cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fyggn2
title: Occurrence Download

description: A dataset containing 129205 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((99.69634 5.441097, 99.67465 5.354996, 99.67223 5.330694, 99.68456 5.148224, 99.75604 4.979884, 99.87876 4.844289, 100.0392 4.756431, 100.0745 4.750481, 100.0784 4.748321, 100.2587 4.717924, 100.2687 4.717924, 100.4283 4.74157, 100.4391 4.746706, 100.459 4.749653, 100.6048 4.818509, 100.7243 4.926675, 100.8074 5.064859, 100.8177 5.105741, 100.8221 5.113024, 100.8297 5.143142, 100.8601 5.193589, 100.8998 5.349607, 100.9014 5.36581, 100.8895 5.548578, 100.8182 5.717291, 100.7911 5.747363, 100.7833 5.765699, 100.6606 5.901752, 100.5 5.989933, 100.4728 5.994527, 100.4517 6.006119, 100.2709 6.03666, 100.2509 6.03666, 100.0918 6.013139, 99.94629 5.944588, 99.93932 5.938305, 99.9354 5.936457, 99.81594 5.828707, 99.73276 5.690999, 99.69299 5.535115, 99.69132 5.518911, 99.69634 5.441097), (100.2509 5.48666, 100.2709 5.48666, 100.2701 5.478558, 100.2801 5.478558, 100.2793 5.470456, 100.3193 5.470456, 100.3159 5.438049, 100.326 5.438049, 100.3251 5.429948, 100.3451 5.429948, 100.3443 5.421846, 100.3543 5.421846, 100.3526 5.405643, 100.3426 5.405643, 100.3418 5.397542, 100.3318 5.397542, 100.331 5.38944, 100.321 5.38944, 100.3144 5.32463, 100.3044 5.32463, 100.2995 5.276024, 100.2895 5.276024, 100.2695 5.276024, 100.2687 5.267924, 100.2587 5.267924, 100.2595 5.276024, 100.2195 5.276024, 100.2219 5.300327, 100.2419 5.300327, 100.2519 5.300327, 100.2528 5.308428, 100.2628 5.308428, 100.2668 5.348934, 100.2768 5.348934, 100.2785 5.365136, 100.2685 5.365136, 100.2734 5.413745, 100.2834 5.413745, 100.2843 5.421846, 100.2943 5.421846, 100.2959 5.438049, 100.2859 5.438049, 100.2868 5.446151, 100.2768 5.446151, 100.2784 5.462355, 100.2684 5.462355, 100.2693 5.470456, 100.2492 5.470456, 100.2484 5.462355, 100.2384 5.462355, 100.2401 5.478558, 100.2501 5.478558, 100.2509 5.48666))",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 129205 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048354-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/loguwc
title: PAN-00142552 - terra sigillata cup type Drag. 27

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00142552&lt;/p&gt;
description: Modified: 2025-10-17T11:45:42+02:00
DOI: 10.15468/dl.x3ek2j
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lagerstroemia microcarpa"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048366-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.29017.17766
title: Una partícula revoltosa nos devuelve el sentido del arte dramático y teatral
DOI: 10.5281/zenodo.17905566
title: AutoSiQ: A Curated Haploid Arabidopsis thaliana Inflorescence Dataset with a Fine-Grained Silique Ontology and a Deep Learning Application for Haploid Fertility Quantification

description: Data generation pipeline for AutoSiQ: annotation processing, color extraction, and YOLO label formatting.

This companion dataset contains the Python and Matlab utilities used to process raw color-annotated Arabidopsis thaliana inflorescence images into YOLOv5-ready bounding boxes and labels. The seven-class ontology supports both the two-class setup (fertile silique, total silique) used in the paper and fine-grained seven-class training.

Seven-class ontology:



Fertile silique (f)

Fertile crack (f_c)

Green fertile (g_f)

Mature non-fertile (m)

Green non-fertile (g)

Crack non-fertile (c)

Flower (fl)


Key scripts:



0_sanatizing.py: Annotation sanitization and cleanup.

