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

description: A dataset containing 1760 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "TaxonKey is Quercus dentata Thunb."
 ]
}

 The dataset includes 1760 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015055-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v6j75v
title: Occurrence Download

description: A dataset listing the 7 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lumbriculus variegatus (Müller, 1774)"
 ]
}

 The dataset's 7 records were derived from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015046-250310093411724/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.28615217
title: FieldscaleSunflowerhead

description: This project includes the framework of the dual-branch YOLOv10 network as well as the original YOLOv10 network, and also includes the core code of point cloud analysis and partially annotated sample sets.
DOI: 10.15468/dl.jzuh45
title: Occurrence Download

description: A dataset listing the 152 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((8.94349 44.39339,8.95314 44.39339,8.95314 44.40063,8.94349 44.40063,8.94349 44.39339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 152 records were derived from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015041-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w3yn6x
title: Occurrence Download

description: A dataset containing 20342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Pteroglossus castanotis Gould, 1834"
 ]
}

 The dataset includes 20342 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015056-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14719219
title: Data & Codification from Stage 2 of the study "Using Real-world Scenarios to Bridge Training and Practice in Evidence-Based Software Engineering"

description: Supplementary materials for the paper “Using Real-world Scenarios to Bridge Training and Practice in Evidence-Based Software Engineering.” This document includes the data and coding for Stage 2 of the empirical study presented in the referenced paper. January 2025.
DOI: 10.5281/zenodo.14719220
title: Data & Codification from Stage 2 of the study "Using Real-world Scenarios to Bridge Training and Practice in Evidence-Based Software Engineering"

description: Supplementary materials for the paper “Using Real-world Scenarios to Bridge Training and Practice in Evidence-Based Software Engineering.” This document includes the data and coding for Stage 2 of the empirical study presented in the referenced paper. January 2025.
DOI: 10.5281/zenodo.15009032
title: CHAMOIS datasets: Pfam domains and ChemOnt-classified metabolites for experimentally-verified BGCs.

description: Overview

CHAMOIS is a fast method for predicting chemical features of natural products produced by Biosynthetic Gene Clusters (BGCs) using only their genomic sequence. It can be used to get chemical features from BGCs predicted in silico with tools such as GECCO or antiSMASH. It is developed by the Zeller Lab at LUMC and EMBL.

This record contains the training data for CHAMOIS version 1.0, as well as the data and scripts supporting the analyses presented in the paper. The code for the CHAMOIS tool can be found in the zellerlab/CHAMOIS repository on GitHub. The various HDF5 files are intended to be opened with the anndata library (Virshup 2024) using the anndata.read_h5ad function. Alternatively, the observations metadata, variables metadata, and data tables are given as tab-separated-values (TSV) files in the same folder under the name obs.tsv, var.tsv and X.tsv respectively.

Contents

Each dataset is an archive containing the following files:



features.hdf5 and features folder : The Pfam v36.0 domain vectors for each BGC of the dataset.

classes.hdf5 and classes folder: The predicted ChemOnt classes for a selected compound of each BGC of the dataset.

compound.json : A JSON file listing all compounds per BGC (as the BGCs in classes.hdf5 only have the classification for a single compound).

types.tsv : The MIBiG types (Polyketide, NRP, RiPP, etc.) for each BGC of the dataset (if any).

taxonomy.tsv : The taxonomy for the host of each BGC of the dataset (if any).


CHAMOIS can be trained and evaluated on these domains directly using the chamois train and chamois cv commands:



chamois train -f features.hdf5 -c classes.hdf5 -o model.json

chamois cv -f features.hdf5 -c classes.hdf5 -o report.tsv


 

Datasets

MIBiG 2.0

This dataset contains 1,517 annotated BGCs released in MIBiG 2.0 (Kautsar 2019), excluding some records from a manually curated list, and with manual corrections in BGC coordinates and compound assignment. It also excludes the BGCs that were deprecated or removed in MIBiG 3.1 to avoid low-quality entries.

