward types x Cognitive Load

description: This is the OpenSesame Task for Flanker and AXCPT Reward types x Cognitive Load
DOI: 10.5281/zenodo.14162479
title: gastrophryne_elegans_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.14162480
title: gastrophryne_elegans_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.14162255
title: fungal-Manuscripts

description: Data belong to the manuscript “Carbon management measures regulate response of fungal community within soil aggregates to short-term nitrogen and phosphorus additions in temperate forest of northeast China” for submission to the journal Catena.

 

microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), soil exchangeable ammonium (AN) and soil pH (pH), soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP).
DOI: 10.5281/zenodo.14162256
title: fungal-Manuscripts

description: Data belong to the manuscript “Carbon management measures regulate response of fungal community within soil aggregates to short-term nitrogen and phosphorus additions in temperate forest of northeast China” for submission to the journal Catena.

 

microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), soil exchangeable ammonium (AN) and soil pH (pH), soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP).
DOI: 10.15468/dl.sjzva3
title: Occurrence Download

description: A dataset containing 137490 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Big Hedgehog Map records"
 ]
}

 The dataset includes 137490 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014428-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14162732
title: Predictability of linguistic complexity: samples of the corpora
DOI: 10.5281/zenodo.14162733
title: Predictability of linguistic complexity: samples of the corpora
DOI: 10.15468/dl.8se3f4
title: Occurrence Download

description: A dataset containing 1023 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dreissena bugensis (Andrusov, 1897)",
 "Country is Canada",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 1023 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014444-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q6jyzm
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Italy, Malta)",
 "TaxonKey is Crocus longiflorus Raf."
 ]
}

 The dataset includes 176 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014445-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/go8s1b
title: Correlation Halla between immune response and microbiota composition in chicken.tab

description: :unav
DOI: 10.6084/m9.figshare.25976608
title: Supplementary data for "<b>On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa</b>"

description: Supplementary data for Benz, Raas, Tripathi, <i>et al. </i>2024 "<b>On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa</b>".<br>This dataset includes:Supplementary File S1: cytoscape network file for HHsearch ("FileS1_HHsearch_network_based_on_TableS3.cys"). Supplementary File S2: cytoscape network file for Foldseek ("FileS2_Foldseek_nework_based_on_TableS5.cys")Supplementary File S3: Zip file for CENP-A-V5 confocal images. ("FileS3.zip")The original files of the main figures ("Main Figures.zip")The original files of the supplementary figures & tables ("Supplementary Figures.zip" & "Supplementary Tables.zip"). <b>Detailed legends of the supplementary tables can be found below.</b>Complete set of predicted structures for all <i>P. papillatum </i>folds as predicted with AlphaFold2 ("P_papillatum_AF2_foldome_rank1_pdbs.tar.gz")HH-suite databases used in the homology search bioinformatics pipelines of KKT alignments, cKT alignments and diplonemid orthologous groups ("kkt_kkip_hhsearch_db.tar.gz", "ckt_hhsearch_db.tar.gz", "Diplonemea_hhsearch_db.tar.gz", respectively)Foldseek database of the full <i>P. papillatum</i> foldome ("P_papillatum_af2_foldseek_db.tar.gz") & of the full foldomes of the representative species + the <i>P. papillatum </i>foldome + the curated kinetochore folds ("repspecies_ppal_kkt-kt_foldseek_db.tar.gz")Curated set of AlphaFold2-predicted structures of kinetochore proteins ("kkt-kt_foldseek_db.tar.gz")Output files from hhsearch and foldseek as performed during hte homology searches ("hhsearch_output.tar.gz" & "foldseek_output.tar.gz", respectively)Transcriptomes of Diplonemea spp. used in the bioinformatics pipeline ("Diplonemea_sequence_database.tar.gz")OrthoFinder output run on the Diplonemea dataset ("orthofinder_diplonemea.tar.gz")<b>Legends for supplementary tables:</b><b>Table S1:</b> source of predicted proteins of eukaryotic transcriptomes and genomes of various eukaryotes used in this study<b>Table S2:</b> Paradiplonema ID infosheet<b>Table S3:</b> HHsearch searches.<br>a: initial search (KT/KKT vs. Diplonemea OGs) reciprocal search (top 10 Diplonemea OGs ← → Diplonemea OGs + KOG/COG + PFAM + KT/KKT). c: bidirectional hits from reciprocal search<br><b>Table S4:</b> HMMsearch –max<b>Table S5:</b> Foldseek searches<br>a: initial search (KT/KKT from representative species vs. <i>P. papillatum</i> AF2 structures). b: reciprocal search (top 10 <i>P. papillatum, </i>AF2 structures ← → KT/KKT from representative species + full proteomes of <i>A.</i> <i>thaliana, H. sapiens, S. cerevisiae</i> and <i>T. brucei</i>). c: bidirectional hits from reciprocal search<br><b>Table S6:</b> Discoba kinetochore evolution - presence/absence table<b>Table S7:</b> Pulldown of CENP-A-V5<b>Table S8:</b> Primer sequences used for endogenous tagging
DOI: 10.6084/m9.figshare.25976608.v1
title: Supplementary data for "<b>On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa</b>"

