Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
52
datasets available to search
ShareScore release 0.7.1
Dataset results
52 results for “history of science”
Science ready spectra of star clusters and their best-fitting models described in the research paper "Using Star Clusters as Tracers of Star Formation and Chemical Evolution: the Chemical Enrichment History of the Large Magellanic Cloud" by Chilingarian & Asa'd
<p>Science ready spectra of star clusters in the Large Magellanic Cloud and their best-fitting templates (alpha-enhanced MILES based simple stellar population models) obtained using the NBursts full spectrum fitting code. Each spectrum is presented as a binary FITS table, which contains a spectrum (wavelength, flux, uncertainties), best-fitting template, best-fitting parameters (radial velocity, age, metallicity), and a pixel mask used in the fitting procedure. For each cluster, 5 spectra are provided, which correspond to [alpha/Fe] values from 0.0 to 0.4 dex with a step of 0.1 dex. The only exception is NGC2249, for which only 3 models are provided. The alpha-enhancement value of a model grid used in the fitting procedure is given in the FITS keyword MGFEGRID.</p>
Data and code for: "Global Sampling Decline Erodes Science Potential of Natural History Collections"
<p># GBIF Specimen Data Analysis and Forecasting<br><br>## Version 2 - modified date ranges for figures 1 and 2 in response to reviewer comments</p> <p>This repository contains the code and data for analysing and forecasting trends in Global Biodiversity Information Facility (GBIF) specimen records across three major taxonomic groups: Chordata, Arthropoda, and Plantae. <br>The analysis pipeline includes data cleaning, anomaly detection, primary analyses, and forecasting based on historical database snapshots.</p> <p>These scripts and data correspond to analyses in the following manuscript:</p> <p>Global Sampling Decline Erodes Science Potential of Natural History Collections</p> <p>Authors:<br>Owen Forbes<br>Andrew G. Young<br>Peter H. Thrall</p> <p><br>## Repository Structure</p> <p>The repository consists of three main Quarto (.qmd) scripts and associated data files:</p> <p>1. `1_DataCleaning_Forbes-et-al_2025.qmd`: Data cleaning and anomaly detection<br>2. `2_PrimaryAnalyses_Forbes-et-al_2025.qmd`: Primary analyses and visualisation<br>3. `3_SnapshotsForecasting_Forbes-et-al_2025.qmd`: Historical snapshot analysis and forecasting</p> <p>## Requirements</p> <p>- R (version 4.3.2 or later)<br>- Required R packages:<br> - tidyverse (v2.0.0) - for data manipulation and visualization<br> - readr (v2.1.5) - for reading CSV/TSV files<br> - ggplot2 (v3.4.0 or v3.5.0) - for creating visualizations<br> - rnaturalearth (v1.0.1) - for accessing natural earth map data<br> - dplyr (v1.1.0 or v1.1.4) - for data manipulation<br> - countrycode (v1.6.0) - for converting country names and codes<br> - spdep (v1.3-3) - for spatial dependence modeling<br> - sp (v1.6-0 or v2.1-3) - for spatial data manipulation<br> - sf (v1.0-15 or v1.0-16) - for simple features access<br> - data.table (v1.14.8) - for fast aggregation of large data<br> - lubridate (v1.9.2) - for date-time manipulation<br> - viridis (v0.6.3) - for color palettes<br> - gridExtra (v2.3) - for arranging multiple plots<br> - ggpubr (v0.6.0) - for creating publication-ready plots<br> - zoo (v1.8-12) - for time series, including moving averages<br> - scales (v1.3.0) - for graphical scales<br> - forecast (v8.22.0) - for ARIMA forecast models<br> - purrr (v1.0.2) - for mapping custom forecast function onto each dataset<br> - arrow - for working with parquet files</p> <p>Install these packages before running the scripts.</p> <p>## How to Use</p> <p>1. Download this repository to your local machine.<br>2. Set your working directory to the location of the scripts.<br>3. Download raw datasets from GBIF (as required)<br>4. Ensure all required R packages are installed.