MIBiG 3.1

This dataset contains 2,068 annotated BGCs released in MIBiG 3.1 (Terlouw 2023), excluding some records from a manually curated list, and with manual corrections in BGC coordinates and compound assignment.

Benchmark 

This dataset contains 52 annotated BGCs, found in literature in their native context (the complete host genome) and used in the BGC screening benchmark of the CHAMOIS paper. The BGCs are distinct from the MIBiG 2.0 and 3.1 datasets, so it can be used as an external validation set if needed, although some clusters still exhibit moderate similarity. The dataset also contains the complete sequences of the 50 genomes containing the BGCs.

PRISM 4

This dataset contains 1,267 annotated BGCs from the "Gold Standard BGCs" published in PRISM 4 (Skinnider 2020). It overlaps with the MIBiG datasets.
DOI: 10.15468/dl.za3scy
title: Occurrence Download

description: A dataset containing 212532 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Geometry POLYGON((9.6867 3.53797,9.99312 3.95288,10.56107 4.52082,11.60229 5.73243,12.41634 7.00084,14.93843 12.07397,14.14835 13.03447,11.5455 9.97307,11.55211 9.63321,10.61456 8.40481,10.88933 8.69368,8.64899 5.37274,8.45677 4.51703,8.50895 4.3998,8.65479 4.08276,9.6867 3.53797))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 212532 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015034-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15040391
title: BLLAST land-atmosphere coupled study cases

description: Study cases in the common format DEPHY. This study cases are adapted to study land-atmosphere coupling in climate models or numerical weather prediction models.
DOI: 10.5281/zenodo.15045485
title: BLLAST land-atmosphere coupled study cases

description: Study cases in the common format DEPHY. This study cases are adapted to study land-atmosphere coupling in climate models or numerical weather prediction models.
DOI: 10.5281/zenodo.15045781
title: MethMotif 2025 Protocol Output Files and Markdown

description: Abstract:

This protocol presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocol is organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) Visualization of methylation-specific TF motifs using TFregulomeR, and (3) Characterization of leucine zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behaviour, and visualize the impact of DNA methylation on binding specificity. The protocol also provides step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through this protocol, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine zipper TFs in a cell-type-specific context.

Data Structure:

This repository contains essential resources from the MethMotif suite, including:





Protocol Output Files (protocol_output.zip): A compressed archive containing the results generated from the MethMotif suite, including processed data, intermediate outputs, and final reports.

Markdown Script (methmotif_protocol_markdown.md): A structured markdown document outlining the MethMotif suite protocol, including methodology, key parameters, and interpretation of results.

R Script (methmotif_protocol_rscript.R): A script written in R used to execute parts of the MethMotif analysis, including data preprocessing, motif discovery, and visualization.



These files facilitate reproducibility and provide a comprehensive guide for running and analyzing data with the MethMotif suite.
DOI: 10.5281/zenodo.15045782
title: MethMotif 2025 Protocol Output Files and Markdown

description: Abstract:

This protocol presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocol is organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) Visualization of methylation-specific TF motifs using TFregulomeR, and (3) Characterization of leucine zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behaviour, and visualize the impact of DNA methylation on binding specificity. The protocol also provides step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through this protocol, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine zipper TFs in a cell-type-specific context.

Data Structure:

This repository contains essential resources from the MethMotif suite, including:





Protocol Output Files (protocol_output.zip): A compressed archive containing the results generated from the MethMotif suite, including processed data, intermediate outputs, and final reports.

Markdown Script (methmotif_protocol_markdown.md): A structured markdown document outlining the MethMotif suite protocol, including methodology, key parameters, and interpretation of results.

R Script (methmotif_protocol_rscript.R): A script written in R used to execute parts of the MethMotif analysis, including data preprocessing, motif discovery, and visualization.



