cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.p45cw8
title: Occurrence Download

description: A dataset containing 3141 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tangara cyanicollis (d'Orbigny & Lafresnaye, 1837)"
 ]
}

 The dataset includes 3141 records from 133 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019506-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2porp
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aiphanes grandis Borchs. & Balslev"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001151-150407101314760/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vtvq2m
title: Occurrence Download

description: A dataset containing 3527 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coptodon rendalli (Boulenger, 1897)"
 ]
}

 The dataset includes 3527 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0167532-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.idq72s
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Aonyx congicus (Lönnberg, 1910)"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030127-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ueym2n
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mimosa scabrella Benth."
 ]
}

 The dataset includes 307 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001151-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p28ebb
title: Occurrence Download

description: A dataset containing 9217 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Aloina rigida (Hedw.) Limpr.",
 "TaxonKey is Anoectangium aestivum (Hedw.) Mitt.",
 "TaxonKey is Anoectangium clarum Mitt.",
 "TaxonKey is Anoectangium kweichowense E.B.Bartram"
 ]
}

 The dataset includes 9217 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028272-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rdufuc
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Montiopsis sericea (Hook. & Arn.) D.I.Ford"
 ]
}

 The dataset includes 146 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049517-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7x79d7
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eutropis lapulapu Barley, Diesmos, Siler, Martinez & Brown, 2020"
 ]
}

 The dataset includes 53 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049522-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xd9fal
title: Occurrence Download

description: A dataset containing 9514 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Colibri thalassinus (Swainson, 1827)"
 ]
}

 The dataset includes 9514 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001151-150422101436696/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbpsqm
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Marmota himalayana (Hodgson, 1841)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 60 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029546-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4dnx33
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Disporum acuminatissimum W.L.Sha"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003047-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syu7jj
title: Occurrence Download

description: A dataset containing 3257 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is fundiv france database"
 ]
}

 The dataset includes 3257 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001151-150512124619364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k7wbad
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chiasognathus grantii Stephens, 1831"
 ]
}

 The dataset includes 71 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0300728-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a3vuqa
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viburnum sempervirens K.Koch",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "or" : [
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Specimen"
 ]
 }
 ]
}

 The dataset includes 59 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001151-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e86nu4
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aedes abnormalis (Theobald, 1909)"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0300751-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mumpzy
title: Occurrence Download

description: A dataset containing 30178529 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 30178529 records from 8817 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001111-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/wgh1dg
title: PAN-00112693 - coin/coin-related, Constans (337-350), nummus

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00112693&lt;/p&gt;
description: Modified: 2025-07-08T08:38:39+02:00
DOI: 10.15468/dl.qn2n8f
title: Occurrence Download

description: A dataset containing 88936 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Larrea tridentata"
 ]
}

 The dataset includes 88936 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023324-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d3q2sm
title: Occurrence Download

description: A dataset containing 2490 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Takifugu niphobles"
 ]
}

 The dataset includes 2490 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023346-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17753531
title: AnnoTEP-DB (Annotation of Transposable Elements in Plants Database - Frozen Release, v1.0): A Precomputed Repository for Lineage-Level Plant Transposable Elements Annotation

description: AnnoTEP-DB (Frozen Release, v1.0): A Precomputed Repository for Lineage-Level Plant Transposable Elements Annotation

This Zenodo record provides a frozen, versioned snapshot of the AnnoTEP-DB resource — a comprehensive database of precomputed transposable element (TE) annotations and lineage-level classifications originally spanning 75 plant and algal genomes.

The full database (≈650 GB) exceeds Zenodo's 50 GB per-record storage limit. Therefore, this deposit includes a curated subset of representative genome-level archives, selected from the full collection to maximize phylogenetic diversity and ensure reproducibility of the main AnnoTEP-DB features.

The database was generated using the EDTA-GUI pipeline integrated with REXdb and RepeatModeler2, enabling lineage-aware TE classification, visualization, and comparative exploration across major plant clades.

To ensure long-term accessibility and reproducibility, the resource was restructured into two components:





AnnoTEP-DB-Interface.tar.gz — the complete interactive web interface (HTML, PHP, JavaScript, DataTables) required to deploy or browse AnnoTEP-DB locally;




Selected genome-level archives (.7z) — each containing the TE annotation outputs for a specific species, including FASTA and GFF3 files, summary tables, repeat landscapes, and TE lineage trees.



Each .7z genome archive (e.g., A_thaliana.7z, T_grandiflorum174.7z, Z_mays.7z) represents a complete standalone dataset comprising:





consensus TE libraries and genomic coordinates;




classification statistics by order, superfamily, and lineage;




repeat landscapes and insertion age profiles;




auxiliary visualization files and EDTA-GUI summary reports.



This frozen snapshot preserves the interface and the selected genome datasets in a format that remains fully accessible even without continued hosting.