<br>5. Run the scripts in RStudio or your preferred R environment.</p> <p>### Data Cleaning (`1_DataCleaning_Forbes-et-al_2025.qmd`)</p> <p>This script cleans the raw GBIF data and identifies anomalies. It produces files containing indexes of dataset records to be removed, which are used in subsequent analyses.</p> <p>**Note**: The raw GBIF exported datasets for contemporary records are not included in this repository due to file size constraints. Download them from the GBIF links provided in the script and place them in the `data/` directory.</p> <p>### Primary Analyses (`2_PrimaryAnalyses_Forbes-et-al_2025.qmd`)</p> <p>This script performs the main analyses and generates visualisations. It uses the outputs from the data cleaning script to filter anomalous records.</p> <p>To reproduce all analysis stages from the original raw .csv files:<br>- Start at the chunks labelled "DATA LOAD AND FILTERING".<br>- Run the pipeline for non-spatial analyses before spatial analyses.<br>- Due to memory constraints, it's recommended to run analyses for one taxonomic group and one analysis stream at a time.</p> <p>To skip to plot generation:<br>- Navigate to sections tagged as "@! SKIP TO PLOTTING !@".<br>- Ensure all required analysis output files are in the `data/` directory.</p> <p>### Forecasting (`3_SnapshotsForecasting_Forbes-et-al_2025.qmd`)</p> <p>This script analyses historical GBIF database snapshots and forecasts future growth. It uses the cleaned snapshot data produced by the data cleaning script.</p> <p>## Data Files</p> <p>### GBIF Exports - Raw Data (not included on Zenodo due to file size, please download directly from GBIF)<br>- `0016915-240425142415019.csv` for Chordata - https://www.gbif.org/occurrence/download/0016915-240425142415019</p> <p>- `0016914-240425142415019.csv` for Plantae - https://www.gbif.org/occurrence/download/0016914-240425142415019 </p> <p>- `0016913-240425142415019.csv` for Arthropoda - https://www.gbif.org/occurrence/download/0016913-240425142415019</p> <p>### Included Data Files</p> <p>#### Raw Data<br>- `GBIF_snapshots.parquet` # Historical snapshots RAW dataset (arrow/parquet format)<br>- `GBIF_integer_to_datasetKey.tsv` # Mapping old dataset IDs onto new datasetKey field</p> <p>#### Contemporary Datasets - data cleaning outputs<br>- `chordata_counts_to_highlight_030724` # List of anomalous Chordata dataset + year indexes to filter<br>- `arthropoda_counts_to_highlight_OG_030724` # List of anomalous Arthropoda dataset + year indexes to filter<br>- `plantae_counts_to_highlight_030724` # List of anomalous Plantae dataset + year indexes to filter</p> <p>#### Cleaned Snapshots<br>- `plantae_snapshots_filter_threshold_IN_040924` # Cleaned Plantae snapshots<br>- `arthropoda_snapshots_filter_threshold_IN_040924` # Cleaned Arthropoda snapshots<br>- `chordata_snapshots_filter_threshold_IN_040924` # Cleaned Chordata snapshots<br>- `gbif_dates_df_anomaly_filtered_090724` # Anomaly-filtered snapshots (combined dataset)<br>- `gbif_dates_df_anomalies_highlighted_090724` # Anomalies highlighted snapshots (combined dataset)</p> <p>#### Analysis Outputs - for skipping straight to plot/figure generation<br>- `arthropoda_specimens_per_year_080724` # Arthropoda specimen counts per year<br>- `arthropoda_unique_species_per_year_080724` # Arthropoda unique species counts per year<br>- `arthropoda_grid_counts_080724` # Arthropoda grid counts<br>- `chordata_specimens_per_year_080724` # Chordata specimen counts per year<br>- `chordata_unique_species_per_year_080724` # Chordata unique species counts per year<br>- `chordata_grid_counts_080724` # Chordata grid counts<br>- `plantae_specimens_per_year_080724` # Plantae specimen counts per year<br>- `plantae_unique_species_per_year_080724` # Plantae unique species counts per year<br>- `plantae_grid_counts_080724` # Plantae grid counts<br>- `chordata_continent_count_080724` # Chordata continent-specific counts<br>- `arthropoda_continent_count_080724` # Arthropoda continent-specific counts<br>- `plantae_continent_count_080724` # Plantae continent-specific counts</p> <p> </p>
