cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10932490
title: Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

description: Graph edition is a vastly studied subject, with many heuristics to compare topologies, and many NP-hard problems. Here, we present a method, relying on the specificities of what a pangenome graph is (a collection of subsequences linked by edges, that represents the embedding of genomes inside a graph structure) to formulate a O(n) solution in this specific case. It allows us to pinpoint dissimilarities between graphs, and we can analyse how such graphs differ when build with different tools, or parameters.

Warning: all graphs are given as they came out of the Minigraph-Cactus and PGGB pipelines. It means, as `rs-pancat-compare` can compare only GFA1.0 that you must perform conversion using the `vg toolkit` (see [commands available on this GitHub](https://github.com/dubssieg/pancat_paper))

Data description:

Archive `yeast_dataset`:

Contains the raw `.fasta` genomes used to build the yeast chromosome 1 graphs described in the publication.

Archive `json_datasets_results`:

Contains the computed distance, variants, and sequence complexity analysis results as `.json` files. 

Archive `reference_impact`:

Contains the `.gfa` graphs used for the comparison of the impact of the reference choice against the secondary genome order in Minigraph-Cactus (fig 1A of the article).

Archive `mgc_vs_pggb`:

Contains the `.gfa` graphs used for the comparison of the impact of the reference choice in Minigraph-Cactus against PGGB (fig 1B of the article).

Archives `growth_replicate_XX` (not kept in paper):

These archives are replicates with varying references of an experiment made by adding more and more genomes to the graphs. The file names ranges from 2 to 15, these numbers being the number of genomes included in the graph. (Yeast dataset, chromosome 1)

Archive `software_evolution` (not kept in paper):

This archive contains graphs made using the same 15 genomes of yeast (chromosome 1) on three different versions of Minigraph-Cactus and three different versions of PGGB.
DOI: 10.15468/dl.wbqm24
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Salmo trutta Linnaeus, 1758"
 ]
}

 The dataset includes 100 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027209-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7266/a1na953z
title: Ammonium concentration measurements in Baffin Bay's porewater obtained from 2020-10-31 to 2022-05-26
DOI: 10.15468/dl.krfgku
title: Occurrence Download

description: A dataset containing 18691 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Stichting Calidris - Longterm biometric data of ringed shorebirds"
 ]
}

 The dataset includes 18691 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027211-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a4mzxh
title: Occurrence Download

description: A dataset containing 569 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora del Banco de Hábitat El Tigrillo - Río Manacacías"
 ]
}

 The dataset includes 569 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027213-241126133413365/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.20137961
title: Swallow and martin roosts detected on WSR in the Great Lakes region from 2000 to 2022

description: This dataset contains the results the following data processing steps:1) Rendering of Weather Surveillance Radar data and using it as input to the machine learning model described in Cheng et al. (2020) that is capable of detecting and tracking swallow and martin roost signatures.2) Manual screening of the model's results, labeling each true positive track according to the type and degree of contamination of the roost by other sources of non-biological scattering.3) Grouping of overlapping tracks that can be considered as the same roost dispersal event.5) Calculation of number of birds per detection, assuming a Purple Martin (<i>Progne subis</i>) radar cross-section (following the procedure proposed by Chilson et al 2012), and summarizing counts across all radar sweeps.These procedures have been described in detail in the following publication: Belotti, M.C.T.D., Deng, Y., Zhao, W., Simons, V.F., Cheng, Z., Perez, G., Tielens, E., Maji, S., Sheldon, D., Kelly, J.F. and Horton, K.G. (2023), Long-term analysis of persistence and size of swallow and martin roosts in the US Great Lakes. <i>Remote Sens Ecol Conserv</i>, 9: 469-482. https://doi.org/10.1002/rse2.323Code for the analysis of these data can be found here: https://gitlab.com/mariabelotti/prjct_number_of_birds<b>References:</b>Cheng, Z., Gabriel, S., Bhambhani, P., Sheldon, D., Maji, S., Laughlin, A., & Winkler, D. (2020). Detecting and Tracking Communal Bird Roosts in Weather Radar Data. <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 34(01), 378–385. https://doi.org/10.1609/aaai.v34i01.5373Chilson, P. B., W. F. Frick, P. M. Stepanian, J. R. Shipley, T. H. Kunz, and J. F. Kelly. (2012). Estimating animal densities in the aerosphere using weather radar: To Z or not to Z? <i>Ecosphere</i>, 3(8):72. http://dx.doi.org/10.1890/ES12-00027.1<br>
DOI: 10.6084/m9.figshare.20137961.v2
title: Swallow and martin roosts detected on WSR in the Great Lakes region from 2000 to 2022

