cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14532347
title: Multi-omics for Understanding Climate Change (MUCC) database v2.0.0

description: This is the Multi-omics for Understanding Climate Change (MUCC database) version 2.0.0. This current version is based on amplicon and metagenomic sequencing of Old Woman Creek (OWC), Prairie Pothole Region(PPR7 and PPR8), Jean Lafitte National Historical Park and Preserve (JLA), AmeriFlux site US-LA2 (LA2), Stordalen Mire (STM-fen and STM-bog), AmeriFlux site-ID US-Twt (TWI), and Peatland Responses Under Changing Environments (SPRUCE) and wetland soils. Additionally, this includes metatranscriptome sequencing from OWC. In the future, this will be expanded to include more data from these sites and from additional wetlands.

OWC, PPR, JLA and LA2 data are deposited in NCBI Bioproject PRJNA1007388

Stordalen Mire MAGs are deposited in BioProject PRJNA386538

AmeriFlux site-ID US-Twt are deposited in SRA SRP003022, SRA SRP010671, SRP010730, SRP010738, SRP010741, SRP010747, SRP010748, SRP010751, SRP010862, SRP010870, and SRP011309. 

SPRUCE data are deposited in PRJNA638786 and PRJNA638601

 

Files and datasets included here: 



16S.zip 16S amplicon sequencing data and site metadata for 1,112 samples (fastq files)

MQ_HQ_MAGs.zip Database of 4745 Medium and High Quality MAGs (fasta files)

MUCC_v2.0.0_HQMQ_genes.faa.zip MAG amino acid gene sequences derived from DRAM gene calls (fasta file)

MUCC_v2.0.0_HQMQ_annotations.tsv MAG DRAM ANNOTATIONS

owc_metat_table_methanoregula_genes.csv Metatranscriptomic expression per genes in Methanoregula across 133 metatranscriptomes (csv table)

gtdbtk.ar53.decorated.tree newick file for GTDB de novo work flow Methanoregula MAG tree

Newick_gene_trees.zip Trees used in blast identification of methylotrophic gene homologs to curate MR for methylotrophy

fasta_reference_genes.zip FASTA reference files of genes used as BLAST query to mine Methanoregula MAGs for genes involved in detoxification of reactive oxygen species (ROS) and methanogenic metabolism of methylated compounds

protpipeliner.py Python script is a modification of protpipeliner.rb for building RAXML trees

classification_w_outgroup.txt Taxonomy and corresponding MAG ID for Methanregula used in the tree (Figure 5B)

Methanoregula_metabolism_summary.xlsx The DRAM annotations of the Methanoregula MAGs from MUCC, GTDB, and JGI

Methanoregula_physiology.txt Curation of Methanoregula MAGS for physliogical functions of interest

Methanoregula_MAGs_list.txt Comprehensive list of all Methanoregula MAGs used and what database they were sourced from

Methanoregula_MAGs_DB.zip Database of 108 Methanregula MAGs
DOI: 10.15468/dl.hxgptj
title: Occurrence Download

description: A dataset containing 21862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pogonias cromis (Linnaeus, 1766)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 21862 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042374-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.svawwh
title: Occurrence Download

description: A dataset containing 4904 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dreissena polymorpha (Pallas, 1771)",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 4904 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042375-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mu6na
title: Occurrence Download

description: A dataset containing 15774 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pollachius pollachius (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 15774 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042376-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d322xt
title: Occurrence Download

description: A dataset containing 666680 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oryctolagus cuniculus (Linnaeus, 1758)"
 ]
}

 The dataset includes 666680 records from 2881 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042365-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4zcbx4
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bemisia tabaci (Gennadius, 1889)"
 ]
}

 The dataset includes 273 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0225771-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cwcxf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Subantarctic Fur sealsat Heard Island, 1987/88"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180500-200613084148143/datasets/export for details.
DOI: 10.15468/dl.4dteyp
title: Occurrence Download

description: A dataset containing 3700 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phellodendron amurense Rupr."
 ]
}

 The dataset includes 3700 records from 166 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0268577-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48px4n
title: Occurrence Download

description: A dataset containing 919 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Catonephele numilia esite Felder, 1869"
 ]
}

