cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29908439.v3
title: Supplementary information-Recent Advances in TROPOMI-Based Methane Source Detection: A Systematic Review

description: This spreadsheet contains data for a review paper on TROPOMI-based methane source detection
DOI: 10.18419/darus-5711
title: Atmospheric transmission models for FIFI-LS: altitude 40kft, 39deg O3

description: &lt;p&gt;This dataset contains atmospheric transmission models calculated by a modified version of ATRAN ("SDC ATRAN"). They are to be used as the default models for FIFI-LS data reduction with &lt;a href="https://github.com/SOFIA-Data-Center/sofia_redux"&gt;SOFIA Redux&lt;/a&gt;
&lt;/p&gt;&lt;p&gt;
The models are generated from a modified "SDC ATRAN" model based on Steve Lord's ATRAN. The most significant modification is a correction of &lt;sup&gt;17&lt;/sup&gt;O&lt;sup&gt;16&lt;/sup&gt;O isotopologue abundance coefficients.
&lt;/p&gt;&lt;p&gt;
The models are stored in FITS binary table format with the columns "wavelength" and "transmission". All models of the same altitude (and same wavelength range) have the same number of wavelength elements.
&lt;/p&gt;&lt;p&gt;
File naming convention:
&lt;pre&gt;
atran_sdc_xxK_yydeg_zzpwv_39deg_2nlayer_40-300mum_bt.fits
&lt;/pre&gt;
where &lt;i&gt;xx&lt;/i&gt; is the flight altitude in kft, &lt;i&gt;yy&lt;/i&gt; is the zenith angle in degree, and &lt;i&gt;zz&lt;/i&gt; the
precipitable water vapor value in micron.
&lt;/p&gt;&lt;p&gt;
This dataset contains models calculated for a 2 layer atmospheric model with an ozone profile identified by "39deg".&lt;/p&gt;
DOI: 10.15468/dl.mqt6jv
title: Occurrence Download

description: A dataset containing 1175 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ecclisopteryx guttulata"
 ]
}

 The dataset includes 1175 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003827-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2xpqyf
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Observation.org, Nature data from around the World",
 "Geometry POLYGON((6.90007 51.31101,6.89946 51.29631,6.91733 51.29563,6.91777 51.31289,6.90851 51.31294,6.90007 51.31299,6.90007 51.31101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 145 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003830-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18712995
title: quercusTOA database: Integrating functional annotations and comparative genomics across oak lineages

description: ·

QuercusTOA is a comprehensive database integrating curated records of Quercus proteins with taxonomic, functional, and structural information. It provides a robust framework for comparative genomics and functional analysis across several oak species and model organisms.

The database is organized into three core datasets:





Sequence Dataset: Contains genomic and proteomic data for Q. suber, Q. robur, Q. lobata, Q. rubra, Q. variabilis, Q. dentata, Q. gilva, Q. longispica, and Q. acutissima. Data were integrated from NCBI, CNCB-NGDC, TAIR10, and CANTATA lncRNA databases using the NGShelper toolset.




Comparative Genomics Dataset: Features gene and CDS relationships established via MMseqs2 clustering and Liftoff. It includes homology mapping between Quercus species and cross-species protein relationships.




Functional Annotation Dataset: Provides high-quality consensus sequences (validated by BUSCO) and annotations derived from InterProScan and eggNOG-mapper. It also includes A. thaliana orthologs and BLAST+/Diamond databases for rapid sequence search.



Access A dynamic version of QuercusTOA is hosted by CESVIMA (UPM) and can be accessed via the official website or the QUERCUSTOA-APP.
DOI: 10.5281/zenodo.18712996
title: quercusTOA database: Integrating functional annotations and comparative genomics across oak lineages

description: ·

QuercusTOA is a comprehensive database integrating curated records of Quercus proteins with taxonomic, functional, and structural information. It provides a robust framework for comparative genomics and functional analysis across several oak species and model organisms.

The database is organized into three core datasets:





Sequence Dataset: Contains genomic and proteomic data for Q. suber, Q. robur, Q. lobata, Q. rubra, Q. variabilis, Q. dentata, Q. gilva, Q. longispica, and Q. acutissima. Data were integrated from NCBI, CNCB-NGDC, TAIR10, and CANTATA lncRNA databases using the NGShelper toolset.




Comparative Genomics Dataset: Features gene and CDS relationships established via MMseqs2 clustering and Liftoff. It includes homology mapping between Quercus species and cross-species protein relationships.




Functional Annotation Dataset: Provides high-quality consensus sequences (validated by BUSCO) and annotations derived from InterProScan and eggNOG-mapper. It also includes A. thaliana orthologs and BLAST+/Diamond databases for rapid sequence search.