description: Supplementary data for Benz, Raas, Tripathi, <i>et al. </i>2024 "<b>On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa</b>".<br>This dataset includes:Supplementary File S1: cytoscape network file for HHsearch ("FileS1_HHsearch_network_based_on_TableS3.cys"). Supplementary File S2: cytoscape network file for Foldseek ("FileS2_Foldseek_nework_based_on_TableS5.cys")Supplementary File S3: Zip file for CENP-A-V5 confocal images. ("FileS3.zip")The original files of the main figures ("Main Figures.zip")The original files of the supplementary figures & tables ("Supplementary Figures.zip" & "Supplementary Tables.zip"). <b>Detailed legends of the supplementary tables can be found below.</b>Complete set of predicted structures for all <i>P. papillatum </i>folds as predicted with AlphaFold2 ("P_papillatum_AF2_foldome_rank1_pdbs.tar.gz")HH-suite databases used in the homology search bioinformatics pipelines of KKT alignments, cKT alignments and diplonemid orthologous groups ("kkt_kkip_hhsearch_db.tar.gz", "ckt_hhsearch_db.tar.gz", "Diplonemea_hhsearch_db.tar.gz", respectively)Foldseek database of the full <i>P. papillatum</i> foldome ("P_papillatum_af2_foldseek_db.tar.gz") & of the full foldomes of the representative species + the <i>P. papillatum </i>foldome + the curated kinetochore folds ("repspecies_ppal_kkt-kt_foldseek_db.tar.gz")Curated set of AlphaFold2-predicted structures of kinetochore proteins ("kkt-kt_foldseek_db.tar.gz")Output files from hhsearch and foldseek as performed during hte homology searches ("hhsearch_output.tar.gz" & "foldseek_output.tar.gz", respectively)Transcriptomes of Diplonemea spp. used in the bioinformatics pipeline ("Diplonemea_sequence_database.tar.gz")OrthoFinder output run on the Diplonemea dataset ("orthofinder_diplonemea.tar.gz")<b>Legends for supplementary tables:</b><b>Table S1:</b> source of predicted proteins of eukaryotic transcriptomes and genomes of various eukaryotes used in this study<b>Table S2:</b> Paradiplonema ID infosheet<b>Table S3:</b> HHsearch searches.<br>a: initial search (KT/KKT vs. Diplonemea OGs) reciprocal search (top 10 Diplonemea OGs ← → Diplonemea OGs + KOG/COG + PFAM + KT/KKT). c: bidirectional hits from reciprocal search<br><b>Table S4:</b> HMMsearch –max<b>Table S5:</b> Foldseek searches<br>a: initial search (KT/KKT from representative species vs. <i>P. papillatum</i> AF2 structures). b: reciprocal search (top 10 <i>P. papillatum, </i>AF2 structures ← → KT/KKT from representative species + full proteomes of <i>A.</i> <i>thaliana, H. sapiens, S. cerevisiae</i> and <i>T. brucei</i>). c: bidirectional hits from reciprocal search<br><b>Table S6:</b> Discoba kinetochore evolution - presence/absence table<b>Table S7:</b> Pulldown of CENP-A-V5<b>Table S8:</b> Primer sequences used for endogenous tagging
DOI: 10.15468/dl.jwzuej
title: Occurrence Download

description: A dataset listing the 3 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acteocina knockeri (E.A.Smith, 1872)"
 ]
}

 The dataset's 3 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014426-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hkuyd5
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "TaxonKey is Tillandsia recurvata (L.) L."
 ]
}

 The dataset's 1 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014429-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hnu8c8
title: Occurrence Download

description: A dataset containing 2 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 (Aspidistra acetabuliformis Y.Wan & C.C.Huang)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014446-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cke7sq
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "TaxonKey is Tillandsia recurvata (L.) L."
 ]
}

 The dataset's 1 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014432-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13891735
title: Table 2 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

description: Table 2. Comparison of fossil Fagus woods from Dietz Hill with Fagus dodgei from Post Hammer (UF 279, late Eocene, Wheeler and Manchester 2021) and Fagus manosii (mid-Miocene, Wheeler and Dillhoff 2009). VTD =vessel tangential diameter in µm, mean (SD); V/mm2 =number of vessels per square mm; Lrg Ray =large ray, number of cells wide; Cmp =compound ray; Lrg Ray Ht. =large ray height in µm, mean (SD, when known), range.
SampleVTDV /mm2Lrg RayLrg Ray Ht.UF 278-8486959 (8)39–536–9, Cmp2214 (580), 1269–3102UF 278-8490349 (13)67–827–12, Cmp2566 (734), 1974–3948UF 278-8487344 (6)86–103to 22, Cmp common1875 (500), 1356–2825UF 278-8488862 (12)61–758–11, Cmp common2358 (311), 1904–2744UF 278-8489653 (8)87–117to 20+, Cmp common1967 (815), 705–3666Fagus dodgei55 (11)39–7918–20, Cmp1560, 740–2690Fagus manosii52 (11)110–130to 16, Cmp absent1700 (max)
description: Published as part of Wheeler, Elisabeth A., Manchester, Steven R. & Baas, Pieter, 2023, A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA, pp. 17 in PaleoBios 40 (14) on page 17, DOI: 10.5070/P9401462457, http://zenodo.org/record/10913330
DOI: 10.15468/dl.qchfdn
title: Occurrence Download

description: A dataset containing 7320438 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "TaxonKey is Insecta"
 ]
}

 The dataset includes 7320438 records from 1380 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014435-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0187176.10fu
title: SH0187176.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0187177.10fu
title: SH0187177.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0187178.10fu
title: SH0187178.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.