cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17162544
title: Microflora Danica

description: Microflora Danica

Scope

Microflora Danica (MFD) is set to create the compendium of the microbial populations of Denmark using 10.000+ metagenomic samples encompassing soils, waters and sediments from natural, agricultural and built environments.

More than 50 subprojects are included in MFD, with various degrees of spatial resolutions, depth of associated data and technical challenges. This wiki is meant to help the researchers in navigating the various subprojects, data and results from MFD.

The first flagship manuscript "Microflora Danica: the atlas of Danish environmental microbiomes" is available as a preprint on bioRxiv. The data are publicly available, its findings can be explored and reproduced starting from The MFD Atlas page of this wiki.

Introduction

Microflora Danica is the Atlas of the enviromental microbiomes of Denmark. It relies upon a large scale dataset encompassing 10,683 shotgun metagenomes, 412 near full-length 16S UMI datasets and 450 bacterial and eukaryotic rRNA operon collections, linked to a detailed 5-level habitat ontology. The manuscript determines that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

Data

This project encompasses additional data files belonging to the Microflora Danica project. Here we deopisted:



Metagenomic assemblies.

Metagenome bins (MQ MAGs). 

The MFG (Microflora Global) 16S rRNA gene reference database (unclustered and clustered at 98.7% ANI).

Metagenomic derived 16S rRNA gene fragments derived from the 10km reference grid representative samples.

Genus-aggregated observational tables of the 16S rRNA gene fragments (counts and relative abundance) as well as versions of these subjected to random subsampling without replacement.

OTU tables of the 16S UMI, 16S and 18S sequences from operons. 

Data used in the analysis for evaluation of the effect of drying performed for the agricultural samples. 

Supplementary data for nitrifier analysis (including packages for GraftM).

Supplementary data for metagenomic marker gene analysis (including package for SingleM). 


Other resources

The sequencing data, and metagenome bins (HQ MAGs, >90 % completeness <5 % contamination) are available in NCBI under bioproject PRJNA1071982. Associated metadata are also available in github (https://github.com/cmc-aau/mfd_wiki).The near-full length 16S UMI as well as the near-full length 16S and 18S from the bacterial and eukaryotic operons has also been deposited in GBIF. 

This project is supported by the Poul Due Jensen/Grundfos foundation.
DOI: 10.15468/dl.8a7jst
title: Occurrence Download

description: A dataset containing 829 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (USA.9_1, USA.8_1, USA.21_1, USA.31_1, USA.39_1, USA.47_1, USA.49_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Lasioglossum marinum"
 ]
}

 The dataset includes 829 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020039-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17152881
title: Replication package for: "Breaking the Iron Rice Bowl: Tenure-Track Systems and the Rise of Academic Innovation in China"

description: This is the replication package for "Breaking the Iron Rice Bowl: Tenure-Track Systems and the Rise of Academic Innovation in China", published in the Economic Journal.
DOI: 10.5281/zenodo.17152882
title: Replication package for: "Breaking the Iron Rice Bowl: Tenure-Track Systems and the Rise of Academic Innovation in China"

description: This is the replication package for "Breaking the Iron Rice Bowl: Tenure-Track Systems and the Rise of Academic Innovation in China", published in the Economic Journal.
DOI: 10.15468/dl.yh5n2u
title: Occurrence Download

description: A dataset containing 7047 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "Country is one of (Colombia)",
 "TaxonKey is one of (Amphibia [GBIF Backbone Taxonomy])",
 "StateProvince is one of (Caldas)"
 ]
 }
 ]
}

 The dataset includes 7047 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020038-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/knbd-r965
title: JWST Observations of 133P - Cycles 2 and 3

description: JWST NIRCam and NIRSpec observations of main-belt comet 133P/Elst-Pizarro when active in 2024
DOI: 10.15468/dl.zm49ps
title: Occurrence Download

description: A dataset containing 3752 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heloderma suspectum"
 ]
}