Access A dynamic version of QuercusTOA is hosted by CESVIMA (UPM) and can be accessed via the official website or the QUERCUSTOA-APP.
DOI: 10.18419/darus-5708
title: Atmospheric transmission models for FIFI-LS: altitude 37kft, 39deg O3

description: &lt;p&gt;This dataset contains atmospheric transmission models calculated by a modified version of ATRAN ("SDC ATRAN"). They are to be used as the default models for FIFI-LS data reduction with &lt;a href="https://github.com/SOFIA-Data-Center/sofia_redux"&gt;SOFIA Redux&lt;/a&gt;
&lt;/p&gt;&lt;p&gt;
The models are generated from a modified "SDC ATRAN" model based on Steve Lord's ATRAN. The most significant modification is a correction of &lt;sup&gt;17&lt;/sup&gt;O&lt;sup&gt;16&lt;/sup&gt;O isotopologue abundance coefficients.
&lt;/p&gt;&lt;p&gt;
The models are stored in FITS binary table format with the columns "wavelength" and "transmission". All models of the same altitude (and same wavelength range) have the same number of wavelength elements.
&lt;/p&gt;&lt;p&gt;
File naming convention:
&lt;pre&gt;
atran_sdc_xxK_yydeg_zzpwv_39deg_2nlayer_40-300mum_bt.fits
&lt;/pre&gt;
where &lt;i&gt;xx&lt;/i&gt; is the flight altitude in kft, &lt;i&gt;yy&lt;/i&gt; is the zenith angle in degree, and &lt;i&gt;zz&lt;/i&gt; the
precipitable water vapor value in micron.
&lt;/p&gt;&lt;p&gt;
This dataset contains models calculated for a 2 layer atmospheric model with an ozone profile identified by "39deg".&lt;/p&gt;
DOI: 10.15468/dl.aw6xwk
title: Occurrence Download

description: A dataset containing 41501 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de Tejidos del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-CT)"
 ]
}

 The dataset includes 41501 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003828-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p7m56d
title: Occurrence Download

description: A dataset containing 29241 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemiramphus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 29241 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003829-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1397366.10fu
title: SH1397366.10FU

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/sh1397367.10fu
title: SH1397367.10FU

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/sh1397368.10fu
title: SH1397368.10FU

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/sh1397371.10fu
title: SH1397371.10FU

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/sh1397372.10fu
title: SH1397372.10FU

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/sh1397374.10fu
title: SH1397374.10FU

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/sh1397378.10fu
title: SH1397378.10FU

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/sh1397380.10fu
title: SH1397380.10FU

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/sh1397382.10fu
title: SH1397382.10FU

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/sh1397386.10fu
title: SH1397386.10FU

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.cm3arr
title: Occurrence Download

description: A dataset containing 7232 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Boa constrictor Linnaeus, 1758"
 ]
}

 The dataset includes 7232 records from 318 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007451-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whpdk6
title: Occurrence Download

description: A dataset containing 1326 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Veronica laxa"
 ]
}

 The dataset includes 1326 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005546-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkvxuf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Setophaga pensylvanica)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005548-250717081556266/datasets/export for details.
DOI: 10.20350/digitalcsic/17434
title: DATASET A complex and dynamic redox network regulates oxygen reduction at photosystem I in Arabidopsis

description: Chemicals and CAS Registry Numbers nicotinamide adenine dinucleotide phosphate 53-59-8 oxygen 7782-44-7 thioredoxin 52500-60-4 Arabidopsis Proteins NADP Oxygen Photosystem I Protein Complex Reactive Oxygen Species Thioredoxins
description: Thiol-dependent redox regulation of enzyme activities plays a central role in regulating photosynthesis. Besides the regulation of metabolic pathways, alternative electron transport is subjected to thiol-dependent regulation. We investigated the regulation of O2 reduction at photosystem I. The level of O2 reduction in leaves and isolated thylakoid membranes depends on the photoperiod in which plants are grown. We used a set of Arabidopsis (Arabidopsis thaliana) mutant plants affected in the stromal, membrane, and lumenal thiol network to study the redox protein partners involved in regulating O2 reduction. Light-dependent O2 reduction was determined in leaves and thylakoids of plants grown in short-day and long-day conditions using a spin-trapping electron paramagnetic resonance assay. In wild-type samples from short-day conditions, reactive oxygen species generation was double that of samples from long-day conditions, while this difference was abolished in several redoxin mutants. An in vitro reconstitution assay showed that thioredoxin m, NADPH-thioredoxin reductase C, and NADPH are required for high O2-reduction levels in thylakoids from plants grown in long-day conditions. Using isolated photosystem I, we also showed that reduction of a photosystem I protein is responsible for the increase in O2 reduction. Furthermore, differences in the membrane localization of m-type thioredoxins and 2-Cys peroxiredoxin were detected between thylakoids of short-day and long-day plants. Overall, we propose a model of redox regulation of O2 reduction according to the reduction power of the stroma and the ability of different thiol-containing proteins to form a network of redox interactions.