description: This dataset contains the results the following data processing steps:1) Rendering of Weather Surveillance Radar data and using it as input to the machine learning model described in Cheng et al. (2020) that is capable of detecting and tracking swallow and martin roost signatures.2) Manual screening of the model's results, labeling each true positive track according to the type and degree of contamination of the roost by other sources of non-biological scattering.3) Grouping of overlapping tracks that can be considered as the same roost dispersal event.5) Calculation of number of birds per detection, assuming a Purple Martin (<i>Progne subis</i>) radar cross-section (following the procedure proposed by Chilson et al 2012), and summarizing counts across all radar sweeps.These procedures have been described in detail in the following publication: Belotti, M.C.T.D., Deng, Y., Zhao, W., Simons, V.F., Cheng, Z., Perez, G., Tielens, E., Maji, S., Sheldon, D., Kelly, J.F. and Horton, K.G. (2023), Long-term analysis of persistence and size of swallow and martin roosts in the US Great Lakes. <i>Remote Sens Ecol Conserv</i>, 9: 469-482. https://doi.org/10.1002/rse2.323Code for the analysis of these data can be found here: https://gitlab.com/mariabelotti/prjct_number_of_birds<b>References:</b>Cheng, Z., Gabriel, S., Bhambhani, P., Sheldon, D., Maji, S., Laughlin, A., & Winkler, D. (2020). Detecting and Tracking Communal Bird Roosts in Weather Radar Data. <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 34(01), 378–385. https://doi.org/10.1609/aaai.v34i01.5373Chilson, P. B., W. F. Frick, P. M. Stepanian, J. R. Shipley, T. H. Kunz, and J. F. Kelly. (2012). Estimating animal densities in the aerosphere using weather radar: To Z or not to Z? <i>Ecosphere</i>, 3(8):72. http://dx.doi.org/10.1890/ES12-00027.1<br>
DOI: 10.6084/m9.figshare.20137961.v1
title: Swallow and martin roosts detected on WSR in the Great Lakes region from 2000 to 2020

description: This dataset contains the resultsresults  three processing steps:
<br>
1) Rendering of Weather Surveillance Radar data and using it as input to the machine learning model described in Cheng et al. (2020) that is capable of detecting and tracking swallow and martin roost signatures.
<br>
2) Manual screening of the model's results, labeling each true positive track according to the type and degree of contamination of the roost by other sources of non-biological scattering.
<br>
3) Grouping of overlapping tracks that can be considered as the same roost dispersal event.
<br>
4) Mean shift clustering of the first detection in each track to find regions of persistent use throughout the years.
<br>
5) Calculation of number of birds per detection, assuming a Purple Martin (<em>Progne subis</em>) radar cross-section (following the procedure proposed by Chilson et al 2012).
<br>
These procedures have been described in detail in the following paper submitted for publication<em>: Long-term analysis of persistence and size of swallow and martin roosts in the US Great Lakes, </em>which has the same authors as this dataset (full citation will be added here once paper is accepted for publication).
  
<br>
<strong>References:</strong>
<br>
Cheng, Z., Gabriel, S., Bhambhani, P., Sheldon, D., Maji, S., Laughlin, A., & Winkler, D. (2020). Detecting and Tracking Communal Bird Roosts in Weather Radar Data. <em>Proceedings of the AAAI Conference on Artificial Intelligence</em>, 34(01), 378–385. https://doi.org/10.1609/aaai.v34i01.5373
<br>
Chilson, P. B., W. F. Frick, P. M. Stepanian, J. R. Shipley, T. H. Kunz, and J. F. Kelly. (2012). Estimating animal densities in the aerosphere using weather radar: To Z or not to Z? <em>Ecosphere</em>, 3(8):72. http://dx.doi.org/10.1890/ES12-00027.1
<br>
DOI: 10.15468/dl.9cse5g
title: Occurrence Download

description: A dataset listing the 41 species recorded in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (BRA.13.44_2, BRA.13.824_2, BRA.13.661_2, BRA.25.491_2)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Mammalia, Reptilia, Amphibia)"
 ]
}

 The dataset's 41 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027192-241126133413365/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.27988724
title: White_Spruce_Phenotype_Pedigree_PLoS2022.TXT

description: White Spruce Phenotype Pedigree
DOI: 10.6084/m9.figshare.27988724.v1
title: White_Spruce_Phenotype_Pedigree_PLoS2022.TXT

description: White Spruce Phenotype Pedigree
DOI: 10.17632/sfzs5chpsm.1
title: Research Data-Zjm

description: Basic physicochemical properties of tested soils and various colloidal particles in paddy field
DOI: 10.15468/dl.upgeu8
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-5.87549 29.8691,-3.81938 29.8691,-3.81938 31.33373,-5.87549 31.33373,-5.87549 29.8691))",
 "TaxonKey is Picus vaillantii (Malherbe, 1847)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027214-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7fw9v
title: Occurrence Download

description: A dataset containing 555 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora del Banco de Hábitat Bosque de Niebla - El Globo de Terrasos"
 ]
}