1_5_json_csv_yolov5_sanity_check_bbox.py: Bounding-box validation and sanity checks.

2_json_csv_yolov5_new_annotation.py: Configurable class mapping — converts JSON/CSV annotations to YOLOv5 format. Adjust class settings to export either two-class (paper setup) or all seven classes.

generate_disttributions.py: Class distribution analysis and reporting.

Matlab utilities (createMask.m, make_patches_and_boundingbox_labels.m): Color-based mask extraction and patch/bounding-box generation.


Example data:



annotated_png/, raw_jpg/: Sample raw and color-annotated images showing the input format.

detection_labels.csv, class_distribution.csv:  Reference annotation and distribution files.


Usage: Run scripts sequentially to convert your color-annotated images to YOLO format with configurable class granularity.
DOI: 10.5281/zenodo.17905565
title: AutoSiQ: A Curated Haploid Arabidopsis thaliana Inflorescence Dataset with a Fine-Grained Silique Ontology and a Deep Learning Application for Haploid Fertility Quantification

description: Data generation pipeline for AutoSiQ: annotation processing, color extraction, and YOLO label formatting.

This companion dataset contains the Python and Matlab utilities used to process raw color-annotated Arabidopsis thaliana inflorescence images into YOLOv5-ready bounding boxes and labels. The seven-class ontology supports both the two-class setup (fertile silique, total silique) used in the paper and fine-grained seven-class training.

Seven-class ontology:



Fertile silique (f)

Fertile crack (f_c)

Green fertile (g_f)

Mature non-fertile (m)

Green non-fertile (g)

Crack non-fertile (c)

Flower (fl)


Key scripts:



0_sanatizing.py: Annotation sanitization and cleanup.

1_5_json_csv_yolov5_sanity_check_bbox.py: Bounding-box validation and sanity checks.

2_json_csv_yolov5_new_annotation.py: Configurable class mapping — converts JSON/CSV annotations to YOLOv5 format. Adjust class settings to export either two-class (paper setup) or all seven classes.

generate_disttributions.py: Class distribution analysis and reporting.

Matlab utilities (createMask.m, make_patches_and_boundingbox_labels.m): Color-based mask extraction and patch/bounding-box generation.


Example data:



annotated_png/, raw_jpg/: Sample raw and color-annotated images showing the input format.

detection_labels.csv, class_distribution.csv:  Reference annotation and distribution files.


Usage: Run scripts sequentially to convert your color-annotated images to YOLO format with configurable class granularity.
DOI: 10.17026/ar/siup7e
title: PAN-00018743 - Roman decorative nail A

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00018743&lt;/p&gt;
description: Modified: 2025-08-11T14:37:44+02:00
DOI: 10.15468/dl.4reze2
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Limonia acidissima"
 ]
}

 The dataset includes 22 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048368-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ud49tx
title: Occurrence Download

description: A dataset containing 5284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Macaranga peltata"
 ]
}

 The dataset includes 5284 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048370-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/17agt9
title: PAN-00173788 - watch key

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00173788&lt;/p&gt;
description: Modified: 2025-05-21T14:36:58+02:00
DOI: 10.15468/dl.bjc4hr
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "TaxonKey is Persea americana"
 ]
}

 The dataset includes 50 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048371-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6xfah
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Magnolia nilagirica"
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048373-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/xqzywo
title: PAN-00112424 - coin/coin-related, Hadrianus (117-138), voor Antoninus Pius, sestertius

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00112424&lt;/p&gt;
description: Modified: 2025-07-08T08:31:33+02:00
DOI: 10.15468/dl.m2fybs
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Manilkara hexandra"
 ]
}

 The dataset includes 37 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048374-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17905672
title: Barcode of Life Data Systems: BOLDS main resource (81) DwCA

description: http://www.boldsystems.org/. The Barcode of Life Data Systems (BOLD), is a web platform that provides an integrated environment for the assembly and use of DNA barcode data. It delivers an online database for collection and management of specimen, distributional, and molecular data as well as analytical tools to support their validation. Over the past few years, BOLD has grown to become a powerful online workbench and the central informatics hub of the DNA barcoding community. BOLD is freely available to any researcher with interests in DNA Barcoding. By providing specialized services, it aids in the publication of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances.
DOI: 10.15468/dl.6bs42c
title: Occurrence Download

description: A dataset containing 362 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mesua ferrea"
 ]
}