 The dataset includes 919 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049637-240506114902167/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.17205713
title: 10 years of decision-making for biodiversity conservation actions: A systematic literature review

description: Data and code to produce figures in manuscript submitted to Conservation Biology:<br>data_decision_examples_with_years.csv: data for all main figures<br>authors.csv: cleaned list of authors to produce network figures in supplementary material<br>interrater_data_lit_review.csv: data to produce figure on inter-rater-reliability in supplementary material<br>chapter1_clean_plots....R: code to wrangle data and produce all figures<br>Short summary of project:Decision-science highlights criteria that enable robust planning and which, if utilized during planning of conservation actions, can increase chances to achieve conservation aims. Five such criteria are 1) a quantifiable objective, 2) a clear assumption about the impact of available actions, 3) consideration of constraints, 4) exploring uncertainty, and 5) deliberation on trade-offs. This review quantified the extent to which these five criteria were utilized in published examples of conservation planning in academic and applied context. Less than 50% of identified examples included all five criteria, with differences between five frequently used decision-aiding frameworks: Adaptive Management, Systematic Conservation Planning, Structured Decision Making, Multi-Criteria-Decision-Analysis and Cost-Effectiveness Analysis. Examples using Structured Decision Making were limited in numbers but had more than 50% uptake of all criteria from the field of decision science. Although Systematic Conservation Planning and Adaptive Management provided the vast majority of examples, they appear to be more prevalent in academic contexts than in real-world management plans, and examples using Adaptive Management had only 7% uptake of all criteria. While academic examples of best practice planning that include all five important criteria exist for many countries around the world, best practice examples of real-world planning were almost exclusively located in the United States and Australia.All data and code used in this project are available here.
DOI: 10.6084/m9.figshare.17205713.v2
title: 10 years of decision-making for biodiversity conservation actions: A systematic literature review

description: Data and code to produce figures in manuscript submitted to Conservation Biology:<br>data_decision_examples_with_years.csv: data for all main figures<br>authors.csv: cleaned list of authors to produce network figures in supplementary material<br>interrater_data_lit_review.csv: data to produce figure on inter-rater-reliability in supplementary material<br>chapter1_clean_plots....R: code to wrangle data and produce all figures<br>Short summary of project:Decision-science highlights criteria that enable robust planning and which, if utilized during planning of conservation actions, can increase chances to achieve conservation aims. Five such criteria are 1) a quantifiable objective, 2) a clear assumption about the impact of available actions, 3) consideration of constraints, 4) exploring uncertainty, and 5) deliberation on trade-offs. This review quantified the extent to which these five criteria were utilized in published examples of conservation planning in academic and applied context. Less than 50% of identified examples included all five criteria, with differences between five frequently used decision-aiding frameworks: Adaptive Management, Systematic Conservation Planning, Structured Decision Making, Multi-Criteria-Decision-Analysis and Cost-Effectiveness Analysis. Examples using Structured Decision Making were limited in numbers but had more than 50% uptake of all criteria from the field of decision science. Although Systematic Conservation Planning and Adaptive Management provided the vast majority of examples, they appear to be more prevalent in academic contexts than in real-world management plans, and examples using Adaptive Management had only 7% uptake of all criteria. While academic examples of best practice planning that include all five important criteria exist for many countries around the world, best practice examples of real-world planning were almost exclusively located in the United States and Australia.All data and code used in this project are available here.
DOI: 10.15468/dl.vlldxk
title: Occurrence Download

description: A dataset containing 2998 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Brazil",
 "Country is Colombia",
 "Country is South Africa",
 "Country is Benin"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Eichhornia crassipes (Mart.) Solms",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2998 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016566-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuxk9f
title: Occurrence Download

description: A dataset containing 4132 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rana draytonii Baird & Girard, 1852"
 ]
}

 The dataset includes 4132 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214541-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rwpz9j
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Koelreuteria paniculata Laxm."
 ]
}

 The dataset includes 16 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270333-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fabq33
title: Occurrence Download

description: A dataset containing 8837 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pusa hispida (Schreber, 1775)"
 ]
}

 The dataset includes 8837 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0189647-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17248245
title: sentiwordnet_it 1.0

description: This repository contains a sentiment lexicon for Italian, based on SentiWordNet 3.0 (Baccianella, Esuli, and Sebastiani 2010; Esuli [2019] 2025) and MultiWordNet (Pianta, Bentivogli, and Girardi 2002). 

Unlike previous resources—SentiWordNet, which provides sentiment scores without Italian lexical coverage, and MultiWordNet, which offers Italian synsets without sentiment annotation—this dataset bridges the two by mapping Italian lexical entries to sentiment scores in a ready-to-use CSV format.

This integration enables direct use in sentiment analysis and other NLP applications for Italian, filling a gap in existing resources.

The included files, in the data/ folder are:



swn_it.csv: A dataset of 35,001 Italian synsets with polarity scores, POS, synset, offset, English synset lemmas, and gloss (in English).

swn_it_tidy.csv: A tidy (one token per row) dataset of 41,725 lemmas, with polarity scores. It is designed for use in R.