 The dataset includes 555 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027215-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g97ae2
title: Occurrence Download

description: A dataset containing 176569 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-70.76095 43.04117,-68.66958 44.0457,-66.59343 44.4722,-67.49387 45.84841,-67.79726 47.39195,-69.19657 47.57756,-70.36715 46.6121,-71.15941 45.23847,-70.76095 43.04117))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2008-2024"
 ]
}

 The dataset includes 176569 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027183-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/mvwwz6djcg
title: Polyphenol Supplement in Equine Asthma

description: effects of a mixed polyphenol supplement on respiratory function and inflammation in horses with and without equine asthma
DOI: 10.17632/mvwwz6djcg.1
title: Polyphenol Supplement in Equine Asthma

description: effects of a mixed polyphenol supplement on respiratory function and inflammation in horses with and without equine asthma
DOI: 10.15468/dl.hucafj
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "StateProvince is Kansas",
 "TaxonKey is Nomia universitatis Cockerell, 1908"
 ]
}

 The dataset includes 17 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027218-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.524469
title: Occurrence Download

description: A dataset containing 670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (University of British Columbia Herbarium (UBC) - Bryophytes Collection, University of British Columbia Herbarium (UBC) - Vascular Plant Collection, University of British Columbia Herbarium (UBC) - Algae Collection, University of British Columbia - Spencer Entomological Collection (UBCZ), University of British Columbia Herbarium (UBC) - Lichen Collection, University of British Columbia Herbarium (UBC) - Fungi Collection, Cowan Tetrapod Collection - Mammals, Cowan Tetrapod Collection - Birds, Cowan Tetrapod Collection - Herpetology, Beaty Biodiversity Museum Fish Collection, Beaty Biodiversity Museum Fossil Collection)",
 {
 "and" : [
 "Year 1990-2024",
 "IucnRedListCategory is one of (EW, EX, CR, EN, VU)"
 ]
 }
 ]
}

 The dataset includes 670 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027219-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/vvymnxycrw.1
title: Li-Isotope Fractionation in Olivine

description: 1. Optimized Crystal structure.
2. Electronic Density of state (DOS).
3. Gamma point phonon frequencies for Li-doped olivine (for 6Li and 7Li). Gamma point frequencies has been used to calculated the reduced partition function ratio and fractionation factor.
DOI: 10.5281/zenodo.14343167
title: AMS_AGY_v1_focus_vs_temperature

description: Zenodo hosts the archival version of this document; for convenient viewing, please visit https://github.com/amsikking/AMS_AGY_v1_focus_vs_temperature

Abstract

Data showing how the focal plane of an AMS-AGY v1 objective moves axially with temperature.
description: v1.0.0: Pre-release to get DOI.

v1.0.1: 1st release with embedded DOI.
DOI: 10.5281/zenodo.14343168
title: AMS_AGY_v1_focus_vs_temperature

description: Zenodo hosts the archival version of this document; for convenient viewing, please visit https://github.com/amsikking/AMS_AGY_v1_focus_vs_temperature

Abstract

Data showing how the focal plane of an AMS-AGY v1 objective moves axially with temperature.
description: v1.0.0: Pre-release to get DOI.
DOI: 10.5281/zenodo.14343303
title: AMS_AGY_v1_focus_vs_temperature

description: Zenodo hosts the archival version of this document; for convenient viewing, please visit https://github.com/amsikking/AMS_AGY_v1_focus_vs_temperature

Abstract

Data showing how the focal plane of an AMS-AGY v1 objective moves axially with temperature.
description: v1.0.0: Pre-release to get DOI.

v1.0.1: 1st release with embedded DOI.
DOI: 10.25810/m7s4-h229
title: FIRED Guernsey Nov 2000 - July 2024

description: This is event-level polygons for the fire event delineation (FIRED) product for GUERNSEY from November 2000  to July 2024. It is derived from the MODIS MCD64A1 burned area product (see https://lpdaac.usgs.gov/products/mcd64a1v061/ for more details). The MCD64A1 is a monthly raster grid of estimated burned dates. Firedpy (https://github.com/earthlab/firedpy) is an algorithm that converts these rasters into events by stacking the entire time series into a spatial-temporal data cube, then uses an algorithm to assign event identification numbers to pixels that fit into the same 3-dimensional spatial temporal window. This particular dataset was created using a spatial parameter of 1 pixels and 5 days. Daily polygons are included and the event identification numbers are the same for both files, but the event-level product has only single polygons for each entire event, while the daily product has separate polygons for each date per event. See the associated paper for more details on the methods and more:

Balch, J.K.; St. Denis, L.A.; Mahood, A.L.; Mietkiewicz, N.P.; Williams, T.M.; McGlinchy, J.; Cook, M.C. FIRED (Fire Events Delineation): An Open, Flexible Algorithm and Database of US Fire Events Derived from the MODIS Burned Area Product (2001–2019). Remote Sens. 2020, 12, 3498. https://doi.org/10.3390/rs12213498
DOI: 10.15468/dl.72tkdf
title: Occurrence Download

description: A dataset containing 20266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Cardellina rubra (Swainson, 1827)"
 ]
}

 The dataset includes 20266 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027221-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/zstt35zk4m.1
title: Table 1

description: Descriptive statistics and odds ratio associated with Trichoteiromania (n=129)
DOI: 10.17632/zstt35zk4m.2
title: Table 1

description: Descriptive statistics and odds ratio associated with Trichoteiromania (n=129)
DOI: 10.6084/m9.figshare.27988727
title: README.txt

description: README file for this collection
DOI: 10.6084/m9.figshare.27988727.v1
title: README.txt

description: README file for this collection
DOI: 10.15468/dl.2u7anq
title: Occurrence Download

description: A dataset containing 1765343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Centaurea stoebe L., Reynoutria japonica Houtt., Heracleum mantegazzianum Sommier & Levier, Impatiens glandulifera Royle, Lythrum salicaria L., Vincetoxicum rossicum (Kleopow) Barbar.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1765343 records from 3425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027173-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/3z1-t1d-sne
title: Oulodus elegans (Walliser, 1964)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q28-n6n-9dq
title: Eoplacognathus pseudoplanus (Viira, 1972)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2z2-dxh-qbb
title: Rhabdinopora flabelliformis aff. bryograptoides (Bulman, 1954)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/aj3-zx0-rhg
title: Cordylodus angulatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.15468/dl.p6r4ee
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.28042 43.26145,3.96148 43.53062,4.41403 43.40823,4.71188 43.90891,3.87149 44.02151,3.43606 44.01098,3.14363 43.77226,3.28042 43.26145))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Luzula forsteri (Sm.) DC.",
 "Year 2015-2025"
 ]
}

 The dataset includes 38 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009990-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/jj7-egr-r2n
title: Costiconus iniquus (Viira, 1974)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xsj-df6-cms
title: Ozarkodina eosteinhornensis (Walliser, 1964)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d8g-0x4-4fa
title: Amorphognathus ordovicicus Branson et Mehl, 1933

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gjt-2vy-knk
title: Variabiloconus variabilis (Lindström, 1955)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7z0-3sz-9ak
title: Iapetognathus aengensis (Lindström, 1955

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/brc-hjw-cdn
title: Paroistodus originalis (Sergeeva, 1963)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26796061.v1
title: Abridged data for Kern, Date, Chao 2024, Effects of Spatial Constraints of Inhibitory Connectivity on the Dynamical Development of Criticality in Spiking Networks

description: Neural systems are hypothesized to operate near criticality, enhancing their capacity for optimal information processing, transmission and storage capabilities. Criticality has typically been studied in spiking neural networks and related systems organized in random or full connectivity, with the balance of excitation and inhibition being a key determinant of the critical point of the system. However, given that neurons in the brain are spatially distributed, with their distances significantly influencing connectivity and signal timing, it is unclear how the spatial organization of excitatory and inhibitory connectivity influences the network’s self-organization towards criticality. Here, we systematically constrain the distance and density of inhibitory connectivity in two-dimensional spiking networks and allow synaptic weights to self-organize with activity-dependent excitatory and inhibitory plasticity in the presence of a low level of stochastic intrinsic activity. We then investigate the relationship between inhibitory connectivity, synaptic weights, and the resulting network activity during and after development. We find that networks with longer-range inhibitory synapses tend towards more supercritical behavior compared to networks with a similar number of shorter-range inhibitory synapses. We show that this distance dependence is a consequence of weaker long-range synapses after development due to the presence of synaptic delays, which shift most spike pairs outside of the potentiation window of the inhibitory learning rule.
DOI: 10.3535/d3x-9xm-ych
title: Paltodus deltifer (Lindström, 1955)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fpq-zm5-vfl
title: Protopanderodus rectus (Lindström, 1955)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nz0-4y7-xgp
title: limestone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zaf-35n-wel
title: Ozarkodina confluens (Branson et Mehl, 1933)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.