cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ftkrx6
title: Occurrence Download

description: A dataset containing 2425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scolymus maculatus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2425 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082043-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6asj6a
title: Occurrence Download

description: A dataset containing 521 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is false",
 "TaxonKey is Lanius ludovicianus Linnaeus, 1766"
 ]
}

 The dataset includes 521 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0276463-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qk8zj4
title: Occurrence Download

description: A dataset containing 130628 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pisum L."
 ]
}

 The dataset includes 130628 records from 392 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008345-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pn6qph
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyperus grossianus Pedersen"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0153868-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whm87x
title: Occurrence Download

description: A dataset containing 13407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scorpiurus muricatus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13407 records from 256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082040-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2gee59
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ukraine, Poland)",
 "TaxonKey is Spalax zemni"
 ]
}

 The dataset includes 450 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016263-250914085247600/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.30161455
title: Supplemental data for Wei et al jc.2025-02127

description: This study evaluates the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.
DOI: 10.6084/m9.figshare.30161455.v1
title: Supplemental data for Wei et al jc.2025-02127

description: This study evaluates the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.
DOI: 10.6084/m9.figshare.30161464
title: Arquivos do corpus paralelo de AntPconc

description: O "Corpus_leis_zh-tkn" (arquivos .txt) é um corpus chinês tokenizado gerado pela ferramenta TagAnt a partir do "Corpus_leis_zh" utilizando a opção "Word" (token), preparado mediante segmentação de palavras para que o AntPConc possa identificar as expressões de busca em chinês. Os arquivos Corpus_leis_zh-tkn.txt e Corpus_leis_pt.txt foram gerados a partir do corpus paralelo previamente alinhado "Corpus_aligned_sentences_zh-tkn-pt" (arquivos .xlsx).
DOI: 10.6084/m9.figshare.30161464.v1
title: Arquivos do corpus paralelo de AntPconc

description: O "Corpus_leis_zh-tkn" (arquivos .txt) é um corpus chinês tokenizado gerado pela ferramenta TagAnt a partir do "Corpus_leis_zh" utilizando a opção "Word" (token), preparado mediante segmentação de palavras para que o AntPConc possa identificar as expressões de busca em chinês. Os arquivos Corpus_leis_zh-tkn.txt e Corpus_leis_pt.txt foram gerados a partir do corpus paralelo previamente alinhado "Corpus_aligned_sentences_zh-tkn-pt" (arquivos .xlsx).
DOI: 10.15468/dl.6parxt
title: Occurrence Download

description: A dataset containing 640 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudofumaria lutea",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 640 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016265-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hv76z2
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Australia",
 "OccurrenceStatus is Present",
 "TaxonKey is Thryptomene",
 "Year 2025-2025"
 ]
}

 The dataset includes 57 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016267-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xxdet9
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016266-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18131/bddnx-t8019
title: JulieKim06 Differential Expression.xlsx
DOI: 10.18131/g3-nezj-4v11
title: JulieKim06 Differential Expression.xlsx
DOI: 10.15468/dl.4bf2m6
title: Occurrence Download

description: A dataset containing 26750 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor"
 ]
}

 The dataset includes 26750 records from 442 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016264-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzhwm3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lathyrus jordanii"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016268-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12078070
title: Pre and Post antibiotic epoch: the historical spread of antimicrobial resistance

description: Genome analysis of pre-antibiotic era (PAE) plasmids from the Murray collection and their modern relatives.

 

This Zenodo archive contains data related to our study on the evolution of PAE plasmids and the origin of antimicrobial resistance vectors:

Cazares, A. et al. Pre and Post antibiotic epoch: insights into the historical spread of antimicrobial resistance. (2025).

This archive contains the Murray plasmid assemblies and cytoscape files of the networks presented in our study.

 

Files list:



Murray_plasmids-Illumina_assemblies-files_list.txt: List of 765 Murray plasmid Illumina assemblies

Illumina_assemblies.tar.gz: Sequences of the 765 Murray plasmid Illumina assemblies

Murray_plasmids-hybrid_assemblies-files_list.txt: List of 218 Murray plasmid hybrid assemblies

hybrid_assemblies.tar.gz: Sequences of the 218 Murray plasmid hybrid assemblies

Networks.tar.gz: Compressed directory with the following networks:



PAEModern_plasmids_similarity_network-Illumina_assemblies.cys: Murray plasmids (Illumina assemblies) and close relatives similarity network

Murray_plasmids_containment_network-Illumina_assemblies.cys: Network of Murray plasmids (Illumina assemblies) containment in Modern-CF plasmids

PAEModern_plasmids_similarity_network-hybrid_assemblies.cys: Murray plasmids (hybrid assemblies) and close relatives similarity network

Murray_plasmids_containment_network-hybrid_assemblies.cys: Network of Murray plasmids (hybrid assemblies) containment in Modern-CF plasmids

Integrated_plasmids_database_similarity_network.cys: Similarity network for the dataset of plasmids collected from the public archive




 

NOTE: Refer to the GitHub repository Murray_plasmids for software and code related to this study.
DOI: 10.5281/zenodo.12078071
title: Pre and Post antibiotic epoch: the historical spread of antimicrobial resistance

description: Genome analysis of pre-antibiotic era (PAE) plasmids from the Murray collection and their modern relatives.

