cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1397472.10fu
title: SH1397472.10FU

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/sh1397479.10fu
title: SH1397479.10FU

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/sh1397483.10fu
title: SH1397483.10FU

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/sh1397485.10fu
title: SH1397485.10FU

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/sh1397490.10fu
title: SH1397490.10FU

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/sh1397494.10fu
title: SH1397494.10FU

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/sh1397495.10fu
title: SH1397495.10FU

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/sh1397501.10fu
title: SH1397501.10FU

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/sh1397514.10fu
title: SH1397514.10FU

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.396yfh
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sorbus glabriuscula)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1981",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))"
 ]
}

 The dataset includes 16 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006080-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1397536.10fu
title: SH1397536.10FU

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: 10.5281/zenodo.16023626
title: active_sites v1.0: enzyme domain sequences with annotated active sites from Pfam v37.1 for benchmarking MSA tools

description: This dataset contains 772 enzyme domain families annotated with 1,376 active sites in Pfam v37.1.

Protein sequences containing Pfam domains were retrieved from UniProt, and active site residues were predicted using Pfam’s pfam_scan.pl tool v1.626 together with the active site database active_site.dat v37.1. For each protein, only the sequence corresponding to the annotated domain was extracted from the full-length protein sequence Domain sequences were excluded if: the annotated domain was shorter than 25% of the length of the corresponding Pfam HMM model, or more than 10% of residues were non-standard amino acids.

Directory structure

The dataset contains two directories:



families/ – domain protein sequences grouped by enzyme family [FASTA format]

active_sites/ – active site residue annotations for each family [TSV format]


A metadata file (metadata.tsv) is also included, providing detailed information for each enzyme family.

Metadata

A metadata file (metadata.tsv) provides:



family_id – Pfam family identifier (e.g., PF02615)

family_name – Pfam family name

seqs_count – total number of domain sequences in the family

seqs_with_active_sites – number of sequences containing at least one annotated active site

seqs_with_active_sites_percent – percentage of sequences with active sites

active_site_ids – comma-separated list of active site identifiers for the family

min_seq_length – minimum domain sequence length

mean_seq_length – average domain sequence length

max_seq_length – maximum domain sequence length


Active sites

Each family has a corresponding TSV file in active_sites/ listing sequence-specific active site annotations:



protein_id – protein sequence identifier

site_id – active site identifier (e.g., 114_H, 42_H)

protein_position – residue position within the sequence

protein_residue – amino acid at the position
DOI: 10.5281/zenodo.16023627
title: active_sites v1.0: enzyme domain sequences with annotated active sites from Pfam v37.1 for benchmarking MSA tools

description: This dataset contains 772 enzyme domain families annotated with 1,376 active sites in Pfam v37.1.

Protein sequences containing Pfam domains were retrieved from UniProt, and active site residues were predicted using Pfam’s pfam_scan.pl tool v1.626 together with the active site database active_site.dat v37.1. For each protein, only the sequence corresponding to the annotated domain was extracted from the full-length protein sequence Domain sequences were excluded if: the annotated domain was shorter than 25% of the length of the corresponding Pfam HMM model, or more than 10% of residues were non-standard amino acids.

Directory structure

The dataset contains two directories:



families/ – domain protein sequences grouped by enzyme family [FASTA format]

active_sites/ – active site residue annotations for each family [TSV format]


A metadata file (metadata.tsv) is also included, providing detailed information for each enzyme family.

Metadata

A metadata file (metadata.tsv) provides:



family_id – Pfam family identifier (e.g., PF02615)

family_name – Pfam family name

seqs_count – total number of domain sequences in the family

seqs_with_active_sites – number of sequences containing at least one annotated active site

seqs_with_active_sites_percent – percentage of sequences with active sites

active_site_ids – comma-separated list of active site identifiers for the family

min_seq_length – minimum domain sequence length

mean_seq_length – average domain sequence length

max_seq_length – maximum domain sequence length


Active sites

Each family has a corresponding TSV file in active_sites/ listing sequence-specific active site annotations:



protein_id – protein sequence identifier

site_id – active site identifier (e.g., 114_H, 42_H)

protein_position – residue position within the sequence

protein_residue – amino acid at the position
DOI: 10.15468/dl.5867ws
title: Occurrence Download

description: A dataset listing the 4047356 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4047356 records were derived from 74609 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005593-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25z55s
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parkinsonia aculeata",
 "Country is Timor-Leste",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005632-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dzgtj7
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mostacillastrum subauriculatum"
 ]
}

