cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1171375.10fu
title: SH1171375.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1171384.10fu
title: SH1171384.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1171387.10fu
title: SH1171387.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1171391.10fu
title: SH1171391.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1171398.10fu
title: SH1171398.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1171400.10fu
title: SH1171400.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.z85nz5
title: Occurrence Download

description: A dataset containing 2540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-73.95809 40.80085,-73.98208 40.76804,-73.97309 40.76411,-73.94898 40.79686,-73.95809 40.80085))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sciurus carolinensis"
 ]
}

 The dataset includes 2540 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061751-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17296470
title: Corpus prensa Construcción discursiva del Día Internacional de la Mujer a través del Paisaje Lingüístico y de la prensa
DOI: 10.5281/zenodo.17296471
title: Corpus prensa Construcción discursiva del Día Internacional de la Mujer a través del Paisaje Lingüístico y de la prensa
DOI: 10.6084/m9.figshare.28624573.v1
title: Genomic characterisation of invasive <i>Neisseria meningitidis</i> in Spain (2011/12-2022/23): Expansion of clonal complex 213 and the potential threat to 4CMenB vaccine strain coverage.

description: Invasive meningococcal disease (IMD) is associated with significant global morbidity and mortality and is addressed by conjugated polysaccharide and subcapsular vaccines. In Spain, data on 4CMenB vaccine strain coverage and antimicrobial susceptibility are limited. This study aimed to describe the genomic epidemiology, predict 4CMenB vaccine strain coverage, and assess antimicrobial susceptibility of 323 <i>Neisseria meningitidis</i> isolates causing IMD, collected from 57 Clinical Microbiology Laboratories in Spain over 12 years (2011/12-2022/23). Whole genome sequencing was performed to identify serogroup, clonal complex (cc), and antimicrobial resistance determinants. Vaccine strain coverage for serogroup B (MenB) isolates was predicted using the genetic Meningococcal Antigen Typing System approach. The most prevalent serogroups were B (57.9%), W (21.4%), C (10.4%), and Y (8.4%). MenB predominated throughout most seasons, except during the 2019/20 season when serogroup W peaked. Post-COVID-19 pandemic, MenB remained the most frequent (70.2%). Thirteen cc were identified among MenB isolates, with cc213 being the most prevalent (40.1%). Only 28.9% of MenB isolates were predicted to be covered by 4CMenB, with cc213 showing an exceptionally low coverage rate (5.3%) due to antigenic variants poorly targeted by the vaccine. Notably, cc213 was responsible for twice the proportion of MenB cases in 4CMenB-vaccinated versus unvaccinated. All isolates were susceptible to third generation cephalosporins, and 13.5% showed penicillin resistance. This study highlights the alarming prevalence of cc213 among MenB IMD cases in Spain and the limited 4CMenB coverage against this cc. The disproportionate representation of cc213 in vaccinated individuals underscores its potential to compromise vaccine effectiveness.
DOI: 10.5281/zenodo.15095844
title: GOPREDSIM Embeddings Adapted to FANTASIA v2

description: This file, embeddings_fantasia_gopredsim_2022.dump, is a PostgreSQL custom-format dump containing a comprehensive relational database. It was generated from the massive TOPGO data provided by the goPredSim project and includes data for 309,278 protein entries along with 2,243,531 annotations, as verified against the original TOPGO file.

In addition, the database incorporates a mechanism developed by our team for generating protein embeddings using the Rostlab/prot_t5_xl_uniref50 model into a relational database supporting vectors. To utilize this dump within Fantasia, simply configure the embeddings_url parameter with the URL of this Zenodo file. Fantasia’s containerized environment fully supports this process through the initialize command, which sets up the necessary database structure and loads the dump automatically.

Restoration Instructions

To load this dump into PostgreSQL, you must use pg_restore v16 or higher. Ensure database is clean and run the following command:



pg_restore -U usuario -h localhost -p 5432 -d BioData ./embeddings_fantasia_gopredsim_2022.dump


Caution: The restoration process requires pg_restore version 16 (or higher) to ensure full compatibility with all database structures contained in this dump.
DOI: 10.5281/zenodo.15095845
title: GOPREDSIM Embeddings Adapted to FANTASIA v2

description: This file, embeddings_fantasia_gopredsim_2022.dump, is a PostgreSQL custom-format dump containing a comprehensive relational database. It was generated from the massive TOPGO data provided by the goPredSim project and includes data for 309,278 protein entries along with 2,243,531 annotations, as verified against the original TOPGO file.