These files facilitate reproducibility and provide a comprehensive guide for running and analyzing data with the MethMotif suite.
DOI: 10.15468/dl.q9h32v
title: Occurrence Download

description: A dataset containing 13678 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Netherlands",
 "Month is one of (January, December, November, October)",
 "TaxonKey is Ciconia ciconia (Linnaeus, 1758)",
 "Year 2009-2014"
 ]
}

 The dataset includes 13678 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015057-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wws9ex
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Campylirhynchus pericarpius O'Brien & Wibmer, 1982",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015058-250310093411724/datasets/export for details.
DOI: 10.15468/dl.pyp4cb
title: Occurrence Download

description: A dataset containing 11342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Country is Denmark",
 "DatasetKey is DOF/BirdLife Denmark - Observations from DOFbasen",
 "GadmGid is DNK",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (VU, NT, EN, CR)",
 "PublishingOrg is 8b734449-479a-4924-8f7a-9a2a64112f8f",
 "TaxonKey is Aves",
 "Year 2000-2000"
 ]
}

 The dataset includes 11342 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015060-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spvr6h
title: Occurrence Download

description: A dataset containing 254782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Opuntia Mill.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 254782 records from 834 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015042-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a5jmbp
title: Occurrence Download

description: A dataset containing 735991 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erinaceus europaeus Linnaeus, 1758"
 ]
}

 The dataset includes 735991 records from 2191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015045-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111298534
title: Sinai Syriac 30: Lives of Holy Women, Sinai Syriac 30: Lives of Holy Women, Syrus Sinaiticus

description: [Text Description:] Stories and meditations on holy women/saints, including those who were martyrs, and those in the Bible and Deuterocanonical literature. ❧ [Text or Publication Number Note:] Sinai Syriac 30: Lives of Holy Women ❧ [Medium:] Parchment ❧ [Script Note:] Syriac: Estrangela ❧ [Physical Object Description:] Palimpsest, with overtext written in Syriac, undertext in Syriac or Greek. Ink on overtext is black, ink on undertext has oxidized to faded brown. ❧ [Physical Object Note:] Many of the pages show some water damage. ❧ [Physical Object Note:] Back cover is still extant, shows evidence of roughly stitched repair. ❧
DOI: 10.15468/dl.tzswgx
title: Occurrence Download

description: A dataset containing 8110 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor (Linnaeus, 1771)"
 ]
}

 The dataset includes 8110 records from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002363-180925134338326/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111318771
title: Cuneiform Tablet H

description: [Text Description:] Cuneiform Tablet H ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.25549/inscriptifact-ouc111318103
title: Cuneiform Tablet D

description: [Text Description:] Cuneiform Tablet D ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.15468/dl.whxunt
title: Occurrence Download

description: A dataset containing 520 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bradypus tridactylus Linnaeus, 1758"
 ]
}

 The dataset includes 520 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002363-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111318277
title: Cuneiform Tablet D

description: [Text Description:] Cuneiform Tablet D ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.15468/dl.34c7d4
title: Occurrence Download

description: A dataset containing 6805533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Zenaida macroura Linnaeus, 1758",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6805533 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002363-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111319833
title: Cuneiform Tablet K

description: [Text Description:] Cuneiform Tablet K ❧ [Medium:] Clay ❧ [Script Note:] Cuneiform, Non-Alphabetic ❧ [Physical Object Description:] Clay tablet with cuneiform script
DOI: 10.25549/inscriptifact-ouc112025308
title: Cuneiform Tablet 1913.14.1507, Spurlock 1913.14.1507

description: [Text Description:] Administrative tablet ❧ [Text or Publication Number Note:] Spurlock 1913.14.1507; CDLI P421359 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish White (10YR 9/1.5) Moderate Yellowish Pink (5YR 7.5/4) Medium Gray (N 5.25/ 22.1% R) ❧ [Physical Object Note:] 10.5 x 7.4 x 2.6 cm (195g)
DOI: 10.15468/dl.aiiaer
title: Occurrence Download

description: A dataset listing the 14818194 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 14818194 records were derived from 1790 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002363-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tvpt8z
title: Occurrence Download