 The dataset includes 129 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005633-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v38pyv
title: Occurrence Download

description: A dataset containing 417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parkinsonia aculeata",
 "Country is Tanzania, United Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 417 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005630-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.exbbt6
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Matthiola flavida"
 ]
}

 The dataset includes 209 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005634-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4cbpb3
title: Occurrence Download

description: A dataset containing 7598 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Flueggea suffruticosa"
 ]
}

 The dataset includes 7598 records from 220 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005631-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6tyh8
title: Occurrence Download

description: A dataset containing 1491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pulmonaria angustifolia",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1491 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005635-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24435/materialscloud:4y-bf
title: Engineering PdAu/CeO2 alloy/oxide interfaces for selective methane-to-methanol conversion with water

description: The direct conversion of methane-to-methanol remains a critical challenge in methane valorization. In this study, we unveil the crucial role of PdAu/CeO2 catalysts in enabling selective methane transformation under mild conditions, using only water as the sole oxidant. Through a combination of experimental techniques, including XPS and catalytic testing, alongside density functional theory (DFT) calculations, we demonstrate that a Pd0.3Au0.7/CeO2 catalyst, which predominantly exposes isolated Pd atoms, achieves remarkable methanol selectivity (∼80%) at 500 K with a 1:1 methaneto-water ratio. While Pd/CeO2 efficiently activates methane, its tendency for overreaction leads to complete methanol decomposition, thereby limiting selectivity. Alloying Pd withAu on ceria mitigates this over-reactivity, preventing methanol degradation while maintaining sufficient catalytic activity. The PdAu/CeO2 composite exhibits a synergistic effect: Pd in contact with the ceria support facilitates methane activation and water dissociation, while Au fine-tunes reactivity to promote methanol formation. DFT calculations confirm that isolated Pd sites at the PdAu/CeO2 interface play a key role in balancing activity and selectivity. This work underscores the importance of alloy/oxide interfaces in controlling selective methane conversion with water and offers valuable insights for designing highly efficient catalysts for methanol synthesis.
DOI: 10.24435/materialscloud:nc-b8
title: Engineering PdAu/CeO2 alloy/oxide interfaces for selective methane-to-methanol conversion with water

description: The direct conversion of methane-to-methanol remains a critical challenge in methane valorization. In this study, we unveil the crucial role of PdAu/CeO2 catalysts in enabling selective methane transformation under mild conditions, using only water as the sole oxidant. Through a combination of experimental techniques, including XPS and catalytic testing, alongside density functional theory (DFT) calculations, we demonstrate that a Pd0.3Au0.7/CeO2 catalyst, which predominantly exposes isolated Pd atoms, achieves remarkable methanol selectivity (∼80%) at 500 K with a 1:1 methaneto-water ratio. While Pd/CeO2 efficiently activates methane, its tendency for overreaction leads to complete methanol decomposition, thereby limiting selectivity. Alloying Pd withAu on ceria mitigates this over-reactivity, preventing methanol degradation while maintaining sufficient catalytic activity. The PdAu/CeO2 composite exhibits a synergistic effect: Pd in contact with the ceria support facilitates methane activation and water dissociation, while Au fine-tunes reactivity to promote methanol formation. DFT calculations confirm that isolated Pd sites at the PdAu/CeO2 interface play a key role in balancing activity and selectivity. This work underscores the importance of alloy/oxide interfaces in controlling selective methane conversion with water and offers valuable insights for designing highly efficient catalysts for methanol synthesis.
DOI: 10.15468/dl.cezhup
title: Occurrence Download

description: A dataset containing 112446 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Salix viminalis"
 ]
}

 The dataset includes 112446 records from 788 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005520-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2ume2
title: Occurrence Download

description: A dataset containing 70642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DNK",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Potentilla erecta"
 ]
}

 The dataset includes 70642 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005607-250717081556266/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.29590835
title: Prevalence and Risk Factors for Pre-diabetes and Undiagnosed Type 2 Diabetes Mellitus among Adults on Antiretroviral Therapy at Bwaila Hospital, Malawi.

description: data saved by data set BMC