FIG. 3 in The d'Orbigny Palaeontological Collection of the National Museum of Natural History and Science, Lisbon, Portugal: Historical perspective and revision of Cretaceous Cephalopoda
FIG. 3. — Cretaceous ammonites of the d'Orbigny Collection of the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência): A-D, Neolissoceras grasianum (d'Orbigny, 1840) in ventral (A), lateral (B) and oral (C) views, and original label (D): Nº 357/Ammonites grasanus (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade S.t Julien (Hautes Alpes); E-G, Pleurohoplites (Pleurohoplites) renauxianus (d'Orbigny, 1840) in lateral (E) and ventral (F) views, and original label (G): Nº 464/Ammonites Renauxianus (d'Orb), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Mont-Blainville (Meuse); H-K, Acanthoceras rhotomagense (Brongniart, 1822) in oral (H), lateral (I) and ventral (J) views, and original label (K): Nº 463/Ammonites rhotomagensis (Lamarck), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Rouen (Seine inf.re). Scale bar: 2 cm.
FIG. 2 in The d'Orbigny Palaeontological Collection of the National Museum of Natural History and Science, Lisbon, Portugal: Historical perspective and revision of Cretaceous Cephalopoda
FIG. 2. — Cretaceous nautiloid and ammonites of the d'Orbigny Collection of the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência): A-C, Angulithes triangularis de Montfort, 1808 in oral (A) and lateral (B) views, and original label (C): Nº 459/Nautilus triangularis (Montf), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Fouras (Charente inf.re); D-G, Phylloceras (Hypophylloceras) tethys (d'Orbigny, 1840) in ventral (D), lateral (E) and oral (F) views, and original label (G): Nº 360/Ammonites Tethys (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade Arredores de [environs of] Sisteron (Basses Alpes); H-K, Ptychophylloceras (Semisulcatoceras) semisulcatum (d'Orbigny, 1840) in ventral (H), lateral (I) and oral (J) views, and original label (K): Nº 359/Ammonites semisulcatus (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade Sisteron (Basses Alpes). Scale bar: 2 cm.
Linked collectors and determiners for: The genus Calosoma (Coleoptera, Carabidae) of the collection of the State Museum of Natural History, National Academy of Sciences of Ukraine.
Natural history specimen data linked to collectors and determiners held within, "The genus Calosoma (Coleoptera, Carabidae) of the collection of the State Museum of Natural History, National Academy of Sciences of Ukraine". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/850eb33c-0cdb-4f8e-9d08-207902b384ef">https://bionomia.net/dataset/850eb33c-0cdb-4f8e-9d08-207902b384ef</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/850eb33c-0cdb-4f8e-9d08-207902b384ef">https://gbif.org/dataset/850eb33c-0cdb-4f8e-9d08-207902b384ef</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Mammals in the collection of Zoological Museum of NSNHM (the National Science and Natural History Museum at the National Academy of Sciences of Ukraine, Kyiv): Muridae..
Natural history specimen data linked to collectors and determiners held within, "Mammals in the collection of Zoological Museum of NSNHM (the National Science and Natural History Museum at the National Academy of Sciences of Ukraine, Kyiv): Muridae.". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/db908fac-ed42-407e-817c-3f10ce74a28e">https://bionomia.net/dataset/db908fac-ed42-407e-817c-3f10ce74a28e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/db908fac-ed42-407e-817c-3f10ce74a28e">https://gbif.org/dataset/db908fac-ed42-407e-817c-3f10ce74a28e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: New Mexico Museum of Natural History and Science (NMMNH&S) Invertebrate specimens (Arctos).