In addition, the database incorporates a mechanism developed by our team for generating protein embeddings using the Rostlab/prot_t5_xl_uniref50 model into a relational database supporting vectors. To utilize this dump within Fantasia, simply configure the embeddings_url parameter with the URL of this Zenodo file. Fantasia’s containerized environment fully supports this process through the initialize command, which sets up the necessary database structure and loads the dump automatically.

Restoration Instructions

To load this dump into PostgreSQL, you must use pg_restore v16 or higher. Ensure database is clean and run the following command:



pg_restore -U usuario -h localhost -p 5432 -d BioData ./embeddings_fantasia_gopredsim_2022.dump


Caution: The restoration process requires pg_restore version 16 (or higher) to ensure full compatibility with all database structures contained in this dump.
DOI: 10.18150/pjgpud
title: Antioxidant activity and iodine and thiamine content in Gnocchi-type dumplings and Ciabatta-type rolls with the addition of iodine-fortified dried carrots, pumpkins, broccoli, cauliflower and beetroots

description: Iodine content (mg kg−1), thiamine (mg kg−1), antioxidant activity tested in ABTS and DPPH tests (mg Trolox/100g dry extract mass) measured in food products such as Gnocchi dumplings and Ciabatta rolls with the addition of iodine-fortified vegetables (pumpkin, broccoli, cauliflower, beetroot, carrot), tested after preparation (raw dough), heat treatment and storage. Heat treatment of Ciabatta rolls is baking, and for Gnocchi dumplings, it is boiling in water. Storage conditions for Ciabatta rolls are 21C/8 days and -21C/100 days and for Gnocchi dumplings -21C/100 days.
DOI: 10.15468/dl.w4kn6y
title: Occurrence Download

description: A dataset containing 57291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphorbia esula L."
 ]
}

 The dataset includes 57291 records from 609 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003878-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bv3qvv
title: Occurrence Download

description: A dataset containing 618 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-36.02201 33.10628,-20.46882 33.10628,-20.46882 42.85134,-36.02201 42.85134,-36.02201 33.10628))",
 "TaxonKey is Chaerophyllum azoricum Trel.",
 "Year 1975-2025"
 ]
}

 The dataset includes 618 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003892-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/c3uhbs
title: Research data for: Quantum-inspired evolutionary optimization of SLMoS2 two-phase structures

description: Research data for paper Quantum-inspired evolutionary optimization of SLMoS2 two-phase structures
DOI: 10.15468/dl.uph4az
title: Occurrence Download

description: A dataset containing 15032 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "Country is Germany",
 "License is CC-BY 4.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Bromus erectus Huds.",
 "Year 1970-2000"
 ]
}

 The dataset includes 15032 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003894-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5rr4ec
title: Occurrence Download

description: A dataset containing 640 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "TaxonKey is Artocarpus altilis (Parkinson) Fosberg",
 "Year 1991-2020"
 ]
}

 The dataset includes 640 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003896-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hj4f7
title: Occurrence Download

description: A dataset containing 3118 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gonioctena quinquepunctata (Fabricius, 1787)"
 ]
}

 The dataset includes 3118 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003897-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hd5z8c
title: Occurrence Download

description: A dataset containing 39876 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is VMM - Rat control occurrences in Flanders, Belgium"
 ]
}

 The dataset includes 39876 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003895-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p9wdazip
title: Hydroacoustic data from central Lake Erie, 2010-2019

description: Hydroacoustic estimates of fish density are used for fisheries management in central Lake Erie. Hydroacoustic data were collected along up to four cross-lake transects in central Lake Erie July 2010 through July 2019. Software-generated raw variables used for calculating estimates of hydroacoustic fish densities are presented here.
DOI: 10.5066/p9yan7vt
title: Hydroacoustic data from central Lake Erie, 2020

description: Hydroacoustic estimates of fish density are used for fisheries management in central Lake Erie. Hydroacoustic data were collected along 8, randomly-selected, 5-kilometer transects and three transects between the US shore and the international border in central Lake Erie in July 2020. Software-generated raw variables used for calculating estimates of hydroacoustic fish densities are presented here. These data are related to a longer-term data set from 2010-2019.
DOI: 10.6084/m9.figshare.28673471
title: pangenome analysis

description: This repository contains data and scripts used for pangenome analysis in the paper 'Characterization of <i>Mycobacterium antarcticum</i> sp. nov., a psychrotolerant member of the genus <i>Mycobacterium</i> isolated from Antarctic soil'.
DOI: 10.6084/m9.figshare.28673471.v1
title: pangenome analysis