 

This Zenodo archive contains data related to our study on the evolution of PAE plasmids and the origin of antimicrobial resistance vectors:

Cazares, A. et al. Pre and Post antibiotic epoch: insights into the historical spread of antimicrobial resistance. (2025).

This archive contains the Murray plasmid assemblies and cytoscape files of the networks presented in our study.

 

Files list:



Murray_plasmids-Illumina_assemblies-files_list.txt: List of 765 Murray plasmid Illumina assemblies

Illumina_assemblies.tar.gz: Sequences of the 765 Murray plasmid Illumina assemblies

Murray_plasmids-hybrid_assemblies-files_list.txt: List of 218 Murray plasmid hybrid assemblies

hybrid_assemblies.tar.gz: Sequences of the 218 Murray plasmid hybrid assemblies

Networks.tar.gz: Compressed directory with the following networks:



PAEModern_plasmids_similarity_network-Illumina_assemblies.cys: Murray plasmids (Illumina assemblies) and close relatives similarity network

Murray_plasmids_containment_network-Illumina_assemblies.cys: Network of Murray plasmids (Illumina assemblies) containment in Modern-CF plasmids

PAEModern_plasmids_similarity_network-hybrid_assemblies.cys: Murray plasmids (hybrid assemblies) and close relatives similarity network

Murray_plasmids_containment_network-hybrid_assemblies.cys: Network of Murray plasmids (hybrid assemblies) containment in Modern-CF plasmids

Integrated_plasmids_database_similarity_network.cys: Similarity network for the dataset of plasmids collected from the public archive




 

NOTE: Refer to the GitHub repository Murray_plasmids for software and code related to this study.
DOI: 10.15468/dl.n2hwsb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Europicardium caparti",
 "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/0016270-250914085247600/datasets/export for details.
DOI: 10.5281/zenodo.13863869
title: Model, Data, and Codes for Kim et al. "Human and Earth System Drivers Jointly Shape Regional and Global Hydropower Futures"

description: Is supplement to Software: https://github.com/gijookim/kim_etal_GCAM_hydropower_SD (URL)
DOI: 10.5281/zenodo.13863868
title: Model, Data, and Codes for Kim et al. "Human and Earth System Drivers Jointly Shape Regional and Global Hydropower Futures"

description: Is supplement to Software: https://github.com/gijookim/kim_etal_GCAM_hydropower_SD (URL)
DOI: 10.15468/dl.yusx7s
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus scrocchii"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016271-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h28kx9
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pyrus syriaca"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016273-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvac77
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudofumaria lutea",
 "Country is Slovakia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016272-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/cnjoz8
title: Phenotypic analysis of petunia plants exposed to chronic drought throughout more than 25 clonal generations

description: This archive reports the data analysis of a 5-year experiment designed to assess whether training petunia plants to drought, through recurrent exposure to water deficit within and across clonal generations (cutting propagation during more than 25 generations), may provide them with transgenerational and adaptive drought memory. The archive contains .xlsx datasets with phenotypic and environmental data, .Rmd scripts for their analysis, and corresponding .html reports.
DOI: 10.25581/ornlsfa.019/1619052
title: Litter Production of Oak-Hickory Forest at Missouri Ozark (MOFLUX) Site: 2003-2022

description: This dataset contains measurements of litter production at the second-growth upland oak-hickory forest at the Missouri Ozark AmeriFlux (MOFLUX) site. The MOFLUX site is located in the University of Missouri Baskett Forest situated in the Ozark Border Region of central Missouri, USA, and is part of the AmeriFlux network (site ID: US-MOz). During 2003, 24 circular vegetation plots (each 0.08 hectares) were established in the MOFLUX forest. The plots were situated 50 meters apart on 5 linear transects radiating out from the flux tower base in southeast, south, southwest, west, and northwest directions—there were 5 plots per transect except for the northwest one, which had only 4 due to the presence of a small pond at the terminus (Fig. 1). Litter measurements were initiated in October 2003 and continue to the present. Data through 2022 are reported in this dataset. On each plot, two subplots were established for the collection of litter. Subplots were setup using a stratified random design to ensure the collectors were not immediately adjacent to one another. Litter collectors were usually emptied at monthly intervals, or less during the autumn leaf drop. Samples were dried to constant mass and then sorted before determining the dry mass of leaf, vegetative and woody litter. These litter data have been valuable in modeling efforts to examine the impacts of intensifying moisture extremes (i.e., moisture excess and deficit conditions) on soil carbon cycling. More recent data will be added periodically with no changes to previously released data or the format and structure of the data file. This dataset contains one data file in comma separate (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.
DOI: 10.15468/dl.xsg3xw
title: Occurrence Download