 The dataset includes 362 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048376-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17667226
title: SEA-Bird: A Machine Learning–Ready Bird Sound Dataset for Ten Common Southeast Asian Species

description: The SEA-Bird dataset is a curated, machine-learning–ready collection of avian vocalizations from ten bird species that are among the most commonly found in Malaysia. Recordings are sourced primarily from Southeast Asia, with a small number from surrounding regions. The dataset comprises 6,000 three-second audio clips sampled at 16 kHz and an additional 5,821 clips at 44.1 kHz, each manually verified to ensure minimal background noise, balanced class representation, and the absence of overlapping species calls.

The SEA-Bird dataset was developed to address the scarcity of machine-learning–ready acoustic datasets from underrepresented tropical regions, particularly in Southeast Asia. It supports research in automated species identification, biodiversity monitoring, and embedded acoustic sensing. The 16 kHz subset is optimized for Edge AI applications on low-power microcontrollers, while the 44.1 kHz version preserves high-frequency detail suitable for advanced spectro-temporal analyses.

All recordings were obtained from the Xeno-canto open repository under Creative Commons licenses and underwent a rigorous curation process involving segmentation and manual spectrogram inspection to ensure vocal clarity and completeness.

The dataset is organized into ten folders, each named after one of the included bird species (e.g., Common_Myna/, Spotted_Dove/). Within each folder, individual clips are labeled using the original Xeno-canto recording ID, followed by the start time in milliseconds from the source recording (e.g., XC123456_15000.wav). This structure preserves traceability and supports easy integration into automated pipelines.

This release does not yet include separate metadata files; a future update will provide a CSV metadata table linking each clip to its source recording and associated attributes.

Preliminary experiments using MobileNetV3-Small achieved classification accuracies above 90%, while benchmark models such as EfficientNet-B0, ResNet-50, and VGG-16 confirmed the dataset’s robustness for deep-learning applications.

Both subsets are released under a Creative Commons Attribution (CC BY 4.0) license and are freely available for academic and applied research. The dataset contributes to the growing body of open bioacoustic resources that promote reproducible, scalable, and inclusive research in tropical biodiversity informatics.
DOI: 10.17026/ar/2m19sy
title: PAN-00172794 - pinch lead

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00172794&lt;/p&gt;
description: Modified: 2025-06-23T11:57:29+02:00
DOI: 10.17026/dans-xn8-3qwj
title: PAN-00120480 - terra sigillata cup type Drag. 27

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00120480&lt;/p&gt;
description: Modified: 2025-05-09T18:05:07+02:00
DOI: 10.5281/zenodo.17786115
title: SEA-Bird: A Machine Learning–Ready Bird Sound Dataset for Ten Common Southeast Asian Species

description: The SEA-Bird dataset is a curated, machine-learning–ready collection of avian vocalizations from ten bird species that are among the most commonly found in Malaysia. Recordings are sourced primarily from Southeast Asia, with a small number from surrounding regions. The dataset comprises 6,000 three-second audio clips sampled at 16 kHz and an additional 5,821 clips at 44.1 kHz, each manually verified to ensure minimal background noise, balanced class representation, and the absence of overlapping species calls.

The SEA-Bird dataset was developed to address the scarcity of machine-learning–ready acoustic datasets from underrepresented tropical regions, particularly in Southeast Asia. It supports research in automated species identification, biodiversity monitoring, and embedded acoustic sensing. The 16 kHz subset is optimized for Edge AI applications on low-power microcontrollers, while the 44.1 kHz version preserves high-frequency detail suitable for advanced spectro-temporal analyses.

All recordings were obtained from the Xeno-canto open repository under Creative Commons licenses and underwent a rigorous curation process involving segmentation and manual spectrogram inspection to ensure vocal clarity and completeness.