description: This repository contains data and scripts used for pangenome analysis in the paper 'Characterization of <i>Mycobacterium antarcticum</i> sp. nov., a psychrotolerant member of the genus <i>Mycobacterium</i> isolated from Antarctic soil'.
DOI: 10.5066/p9s2nftp
title: Hydroacoustic data from central Lake Erie, 2021

description: Hydroacoustic estimates of fish density are used for fisheries management in central Lake Erie. Hydroacoustic data were collected along 10, randomly-selected, 5-kilometer transects and two cross-basin transects between the US and Canadian shorelines in central Lake Erie during July 2021. Software-generated raw variables were used for calculating estimates of hydroacoustic fish densities presented here in tabular form. These data are related to a longer-term data set from 2010-2019, and a data set from 2020.
DOI: 10.5066/p13ymgsu
title: Lake Erie Pelagic Prey Fish Community Data, 2022-2023

description: Since 2005, the U.S. Geological Survey - Great Lakes Science Center's Lake Erie Biological Station (LEBS) has participated in a collaborative, multiagency effort to assess pelagic prey fish populations in the western (WB), central (CB), and eastern (EB) basins of Lake Erie through a combination of hydroacoustic and midwater trawl sampling. Assessing lake-wide distribution and abundance of pelagic prey species over time facilitates evaluation of large-scale drivers of fish production while also considering food-web dynamics at a smaller sub-basin scale. Information from this survey will support decision making within an ecosystem-based fishery management framework. In support of binational Great Lakes fishery management, the objectives of this survey are to provide density estimates of key pelagic prey species across Lake Erie, to assess spatial distributions of fishes, and annual fluctuations in abundance. A stratified-random sampling approach including 24 strata was carried out during July (Summer), starting in 2022. This data release adds 2023 data to the set for a total of 2 years using the standardized survey design and data processing workflow.
DOI: 10.15468/dl.tfgw8f
title: Occurrence Download

description: A dataset containing 866928 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Depth is greater than 200m",
 "BasisOfRecord is Machine Observation",
 "HasGeospatialIssue is FALSE",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 866928 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003891-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15085843
title: Data for "Classification and Evolution of CRISPR systems: Discoveries in the Tail of the Distribution"
DOI: 10.5066/p14hmdbt
title: Grass Carp (Ctenopharyngodon idella) Egg Diameter Estimates from the Huron River (Ohio), 2022

description: These data include egg diameter estimates from Grass Carp (Ctenopharyngodon idella) eggs collected during bongo net sampling in the Huron River (Ohio; 41.3305, -82.5812) on May 23, 2022 near Milan, Ohio. Egg diameters were estimated from photographs using proportional relationships of pixel lengths with a known length scale bar in millimeters. Given that eggs were not perfectly spherical, egg diameters were measured across two perpendicular axes and an average was calculated to represent an estimate of egg diameter (mm).
DOI: 10.5066/p98f9nsz
title: Grass Carp (Ctenopharyngodon idella) egg capture data from Great Lakes tributaries, 2021-2022 (ver. 1.1, November 2023)

description: The data includes dates, places, and times of sampling events for eggs of invasive Grass Carp (Ctenopharyngodon idella) in tributaries to the Great Lakes in 2021 and 2022. Reference data on locations and dates sampled, gears used, and effort are included. Developmental stages for a subset of undamaged, fertilized eggs are provided. Tables include common fields to allow for integration into a relational database to aid data extraction and associating data among tables.
DOI: 10.15468/dl.43khrf
title: Occurrence Download

description: A dataset containing 509 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centrochelys sulcata (Miller, 1779)"
 ]
}

 The dataset includes 509 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003899-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18167/dvn1/p0pmd3
title: "Grand Plateau" permanent plots second census, 2000-01, Nouragues forest

description: Forest censuses from the Nouragues research station, CNRS, French Guiana, in the Guyafor network. This dataset gathered trees location, botanical identification and size measurement from the 2000-01 census. The mission of the Nouragues research Station is to foster scientific research in tropical rain forests, at a site remote from major human activities. Guyafor Data Dictionary
DOI: 10.5281/zenodo.15025599
title: CHIRPS Daily Precipitation for Boeotikos Kifissos River Basin

description: Contains data from Climate Hazards Center InfraRed Precipitation with Station data (CHIRPS) precipitation dataset. CHIRPS integrates 0.05° resolution satellite imagery with ground station data to generate gridded rainfall time series.

The datacude includes daily precipitation measurements from 01-Oct-2019 to 30-Sep-2021 for the Boeotikos Kifissos river basin.

 

 



Dimentions:



time: 1096

latitude: 9

longitude: 19



Data variables: (time, latitude, longitude)

Size: 759kB


Dimensions: (time: 1096, latitude: 9, longitude: 19)