cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10700674
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip TBD

ppi_10A_stats.zip TBD

How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.12587821
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip TBD

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.12601152
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip TBD

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.12746715
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB downloaded in June 2024.

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.12821413
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description

ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB downloaded in June 2024.

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.13208732
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description



ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the ppi_6A dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB downloaded in June 2024.

ppi_10A_stats.zip stores the statistics about the ppi_10A dataset. This includes iDist embeddings, as well as a .csv file with main statistics for all interfaces.

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

pdb_redo_ppi_10A_stats.zip stores the statistics about the pdb_redo_ppi_10A dataset. This includes iDist embeddings, as well as a .csv file with main statistics for all interfaces.

skempi2.zip stores PPI interfaces from the SKEMPI v2.0 dataset


How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.5281/zenodo.14845086
title: PPIRef

description: PPIRef is a dataset of 3D structures of protein-protein interfaces. See the GitHub repository for more details.

 

File description



ppi_6A.zip stores the PPIRef dataset: .pdb files with all 6A-distance interfaces from PDB as of Jan 2024.

ppi_6A_stats.zip stores the statistics about the ppi_6A dataset. This includes the indexes for fast search with MMseqs2 and iDist, as well as a .csv file with main statistics for all interfaces.

ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB downloaded in June 2024.

ppi_10A_stats.zip stores the statistics about the ppi_10A dataset. This includes iDist embeddings, as well as a .csv file with main statistics for all interfaces.

pdb_redo_ppi_10A.zip: .pdb files with all 10A-distance interfaces from PDB-REDO downloaded in June 2024.

pdb_redo_ppi_10A_stats.zip stores the statistics about the pdb_redo_ppi_10A dataset. This includes iDist embeddings, as well as a .csv file with main statistics for all interfaces.

skempi2.zip stores PPI interfaces from the SKEMPI v2.0 dataset

benchmark_similarity_6A.zip: Results of benchmarking methods to calculate pairwise PPI similarity. The comparisons were performed on 2M 6A-interfaces. The directory contains results of iAlign and iDist. Please note that some values for iAlign are missing due to iAlign errors. Please see this GitHub issue for details of the benchmark construction.


How to useIt is recommended to download and extract the files in the PPIRef/ppiref/data/ppiref directory. This can be done automatically via the ppiref package. For example, to download and extract the ppi_6A.zip archive run:from ppiref.utils.misc import download_from_zenododownload_from_zenodo('ppi_6A.zip')
DOI: 10.15468/dl.2pcgy5
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Acropora arabensis Hodgson & Carpenter, 1995"
 ]
}

 The dataset includes 50 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023045-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2v8rpn
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "Country is Peru",
 "OccurrenceStatus is Present",
 "TaxonKey is Stenocercus modestus (Tschudi, 1845)",
 "Year 2015-2025"
 ]
}

 The dataset includes 67 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023047-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13620983
title: Supporting data and R code for: Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment

description: Data and R code to replicate analyses in Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment. CSAS Research Document. Publication info and link to follow when prepared.
DOI: 10.5281/zenodo.14536239
title: Supporting data and R code for: Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment

description: Data and R code to replicate analyses in Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment in 2024. CSAS Research Document. Publication info and link to follow when prepared.
DOI: 10.5281/zenodo.14847020
title: Supporting materials and R code for: Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment

description: Reference materials, data, and R code to replicate analyses in Brown et al. West Coast of Vancouver Island Natural-Origin Chinook Salmon (Oncorhynchus tshawytscha) Stock Assessment in 2024. CSAS Research Document. Publication info and link to follow when prepared.
DOI: 10.15468/dl.vzuvfu
title: Occurrence Download

description: A dataset containing 350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((46.47599 22.90611,62.45119 22.90611,62.45119 31.03171,46.47599 31.03171,46.47599 22.90611))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acropora Oken, 1815"
 ]
}

 The dataset includes 350 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023048-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/b235a50888db1a0abbb46f54158ef4a8
title: High-frequency, hourly, and daily measurements from Taylor Glacier Meteorological Station (TARM), McMurdo Dry Valleys, Antarctica (1994-2024, ongoing)