Repository structure





AnnoTEP-DB-Interface.tar.gz — frozen interactive interface




Selected genome archives in .7z format (subset of the original 75 genomes)



Total compressed size of this deposit: ≤ 50 GB (Zenodo limit)Original full database size: ≈ 650 GBAnnotation pipeline: EDTA-GUI v2.1 File formats: .tar.gz, .7zLicense: Creative Commons Attribution 4.0 (CC BY 4.0)DOI of this release: 10.5281/zenodo.17753532

 

Reconstruction of the split Z_mays archive

The Z_mays dataset exceeded Zenodo’s file-size constraints and was therefore uploaded in multiple parts.To reconstruct the original archive, download all parts into the same folder and run:

cat Z_mays.7z.part_* > Z_mays.7z7z x Z_mays.7z

After extraction, the genome files can be placed in the directory/src/assets/pagesto enable full functionality of the AnnoTEP-DB interface.
DOI: 10.5281/zenodo.17753532
title: AnnoTEP-DB (Annotation of Transposable Elements in Plants Database - Frozen Release, v1.0): A Precomputed Repository for Lineage-Level Plant Transposable Elements Annotation

description: AnnoTEP-DB (Frozen Release, v1.0): A Precomputed Repository for Lineage-Level Plant Transposable Elements Annotation

This Zenodo record provides a frozen, versioned snapshot of the AnnoTEP-DB resource — a comprehensive database of precomputed transposable element (TE) annotations and lineage-level classifications originally spanning 75 plant and algal genomes.

The full database (≈650 GB) exceeds Zenodo's 50 GB per-record storage limit. Therefore, this deposit includes a curated subset of representative genome-level archives, selected from the full collection to maximize phylogenetic diversity and ensure reproducibility of the main AnnoTEP-DB features.

The database was generated using the EDTA-GUI pipeline integrated with REXdb and RepeatModeler2, enabling lineage-aware TE classification, visualization, and comparative exploration across major plant clades.

To ensure long-term accessibility and reproducibility, the resource was restructured into two components:





AnnoTEP-DB-Interface.tar.gz — the complete interactive web interface (HTML, PHP, JavaScript, DataTables) required to deploy or browse AnnoTEP-DB locally;




Selected genome-level archives (.7z) — each containing the TE annotation outputs for a specific species, including FASTA and GFF3 files, summary tables, repeat landscapes, and TE lineage trees.



Each .7z genome archive (e.g., A_thaliana.7z, T_grandiflorum174.7z, Z_mays.7z) represents a complete standalone dataset comprising:





consensus TE libraries and genomic coordinates;




classification statistics by order, superfamily, and lineage;




repeat landscapes and insertion age profiles;




auxiliary visualization files and EDTA-GUI summary reports.



This frozen snapshot preserves the interface and the selected genome datasets in a format that remains fully accessible even without continued hosting.

Repository structure





AnnoTEP-DB-Interface.tar.gz — frozen interactive interface




Selected genome archives in .7z format (subset of the original 75 genomes)



Total compressed size of this deposit: ≤ 50 GB (Zenodo limit)Original full database size: ≈ 650 GBAnnotation pipeline: EDTA-GUI v2.1 File formats: .tar.gz, .7zLicense: Creative Commons Attribution 4.0 (CC BY 4.0)DOI of this release: 10.5281/zenodo.17753532

 

Reconstruction of the split Z_mays archive

The Z_mays dataset exceeded Zenodo’s file-size constraints and was therefore uploaded in multiple parts.To reconstruct the original archive, download all parts into the same folder and run:

cat Z_mays.7z.part_* > Z_mays.7z7z x Z_mays.7z

After extraction, the genome files can be placed in the directory/src/assets/pagesto enable full functionality of the AnnoTEP-DB interface.
DOI: 10.15468/dl.c9tc9d
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Postenterogonia orbicularis"
 ]
}

 The dataset includes 79 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023347-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cx5ycz
title: Occurrence Download

description: A dataset containing 400 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Haiti",
 "OccurrenceStatus is Present",
 "TaxonKey is Primulaceae"
 ]
}

 The dataset includes 400 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023348-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17793324
title: Input files for the Dream challenge data, TCGA-HNSC deconvolution and GSE103322 single cell data clustering using DualSimplex package

description: These are files not included into the main paper repository due to size limitations.
DOI: 10.5281/zenodo.17793325
title: Input files for the Dream challenge data, TCGA-HNSC deconvolution and GSE103322 single cell data clustering using DualSimplex package

description: These are files not included into the main paper repository due to size limitations.
DOI: 10.71929/rubin/2570545
title: PSTN-019: The LSST Science Pipelines Software: Optical Survey Pipeline Reduction and Analysis Environment

description: The NSF-DOE Vera C. Rubin Observatory will produce the Legacy Survey of Space and Time (LSST), producing 11 data releases over the ten-year survey. The LSST Science Pipelines Software, the Optical Survey Pipeline Reduction and Analysis Environment (OSPRAE), will be used to create these data releases and to perform the nightly alert production. This paper provides an overview of the LSST Science Pipelines Software, describing the components and how they are combined to form pipelines
DOI: 10.15468/dl.cty4s7
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ukraine",
 "OccurrenceStatus is Present",
 "TaxonKey is Corvus monedula",
 "Year 2020-2025"
 ]
}