Natural history specimen data linked to collectors and determiners held within, "New Mexico Museum of Natural History and Science (NMMNH&S) Invertebrate specimens (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/fc65374a-64af-4131-9c4e-e206945ac0b3">https://bionomia.net/dataset/fc65374a-64af-4131-9c4e-e206945ac0b3</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/fc65374a-64af-4131-9c4e-e206945ac0b3">https://gbif.org/dataset/fc65374a-64af-4131-9c4e-e206945ac0b3</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: New Mexico Museum of Natural History and Science (NMMNHS) Paleontology specimens (Arctos).
Natural history specimen data linked to collectors and determiners held within, "New Mexico Museum of Natural History and Science (NMMNHS) Paleontology specimens (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3774eeec-8a91-45d0-b3d5-a3903cfc220d">https://bionomia.net/dataset/3774eeec-8a91-45d0-b3d5-a3903cfc220d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3774eeec-8a91-45d0-b3d5-a3903cfc220d">https://gbif.org/dataset/3774eeec-8a91-45d0-b3d5-a3903cfc220d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: New Mexico Museum of Natural History and Science (NMMNHS) Insect specimens (Arctos).
Natural history specimen data linked to collectors and determiners held within, "New Mexico Museum of Natural History and Science (NMMNHS) Insect specimens (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/04daaaf2-0d57-414d-8656-28c0137b638a">https://bionomia.net/dataset/04daaaf2-0d57-414d-8656-28c0137b638a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/04daaaf2-0d57-414d-8656-28c0137b638a">https://gbif.org/dataset/04daaaf2-0d57-414d-8656-28c0137b638a</a>. Formatted as a Frictionless Data package.
Natural history and community science records confirm rapid geographic shifts in the distribution of Bachman's Sparrow (Peucaea aestivalis) since 1850
<p>North American grassland birds colonized emerging habitat created by expanding agriculture in a pattern of eastward expansions from the mid-1800s to mid-1900s. These birds have been declining, since at least the mid1900s, largely as result of anthropogenic landscape change. Only one bird that now breeds predominantly in southeastern pine savannas is thought to have experienced a concurrent range expansion into this region: <em>Peucaea aestivalis </em>(Bachman's Sparrow). However, our understanding of the <em>P. aestivalis</em> expansion, and subsequent retraction to the southeastern United States, is largely based on a contemporaneous review of only a subset of historical records from beyond its modern, northern limit. We suggest an alternative explanation for these historical records is that <em>P. aestivalis</em> historically occurred more broadly than was recognized in contemporaneous literature. To evaluate these hypotheses, we reviewed field observations from literature, natural history collections, and eBird to show how <em>P. aestivalis </em>presence throughout eastern North America has shifted since the mid-1800s. To confirm that these findings were not the result of detection bias, we repeated our analysis on a common sparrow species (<em>Spizella pusilla</em>) with a largely overlapping breeding range, but no history of expansion and retraction. We confirm that <em>P. aestivalis</em> expanded its range, but add that prior to that expansion, its historical distribution was broader than commonly acknowledged today. As a result, we identify the northwestern historical limit of <em>P. aestivalis</em>, the Ouachita and Ozark highlands, as a potential source region for an eastward expansion that is consistent with those of other North American grassland birds of the era. We discuss the potential evolutionary and conservation implications of this range expansion on <em>P. aestivalis</em> given our more nuanced understanding of it. Anthropogenic landscape change initially provided additional habitat for <em>P. aestivalis</em> but has ultimately resulted in a reduction of the <em>P. aestivalis</em> distribution.</p>
Natural history and community science records confirm rapid geographic shifts in the distribution of Bachman’s Sparrow (Peucaea aestivalis) since 1850
Open the record for dataset details and reuse information.
FIGURES 6–8 in Karawajew's ant type specimens (Hymenoptera, Formicidae) in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 6–8. The current storage method for the Karawajew's type material: 6—one of the boxes with the recently mounted material; 7—new container with vials; 8—example of the new labels for mounted and fluid-stored type material.