description: A dataset containing 998767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Philothermus Aubé, 1843, Ostomopsis Scott, 1922, Strangalia Audinet-Serville, 1835, Spondylis Fabricius, 1775, Oberea Dejean, 1835, Xylotrechus Chevrolat, 1860, Dorysthenes Vigors, 1826, Cicindela Linnaeus, 1758, Omoglymmius Ganglbauer, 1891, Elaphrus Fabricius, 1775, Carabus Linnaeus, 1758, Clivina Latreille, 1802, Pheropsophus Solier, 1833, Dischissus Bates, 1873, Pentagonica Schmidt-Goebel, 1846, Lebia Latreille, 1802, Ichthyurus Westwood, 1848, Malthinus Latreille, 1806, Heteromastix Boheman, 1858, Laemoglyptus Fairmaire, 1886, Fissocantharis Pic, 1921, Prothemus Champion, 1926, Lycocerus Gorham, Themus Motschulsky, 1857, Simianus Blanchard, 1853, Ennometes Pascoe, 1866, Haematoides Deyrolle & Fairmaire, 1878, Cytilus Erichson, 1847, Notolioon Lawrence, Slipinski, Jäger & Pütz, 2013, Microchaetes Hope, 2019, Dicerca Eschscholtz, 1829, Trachys Fabricius, 1801, Coroebus Gory & Laporte, 1839, Cylas Latreille, 1802, Baryrhynchus Lacordaire, 1865, Apion Herbst, 1797, Deretaphrus Newman, 1842, Ascetoderes Pope, 1961, Polycaon Laporte, 1836, Lyctus Fabricius, 1792, Synercticus Newman, 1842, Paracucujus Sen Gupta & Crowson, 1966, Biphyllus Dejean, 1821, Althaesia Pascoe, 1860, Rhinotia W.Kirby, 1819, Phymatapoderus E.Voss, 1926, Paratrachelophorus E.Voss, 1924, Involvulus F.P.Schrank, 1798, Byctiscus C.G.Thomson, 1859, Eurypogon Motschulsky, 1859, Artematopus Perty, 1832, Wattianus Kaszab, 1981, Acorynus C.J.Schoenherr, 1833, Ozotomerus B.P.Perroud, 1853, Xylinada A.A.Berthold, 1827, Peribathys K.Jordan, 1937, Macratria Newman, 1838, Trichananca Blackburn, 1891, Lemodes Boheman, 1858)"
 ]
}

 The dataset includes 998767 records from 2464 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029905-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/s3t-c3z-2xm
title: Mythimna (Mythimna) pallens Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bwh-k66-g5d
title: Hadena (Hadena) bicruris Hufnagel, 1766

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kvq-ssj-x2s
title: Xylena exsoleta Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xdf-7emr
title: Kreiel 14, Wintelre

description: &lt;p&gt;Omdat het plangebied al onder het archeologisch sporenniveau is verdiept en het plangebied zwaar verstoord blijkt te zijn, beveelt ArcheoPro aan om het plangebied vrij te geven. Geadviseerd wordt om in de omringende percelen rekening te houden met de aanwezigheid van archeologische waarden uit de Nieuwe tijd.&lt;/p&gt;
description: Date: 23/08/2013 (veldwerk)
description: Date: 17/11/2014 (veldwerk)
DOI: 10.3535/jdv-1da-rsr
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r3j-klq-rwn
title: Hadena (Hadena) bicruris Hufnagel, 1766

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fha-xqs-9vd
title: Orthosia (Semiophora) gothica Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/te1-vrk-g8c
title: Mythimna (Hyphilare) ferrago Fabricius, 1787

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/574-0sd-za7
title: Cucullia Schrank, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v8k-ebs-gt2
title: Anarta (Calocestra) trifolii Hufnagel, 1766

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xdf-7w75
title: PAN-00002724 - arched bow brooch B

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00002724&lt;/p&gt;
description: Modified: 2019-04-25T10:19:57+02:00