description: As part of the McMurdo Dry Valleys Long-Term Ecological Research program, a spatially distributed, long-term climate monitoring network was established across the McMurdo Dry Valleys region of Antarctica, consisting of fourteen research-grade weather stations that continuously measure a standard suite of environmental parameters. Ecosystem processes in this region are strongly regulated by climatic drivers that exhibit high variability across both time and space, making accurate measurement of environmental variables at high temporal and spatial resolution essential to understanding the biophysical dynamics of this polar desert ecosystem. This data package includes measurements from the Taylor Glacier Meteorological Station (TARM), which was established in 1994 on the lower section of Taylor Glacier in the Bonney Basin of Taylor Valley, McMurdo Dry Valleys, Antarctica. Parameters include air temperature, relative humidity, incoming and outgoing shortwave radiation, wind speed and direction, surface (snow/ice) temperature, and surface distance. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. Since there is no universally accepted standard for handling gaps in time-series data, users are encouraged to work with the high-frequency data and establish their own criteria for acceptable data completeness to minimize any potential bias.
DOI: 10.5281/zenodo.14840039
title: unimpeded: nlcdm bao.sdss_dr16+planck_2018_CamSpec

description: cosmological model:nlcdm, dataset:bao.sdss_dr16+planck_2018_CamSpec
DOI: 10.5281/zenodo.14840040
title: unimpeded: nlcdm bao.sdss_dr16+planck_2018_CamSpec

description: cosmological model:nlcdm, dataset:bao.sdss_dr16+planck_2018_CamSpec
DOI: 10.15468/dl.vpvm6j
title: Occurrence Download

description: A dataset containing 108627 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lymantria dispar Linnaeus, 1758"
 ]
}

 The dataset includes 108627 records from 728 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023043-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecbshy
title: Occurrence Download

description: A dataset containing 22961 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Arabidopsis thaliana (L.) Heynh."
 ]
}

 The dataset includes 22961 records from 510 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023049-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cbu9m7
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euryalida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 278 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257044-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2q42n
title: Occurrence Download

description: A dataset containing 514 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gentianella turkestanorum (Gand.) Holub"
 ]
}

 The dataset includes 514 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0226588-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbhf7r
title: Occurrence Download

description: A dataset containing 14161 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aphrophora alni (Fallén, 1805)"
 ]
}

 The dataset includes 14161 records from 256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0271790-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ev57jt
title: Occurrence Download

description: A dataset containing 580 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is China",
 "TaxonKey is Picea purpurea Mast."
 ]
}

 The dataset includes 580 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263193-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hc7xz
title: Occurrence Download

description: A dataset containing 280 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhinopithecus A.Milne-Edwards, 1872"
 ]
}

 The dataset includes 280 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0235979-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kn44kp
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliacus caelatus (Hinds, 1844)"
 ]
}

 The dataset includes 41 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263227-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gjcmx2
title: Occurrence Download

description: A dataset listing the 11 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Mammalogy Collection - Royal Ontario Museum",
 "TaxonKey is Eptesicus Rafinesque, 1820"
 ]
}

 The dataset's 11 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007820-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvhngp
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis (Parkinson) Fosberg, Artocarpus communis, Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R. & G.Forst., Artocarpus communis J.R. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., 1776, 161100371, Artocarpus communis J.R Forst. & G. Forst, Artocarpus communis J.R. & G.Forst., Artocarpus communis J.R. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J. R. Forst. & G. Forst., Artocarpus communis J.R.Forst. & G.Forst., 1776, Artocarpus communis J.R & G.Forster, 1776, 197223023, Artocarpus communis J.R.Forst. & G.Forst., Artocarpus communis J.R.Forst. & G.Forst., 1776, Pseudococcus lilacinus Cockerell, 1905, Dobsonia exoleta K.Andersen, 1909, Xenothictis gnetivora Brown, Miller & Horak, 2003, Pseudococcus lilacinus Cockerell, Bolothrips artocarpi Moulton, 1942, Bolothrips artocarpi Moulton 1942, Dobsonia exoleta K. Andersen 1909, Artocarpus altilis (Parkinson) Fosberg)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 127 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240118-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2j5d5b
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Iris hymenospatha B.Mathew & Wendelbo"
 ]
}

 The dataset includes 21 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254430-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryj3qd
title: Occurrence Download

description: A dataset containing 965 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mysida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 965 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257020-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqgmbc
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Holasteroida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 37 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257021-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdxue6
title: Occurrence Download

description: A dataset containing 56571 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microtus arvalis (Pallas, 1779)"
 ]
}

 The dataset includes 56571 records from 700 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007850-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.92p5vm
title: Occurrence Download

description: A dataset containing 8468 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Spheniscus demersus (Linnaeus, 1758)"
 ]
}

 The dataset includes 8468 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241716-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7artj9
title: Occurrence Download

description: A dataset containing 3506 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudastur occidentalis (Salvin, 1876)"
 ]
}

 The dataset includes 3506 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007855-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpj466
title: Occurrence Download

description: A dataset containing 350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chimaeriformes",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 350 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257037-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w72vq4
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rosa ×hybrida Schleich. ex W.D.J.Koch & Ziz",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 208 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263201-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8g7p2y
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Palaeonemertea",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257058-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.