FIGURES 1–5 in Karawajew's ant type specimens (Hymenoptera, Formicidae) in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 1–5. Examples of original vials and labels from the Karawajew's ant collection: 1—original vials; 2–5—original labels of the type material.
Quantifying how natural history traits contribute to bias in community science engagement: a case study using native and introduced orb weaver spiders in North America
<p>Raw data and R scripts for manuscript.</p>
Book of Abstracts from Conference for the Society for the Preservation of Natural History Collections (SPNHC), International Partner – BHL (Biodiversity Heritage Library) and National Partner – NatSCA (Natural Sciences Collections Association) 2022
<p>The complete book of abstracts (Posters & Oral Presentations). </p>
FIGURES 66–69 in A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 66–69. Philonthus rutilipennis (Figs 66a–d), Aleochara solida (Figs 67a–b), Philonthus subopacus (Figs 68a–d), Myrmedonia subtumida (Figs 69a–f): 66a, 67a, 68a, 69a—habitus, 66b, 68c, 69e—aedeagus, 68b—left antennomere, 66c, 68d—apical abdominal segments, 66d, 67b, 68d, 69b, 69f–labels. Scale bars: 1.0 mm (Figs 66a, 68a, 69a, 68c), 0.2 mm (Figs 66b–c, 68b–c, 68d–e).
FIGURES 70–73 in A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 70–73. Brachyusa concolor (Figs 70a–e), Philonthus tanaicus (Figs 71a–b), Trogophloeus tarsalis (Figs 72a–c), Philonthus transbaicalia (Figs 73a–f): 70a, 70d, 71a, 72a, 73a, 73e—habitus, 70b, 73c—aedeagus, 72b—hind leg and apical abdominal segments, 73b—apical abdominal segment, 70c, 70e, 71b, 72c, 73d, 73f—labels. Scale bars: 1.0 mm (Figs. 70a, 70d, 71a, 72a, 73a, 73e), 0.2 mm (Figs. 70b, 72b, 73b–c).
FIGURES 52–55 in A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 52–55. Stenus minutus (Figs 52a–b), Aleochara notatipennis (Figs 53a–c), Lathrobium pallidipenne (Figs 54a–d), Ocypus philonthoides (Figs 55a–c): 52a–b, 53a, 54a, 55a—habitus, 53b, 54b—aedeagus, lateral view, 54c—apical abdominal segment, 55b–antennomeres, apical part of abdomen and aedeagus, 53c, 54d, 55c—labels. Scale bars: 2.0 mm (55a), 1.0 mm (Figs 52a–b, 53a, 54a), 0.5 mm (Figs 53b, 54b–c).
FIGURES 8–11 in A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 8–11. Staphylinus callistus (Figs 8a–b), Trogophloeus caucasicus (Figs 9a–f), Homaeotarsus chaudoirii (Figs 10a– d), Staphylinus chalcopygus (Figs 11a–d): 8a, 9a, 9d, 10a, 11a—habitus, 11b—forebody, 9e—abdominal tergite VIII, 9b–antenna, 10b–c–aedeagus (10b—lateral view, 10c—parameral view), 8b, 9c, 9f, 10d, 11c—labels. Scale bars: 1.0 mm (Figs 8a, 9a, 9d, 10a, 11a), 0.5 mm (Figs 9b, 9e, 11b).
FIGURES 1–4 in A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine
FIGURES 1–4. Dolicaon angusticollis (Figs 1a–b), Oxypoda angusticollis (Figs 2a–b), Stenus arctulus (Figs 3a–e.), Philonthus armeniacus (Figs 4a–e): 1a, 2a, 3a, 4a—habitus (dorsal view), 3b, 4c–aedeagus (parameral view), 3d, 4b—apical segments of abdomen, 3c—antenna, 1b, 2b, 3e, 4d–labels. Scale bars: 1.0 mm (Figs 1a, 2a, 3a, 4a), 0.2 mm (Figs 3b, 3c, 3d, 4b, 4c).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.