The dataset is organized into ten folders, each named after one of the included bird species (e.g., Common_Myna/, Spotted_Dove/). Within each folder, individual clips are labeled using the original Xeno-canto recording ID, followed by the start time in milliseconds from the source recording (e.g., XC123456_15000.wav). This structure preserves traceability and supports easy integration into automated pipelines.

This release does not yet include separate metadata files; a future update will provide a CSV metadata table linking each clip to its source recording and associated attributes.

Preliminary experiments using MobileNetV3-Small achieved classification accuracies above 90%, while benchmark models such as EfficientNet-B0, ResNet-50, and VGG-16 confirmed the dataset’s robustness for deep-learning applications.

Both subsets are released under a Creative Commons Attribution (CC BY 4.0) license and are freely available for academic and applied research. The dataset contributes to the growing body of open bioacoustic resources that promote reproducible, scalable, and inclusive research in tropical biodiversity informatics.
DOI: 10.15468/dl.m2at8d
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Moringa concanensis"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048377-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/reew9z
title: PAN-00110900 - miniature plate/dish (Late Medieval/Modern)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00110900&lt;/p&gt;
description: Modified: 2025-06-14T09:29:33+02:00
DOI: 10.34740/kaggle/dsv/14119150
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.8ug6es
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((77.84867 7.75339,78.99942 8.95887,79.36495 9.05247,79.48951 9.12513,79.51447 9.31127,79.55575 9.83067,80.27537 10.7264,80.36021 11.99472,80.79882 13.8141,77.98131 12.73443,76.76155 12.77617,74.20822 13.86989,75.61449 10.49672,76.32104 7.66218,77.84867 7.75339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mundulea sericea"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048378-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15778204
title: SIGnature Datasets (Tutorial)

description: This dataset is designed for use with the SIGnature package, which enables rapid querying of gene sets across many scRNA-seq datasets by leveraging precomputed gene attribution scores. 

The SIGnature tutorials utilize two cell type attribution folders and one h5ad file:

1. celltype_attributions_lung.tar.gz: this file can be extracted by running "tar -xzf celltype_attributions_lung.tar.gz". This will produce a folder titled "celltype_attributions_lung" that contains data for 2 cell types:



pulmonary ionocyte

type I pneumocyte


2. celltype_attributions.tar.gz: this file can be extracted by running "tar -xzf celltype_attributions.tar.gz". This will produce a folder titled "celltype_attributions" that contains data for 5 cell types:



alveolar macrophage

classical monocyte

intermediate monocyte

macrophage

non-classical monocyte


3. tutorial_dataset.h5ad: small h5ad of simulated data to use during signature tutorials

The SIGnature tutorial can then be run by pointing the code to your extracted data.
DOI: 10.5281/zenodo.17905668
title: SIGnature Datasets (Tutorial)

description: This dataset is designed for use with the SIGnature package, which enables rapid querying of gene sets across many scRNA-seq datasets by leveraging precomputed gene attribution scores. 

The SIGnature tutorials utilize two cell type attribution folders and one h5ad file:

1. celltype_attributions_lung.tar.gz: this file can be extracted by running "tar -xzf celltype_attributions_lung.tar.gz". This will produce a folder titled "celltype_attributions_lung" that contains data for 2 cell types:



pulmonary ionocyte

type I pneumocyte


2. celltype_attributions.tar.gz: this file can be extracted by running "tar -xzf celltype_attributions.tar.gz". This will produce a folder titled "celltype_attributions" that contains data for 5 cell types:



alveolar macrophage

classical monocyte

intermediate monocyte

macrophage

non-classical monocyte


3. tutorial_dataset.h5ad: small h5ad of simulated data to use during signature tutorials

The SIGnature tutorial can then be run by pointing the code to your extracted data.
DOI: 10.17026/ar/6wfdtq
title: PAN-00002685 - coin/coin-related, Victorinus (269-271)/Tetricus I (271-274), naar, antoninianus

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00002685&lt;/p&gt;
description: Modified: 2025-08-19T08:14:13+02:00