It also contains a folder with examples in R, and scripts to use and manipulate the datasets:



examples-R/:



custom_dataset.R: Create a custom tidy dataset from the original one, for treating duplicate entries differently.

example.R: Examples of how to use the dataset for sentiment analysis on a sample text.

uso.md: Instructions for using the dataset in R (in Italian), referred to in example.R.
DOI: 10.15468/dl.r657bd
title: Occurrence Download

description: A dataset containing 182828 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Viola arvensis Murray"
 ]
}

 The dataset includes 182828 records from 636 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211900-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xgbfnh
title: Occurrence Download

description: A dataset containing 5237771 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5237771 records from 383 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024936-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vptryc
title: Occurrence Download

description: A dataset containing 129360 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hippocrepis comosa L."
 ]
}

 The dataset includes 129360 records from 391 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211259-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jyiz5a
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Junonia lemonias (Linnaeus, 1758)"
 ]
}

 The dataset includes 295 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024936-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcvkzc
title: Occurrence Download

description: A dataset containing 990 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Viola ambigua Waldst. & Kit."
 ]
}

 The dataset includes 990 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211896-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.am5dgn
title: Occurrence Download

description: A dataset containing 1015 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Junonia hierta Fabricius, 1798"
 ]
}

 The dataset includes 1015 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024937-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g98d76
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apium inundatum Linnaeus, 1753"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211237-200613084148143/datasets/export for details.
DOI: 10.15468/dl.gns3hb
title: Occurrence Download

description: A dataset containing 11363104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11363104 records from 2777 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211905-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rj7ke6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, 197288244, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, 199476485, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, Caracanthidae, 161421530, Caracanthidae Gill, 1885)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((105.5 17,110.5 17,110.5 22,105.5 22,105.5 17))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239537-220831081235567/datasets/export for details.
DOI: 10.25549/inscriptifact-ouc111304929
title: The Church of the Holy Cross, Timios Stavros, Pelendria

description: [Text Description:] A complex church in Pelendri dedicated to the Holy Cross, 12th c. ❧ [Medium:] Stone ❧ [Script Note:] Greek, Non-Text ❧ [Physical Object Description:] Located in Pelendri. Originally a single-aisled domed building with arched recesses in the side walls. ❧ [Physical Object Note:] In the 14th c. it was extended to the north. A similar aisle was added to the south probably in 16th c. ❧ [Physical Object Note:] Built and painted in the 12th c., and repainted in the 14th-15th centuries. ❧
DOI: 10.15468/dl.2ycgb7
title: Occurrence Download

description: A dataset containing 373 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bothrops atrox (Linnaeus, 1758)"
 ]
}

 The dataset includes 373 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039434-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111134097
title: Tribute-Bearers and Camels in Upper Register from the Southwest Wall of the Corridor (Room 10), OI A7362

description: [Text Description:] Five tribute bearers following a man driving three camels. ❧ [Text or Publication Number Note:] OI A7362 ❧ [Excavation Description:] Found during Oriental Institute's 1928-1935 excavations at the site of ancient Dur-Sharrukin (Fort Sargon), modern Khorsabad, Iraq ❧ [Medium:] Stone ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Stone bas relief, of limestone. Rectangular. Fragment of inscription on bottom left. ❧ [Physical Object Note:] 3.307 m x 1.65 m
DOI: 10.15468/dl.xp6eyh
title: Occurrence Download

description: A dataset containing 3276 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Charadrius nivosus nivosus"
 ]
}

 The dataset includes 3276 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237191-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mtwbyj
title: Occurrence Download

description: A dataset containing 631 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cordia africana Lam.",
 "Year 1900-2020"
 ]
}

 The dataset includes 631 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035822-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111134244
title: Tribute-Bearers and Camels in Upper Register from the Southwest Wall of the Corridor (Room 10), OI A7362

description: [Text Description:] Five tribute bearers following a man driving three camels. ❧ [Text or Publication Number Note:] OI A7362 ❧ [Excavation Description:] Found during Oriental Institute's 1928-1935 excavations at the site of ancient Dur-Sharrukin (Fort Sargon), modern Khorsabad, Iraq ❧ [Medium:] Stone ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Stone bas relief, of limestone. Rectangular. Fragment of inscription on bottom left. ❧ [Physical Object Note:] 3.307 m x 1.65 m
DOI: 10.15468/dl.lrhqmp
title: Occurrence Download

description: A dataset containing 141 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Atlas communaux de la Biodiversité du Parc Naturel Régional des Landes de Gascogne (PNRLG)-Inventaire des amphibiens 2014"
 ]
}

 The dataset includes 141 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016905-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.