 The dataset includes 3752 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020041-250914085247600/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.19790524
title: ANIPBE0-MLXDM dataset. _v2 contains atomic M1, M2, M3, and Veff

description: The dataset for training the ANIPBE0-MLXDM Neural Network Potential
DOI: 10.6084/m9.figshare.19790524.v2
title: ANIPBE0-MLXDM dataset. _v2 contains atomic M1, M2, M3, and Veff

description: The dataset for training the ANIPBE0-MLXDM Neural Network Potential
DOI: 10.6084/m9.figshare.19790524.v1
title: ANIPBE0-MLXDM dataset

description: The dataset for training the ANIPBE0-MLXDM Neural Network Potential
DOI: 10.15468/dl.hqjmcw
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Bangladesh",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020042-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zc6dj9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paphia schnelliana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020043-250914085247600/datasets/export for details.
DOI: 10.15468/dl.xnutqb
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Barbados",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020044-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17162583
title: Fatality Analysis Reporting System (FARS) Processed Data – rfars

description: The Fatality Analysis Reporting System (FARS) is a nationwide census of all U.S. motor vehicle crashes resulting in a fatality, maintained by the National Highway Traffic Safety Administration (NHTSA). While the raw FARS data are publicly available, they are distributed in formats that require significant preprocessing before analysis. This dataset provides a processed version of the FARS database (2014-2023), optimized for immediate use in R, Python, Excel, and other modern data tools. It was prepared by the rfars R package, enabling researchers, policymakers, and educators to access and analyze fatal crash data more efficiently and reproducibly.

This dataset is provided in three different file formats to support a wide range of users and analysis environments:



CSV (.csv) - a plain text format, with each of the five tables saved separately. These files are the most universally compatible and can be opened directly in Excel, though they are larger.

Parquet (.parquet) - a modern, compressed, cross-platform columnar format. Each of the five tables is provided separately (fars_accident.parquet, fars_vehicle.parquet, etc.). This version is recommended for Python, SQL, and advanced R users, as it is smaller than CSV and loads quickly in most data science environments.

RDS (.rds) - a native R format containing the full dataset as a list of five related tables (accident, vehicle, person, drugs, distract). This version is recommended for R users, since it can be loaded in one step with readRDS() and preserves all variable types exactly as processed.
description: Version 2025.3 fixes a data processing bug.
DOI: 10.5281/zenodo.15533780
title: antiSMASH and eggNOG mapper annotations from an ultra-deep sequencing effort of a forest sample in Schönbuch, Germany

description: This dataset contains biosynthetic gene cluster (BGC) and other functional annotations of the total microbiome from a deeply sequenced soil sample collected from Schönbuch forest in southwestern Germany.
DOI: 10.5281/zenodo.17162541
title: antiSMASH and eggNOG mapper annotations from an ultra-deep sequencing effort of a forest sample in Schönbuch, Germany

description: This dataset contains biosynthetic gene cluster (BGC) and other functional annotations of the total microbiome from a deeply sequenced soil sample collected from Schönbuch forest in southwestern Germany.
DOI: 10.5517/ccdc.csd.cc2kdlf0
title: CCDC 2365592: Experimental Crystal Structure Determination

description: Related Article: Arevik S. Saakian, Dimitri N. Laikov, Mikhail S. Nechaev, Victor A. Tafeenko, Elena K. Beloglazkina, Alexander V. Finko|2025|J.Org.Chem.|90|12621|doi:10.1021/acs.joc.5c01225
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kdlg1
title: CCDC 2365593: Experimental Crystal Structure Determination

description: Related Article: Arevik S. Saakian, Dimitri N. Laikov, Mikhail S. Nechaev, Victor A. Tafeenko, Elena K. Beloglazkina, Alexander V. Finko|2025|J.Org.Chem.|90|12621|doi:10.1021/acs.joc.5c01225
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kdlj3
title: CCDC 2365595: Experimental Crystal Structure Determination

description: Related Article: Arevik S. Saakian, Dimitri N. Laikov, Mikhail S. Nechaev, Victor A. Tafeenko, Elena K. Beloglazkina, Alexander V. Finko|2025|J.Org.Chem.|90|12621|doi:10.1021/acs.joc.5c01225
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kdlwg
title: CCDC 2365606: Experimental Crystal Structure Determination

description: Related Article: Arevik S. Saakian, Dimitri N. Laikov, Mikhail S. Nechaev, Victor A. Tafeenko, Elena K. Beloglazkina, Alexander V. Finko|2025|J.Org.Chem.|90|12621|doi:10.1021/acs.joc.5c01225
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kdlxh
title: CCDC 2365607: Experimental Crystal Structure Determination