 The dataset includes 542 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023349-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.71929/rubin/2587850
title: LDM-148: Rubin Observatory Data Management System Design

description: The Rubin Observatory LSST Data Management System (DMS) is a set of services employing a variety of software components running on computational and networking infrastructure that combine to deliver science data products to the observatory's users and support observatory operations. This document describes the components, their service instances, and their deployment environments as well as the interfaces among them, the rest of the LSST system, and the outside world.
DOI: 10.71929/rubin/2587108
title: LDM-151: Data Management Science Pipelines Design

description: The LSST Science Requirements Document (the LSST SRD) specifies a set of data product guidelines, designed to support science goals envisioned to be enabled by the LSST observing program. Following these guidelines, the details of these data products have been described in the LSST Data Products Definition Document (DPDD), and captured in a formal flow-down from the SRD via the LSST System Requirements (LSR), Observatory System Specifications (OSS), to the Data Management System Requirements (DMSR). The LSST Data Management subsystem's responsibilities include the design, implementation, deployment and execution of software pipelines necessary to generate these data products. This document describes the design of the scientific aspects of those pipelines.
DOI: 10.71929/rubin/2998139
title: LDM-612: Plans and Policies for LSST Alert Distribution

description: A major product of the nightly processing of LSST images is a world-public stream of alerts from transient, variable, and moving sources. Science users will access these alerts through community brokers or through a simple filtering service provided by LSST. This document provides a guide to the plans and policies for the alert distribution system to aid science users, broker developers, funding agencies, and LSST Project personnel. It describes the components of the alert distribution system and the data rights required to access specific scientific products. It provides guidelines for organizations developing community brokers and describes the planned capabilities of the LSST simple alert filtering service and Science Platform to aid science users in planning for LSST science.
DOI: 10.71929/rubin/2583432
title: DMTN-015: Flavors of Coadds

description: A glossary of different kinds of coadded images, with brief descriptions of the algorithms behind them.
DOI: 10.71929/rubin/2586490
title: DMTN-021: Implementation of Image Difference Decorrelation

description: Herein, we describe a method for decorrelating image differences produced by the Alard and Lupton (1998) method of PSF matching. Inspired by the recent work of Zackay et al. (2016) and the prior work of Kaiser [2004], this proposed method uses a single post-subtraction convolution of an image difference to remove the neighboring pixel covariances in the image difference that result from the convolution of the template image by the PSF matching kernel. We describe the method in detail, analyze its effects on image differences (both real and simulated) as well as on detections and photometry of detected sources in decorrelated image differences. We also compare the decorrelated image differences with those resulting from a basic implementation of Zackay et al. (2016). We describe the implementation of the new correction in the LSST image differencing pipeline, and discuss potential issues and areas of future research.
DOI: 10.71929/rubin/2586578
title: DMTN-031: Pessimistic Pattern Matching for LSST

description: The current reference catalog matcher used by LSST for astrometry has been found to not be adequately robust and fails to find matches on several current datasets. This document describes a potential replacement algorithm, and compares its performance with the current implementation.
DOI: 10.71929/rubin/2586685
title: DMTN-036: jointcal: Simultaneous Astrometry & Photometry for thousands of Exposures with Large CCD Mosaics

description: The jointcal package simultaneously optimizes the astrometric and photometric calibrations of a set of astronomical images. In principle and often in practice, this approach produces distortion and thoroughput models which are more precise than when fitted independently. This is especially true when the images are deeper than the astrometric reference catalogs. In the "Astromatic" software suite, this simultaneous astrometry functionality is fulfilled by "SCAMP". The code we describe here has similar aims, but follows a slightly different route. Jointcal is built on top of the the LSST Data Management software stack.
DOI: 10.71929/rubin/2997573
title: DMTN-065: Data Management for LSST Special Programs

description: Special Programs are additional survey areas and/or observing strategies that are driven by specific science goals which build on, or are beyond, the core science pillars of the Wide Fast Deep Main Survey. In order to meet the requirements and enable science related to Special Programs, this document provides recommendations for Rubin Data Management regarding processing and serving data products for Special Programs. Hardware and processing boundaries on the potential diversity of data from Special Programs are discussed along with scenarios in which user-generated processing and data products might be needed to meet Special Programs' science goals.