description: A dataset containing 2589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudofumaria lutea",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2589 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016274-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j83k8p
title: Occurrence Download

description: A dataset containing 11718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudofumaria lutea",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11718 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016275-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfhgdc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Europicardium serrulatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016278-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14916528
title: METL Rosetta datasets

description: This repository contains the biophysical attributes used to pretrain METL-Local and METL-Global models. We provide raw Rosetta data as well as processed Rosetta datasets that have duplicates, outliers, and NaN values removed.

Users of these datasets should cite both METL and Rosetta.

The repository also contains packaged conda environment files needed to generate new Rosetta simulation data in the OSPool with our Jupyter notebook.



Raw Rosetta data

Raw Rosetta data comes in the form of SQLite databases in the .db format. There are separate databases for each of the local datasets as well as the global dataset. Note the GB1-IgG binding raw data only contains the binding scores, whereas the processed GB1-IgG binding dataset listed below contains both the binding and standard scores. The processed dataset was created by combining the raw GB1-IgG binding data with the raw GB1 standard data.



Processed Rosetta datasets




Each processed Rosetta dataset has its own directory containing the following:



The dataset in three formats (.tsv, .db, and .h5 files), all containing the same data

A list of PDB files corresponding to the variants in the dataset (pdb_fns.txt)

A splits directory containing train, validation, and test splits we used for pretraining

Standardization parameters computed on the train set (in the splits directory)


Processed Rosetta datasets can be used directly with the main metl GitHub repository to pretrain models. That repository also contains a small example dataset.

Our metl-pub GitHub repository has a mapping from the dataset names to these filenames and instructions for reading the files.

conda environment files

clean_pdb_2025-02-13.tar.gz and metl-sim_2025-02-13.tar.gz are packaged conda environment files from the metl-sim GitHub repository.
DOI: 10.5281/zenodo.10967412
title: METL Rosetta datasets

description: This repository contains the biophysical attributes used to pretrain METL-Local and METL-Global models. We provide raw Rosetta data as well as processed Rosetta datasets that have duplicates, outliers, and NaN values removed.

Users of these datasets should cite both METL and Rosetta.

The repository also contains packaged conda environment files needed to generate new Rosetta simulation data in the OSPool with our Jupyter notebook.



Raw Rosetta data

Raw Rosetta data comes in the form of SQLite databases in the .db format. There are separate databases for each of the local datasets as well as the global dataset. Note the GB1-IgG binding raw data only contains the binding scores, whereas the processed GB1-IgG binding dataset listed below contains both the binding and standard scores. The processed dataset was created by combining the raw GB1-IgG binding data with the raw GB1 standard data.



Processed Rosetta datasets




Each processed Rosetta dataset has its own directory containing the following:



The dataset in three formats (.tsv, .db, and .h5 files), all containing the same data

A list of PDB files corresponding to the variants in the dataset (pdb_fns.txt)

A splits directory containing train, validation, and test splits we used for pretraining

Standardization parameters computed on the train set (in the splits directory)


Processed Rosetta datasets can be used directly with the main metl GitHub repository to pretrain models. That repository also contains a small example dataset.

Our metl-pub GitHub repository has a mapping from the dataset names to these filenames and instructions for reading the files.

conda environment files

clean_pdb_2025-02-13.tar.gz and metl-sim_2025-02-13.tar.gz are packaged conda environment files from the metl-sim GitHub repository.
DOI: 10.15468/dl.mva795
title: Occurrence Download

description: A dataset containing 41422 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Actaea rubra"
 ]
}

 The dataset includes 41422 records from 355 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016277-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjgwr3
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Limonium malacitanum"
 ]
}

 The dataset includes 144 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016279-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kaz5dn
title: Occurrence Download

description: A dataset containing 711 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phrynosoma asio"
 ]
}

 The dataset includes 711 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016281-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8ayszc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Roemeria refracta",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016285-250914085247600/datasets/export for details.
DOI: 10.15468/dl.5tc7ad
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Roemeria refracta",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016286-250914085247600/datasets/export for details.