description: Related Article: Arevik S. Saakian, Dimitri N. Laikov, Mikhail S. Nechaev, Victor A. Tafeenko, Elena K. Beloglazkina, Alexander V. Finko|2025|J.Org.Chem.|90|12621|doi:10.1021/acs.joc.5c01225
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.c27dcd
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Belize",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020045-250914085247600/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.30168448
title: Wetherspoons_Kids_Menu.pdf

description: Wetherspoons is a pub chain restaurant all across the UK. it provides best and amazing food plus drinks in the UK in very affordable prices.
DOI: 10.6084/m9.figshare.30168448.v1
title: Wetherspoons_Kids_Menu.pdf

description: Wetherspoons is a pub chain restaurant all across the UK. it provides best and amazing food plus drinks in the UK in very affordable prices.
DOI: 10.15468/dl.v3bzg6
title: Occurrence Download

description: A dataset containing 1959 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Chrysolophus pictus"
 ]
}

 The dataset includes 1959 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020047-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zywng6
title: Occurrence Download

description: A dataset containing 953 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Specimen)",
 "Geometry POLYGON((-78.24515 62.39828,-82.1432 55.67307,-94.35137 58.5859,-91.36127 35.638,-91.40411 30.84039,-80.93042 25.102,-79.68136 32.30688,-66.89368 42.56534,-62.31026 44.1931,-54.94252 45.34966,-48.90268 48.21966,-67.23637 62.01276,-78.24515 62.39828))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Cardamine douglassii, Cardamine micranthera, Cardamine maxima, Cardamine flagellifera, Cardamine dentata, Cardamine clematitis, Cardamine longii)"
 ]
}

 The dataset includes 953 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020040-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpwj55
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Comoros",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020048-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a5v8md
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paphia semirugata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020050-250914085247600/datasets/export for details.
DOI: 10.15468/dl.d6ua8s
title: Occurrence Download

description: A dataset containing 840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Syrmaticus reevesii"
 ]
}

 The dataset includes 840 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020049-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17162584
title: Crash Report Sampling System (CRSS) Processed Data – rfars

description: The General Estimates System (GES), redesigned as the Crash Report Sampling System (CRSS) in 2016, is a nationally representative sample of police-reported motor vehicle crashes in the U.S., maintained by the National Highway Traffic Safety Administration (NHTSA). While the raw GES/CRSS data are publicly available, they are distributed in formats that require significant preprocessing before analysis. This dataset provides a processed version of the GES/CRSS database (2014-2023), optimized for immediate use in R, Python, Excel, and other modern data tools. It was prepared by the rfars R package, enabling researchers, policymakers, and educators to access and analyze crash data more efficiently and reproducibly.

This dataset is provided in three different file formats to support a wide range of users and analysis environments:



CSV (.csv) - a plain text format, with each of the five tables saved separately. These files are the most universally compatible and can be opened directly in Excel, though they are larger.

Parquet (.parquet) - a modern, compressed, cross-platform columnar format. Each of the five tables is provided separately (fars_accident.parquet, fars_vehicle.parquet, etc.). This version is recommended for Python, SQL, and advanced R users, as it is smaller than CSV and loads quickly in most data science environments.

RDS (.rds) - a native R format containing the full dataset as a list of five related tables (accident, vehicle, person, drugs, distract). This version is recommended for R users, since it can be loaded in one step with readRDS() and preserves all variable types exactly as processed.
description: Version 2025.3 fixes a data processing bug.
DOI: 10.15468/dl.rdcpfy
title: Occurrence Download

description: A dataset containing 780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Tetraophasis obscurus"
 ]
}

 The dataset includes 780 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020051-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpfsrh
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Costa Rica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 111 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020053-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.36tac8
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paratapes undulatus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 116 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020054-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7h92z2
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020055-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aqwf72
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is Guinea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020056-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npuvz6
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleus scutellarioides",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 135 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020057-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/vqx6hj
title: Replication Data for: Impact of Mobile Policing Bases in the metropolitan area of Belo Horizonte Minas Gerais

description: Raw data and R coding used on the paper
DOI: 10.15468/dl.cmfk3p
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 "TaxonKey is one of (Abronia graminea [GBIF Backbone Taxonomy])"
 ]
}

 The dataset includes 343 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020058-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.