cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.b3n43n
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.2_1",
 "TaxonKey is Sophora japonica L.",
 "Year 1970-2024"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011959-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ppged7
title: Occurrence Download

description: A dataset containing 1243541 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphipoda",
 "Year 1901-2024"
 ]
}

 The dataset includes 1243541 records from 1710 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011953-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eagxa9
title: Occurrence Download

description: A dataset containing 9262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cannabis sativa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "CoordinateUncertaintyInMeters is less than 1000",
 "BasisOfRecord is one of (Human Observation, Specimen, Material sample, Occurrence evidence)"
 ]
}

 The dataset includes 9262 records from 194 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051144-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nqcbbs
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera staphyleoides",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051145-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phprz7
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clausena excavata",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051146-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wegpp
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clausena excavata",
 "Country is Madagascar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 36 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051147-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ewp3eg
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clausena excavata",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051148-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17095594
title: Artifact for paper: Evolution-Aware Heuristics for GR(1) Realizability Checking
DOI: 10.15468/dl.bnvgwj
title: Occurrence Download

description: A dataset containing 11881 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alnus cordata"
 ]
}

 The dataset includes 11881 records from 390 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051150-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17088816
title: Supporting data for paper: Out of the Crystalline Comfort Zone: Sampling the Initial Oxide Formation at Cu(111)

description: The final mace model with corresponding training, test and validation data. Uncorrelated snapshots from the REMD simulations and the correspoinding geometry optimized configurations.
DOI: 10.5281/zenodo.17088817
title: Supporting data for paper: Out of the Crystalline Comfort Zone: Sampling the Initial Oxide Formation at Cu(111)

description: The final mace model with corresponding training, test and validation data. Uncorrelated snapshots from the REMD simulations and the correspoinding geometry optimized configurations.
DOI: 10.25612/837.weerzdddrndw
title: HCAD - Property Characteristics and Tax Assessments 2024

description: The data documents the information needed for discovering and appraising property for ad valorem tax purposes for each taxing unit within the boundaries of the district in 2024.
DOI: 10.15468/dl.nqf773
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Belize",
 "DatasetKey is one of (iNaturalist Research-grade Observations, NMNH Extant Specimen Records (USNM, US), Tropicos MO Specimen Data, University of Michigan Herbarium, UTEP Plants (Arctos), Louisiana State University, Shirley C. Tucker Herbarium - Vascular Plants, Royal Botanic Gardens, Kew - Herbarium Specimens, Naturalis Biodiversity Center (NL) - Botany, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (Plantas vasculares), Tropicos Specimens Non-MO)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cordia dodecandra"
 ]
}

 The dataset includes 39 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051152-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.znq2qt
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera stenophylla",
 "HasCoordinate is true"
 ]
}

 The dataset includes 75 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051151-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bympa2
title: Occurrence Download

description: A dataset containing 950672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Specimen, Material citation, Material sample, Human Observation, Machine Observation)",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Elapidae, Colubridae, Viperidae)"
 ]
}

 The dataset includes 950672 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051130-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ww6mrp
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleonema album",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051153-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jeecgk
title: Occurrence Download

description: A dataset containing 8609 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Hygrophorus eburneus"
 ]
}

 The dataset includes 8609 records from 224 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051154-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/zj2p-hf65
title: Direct Spectroscopy of 51 Eridani b with JWST / NIRSpec

description: Datasets are all taken in GO program number 3522
DOI: 10.15468/dl.uv5bsx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Telestes dabar)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051155-250827131500795/datasets/export for details.
DOI: 10.15468/dl.72etx4
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Belize",
 "DatasetKey is one of (NMNH Extant Specimen Records (USNM, US), Tropicos Specimens Non-MO)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cordia gerascanthus"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051157-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8z7xta
title: Occurrence Download

description: A dataset containing 4110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Inocybe napipes"
 ]
}

 The dataset includes 4110 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051158-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9afv7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Belize",
 "DatasetKey is Tropicos MO Specimen Data",
 "OccurrenceStatus is Present",
 "TaxonKey is Cordia panamensis"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051160-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w5fu9t
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleonema pulchellum",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 247 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051161-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4rbsrf
title: Occurrence Download

description: A dataset containing 683 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera submoniliformis",
 "HasCoordinate is true"
 ]
}

 The dataset includes 683 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051159-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18738/t8/nikfzr
title: Data for "Opportunities and limitations of NMR in astrobiology"

description: NMR data for "Opportunities and limitations of nuclear magnetic resonance spectroscopy in astrobiology" by Cornelia Rasmussen and David Hoffman
DOI: 10.5281/zenodo.15174758
title: LigPCDS: Labeled Dataset of X-ray Protein Ligand Images in 3D Point Cloud and Validated Deep Learning Models

description: The difference electron density from X-ray protein crystallography was used to create the first dataset of labeled ligand images in 3D point clouds, named LigPCDS. The dataset contain 244,226 entries of free organic ligands containing 3D representations labeled with two major labeling approaches: SP-based and AtomSymbol-based.

 

The data from free organic molecules (non-covalent ligands) was retrieved from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) in december 2019 with resolutions ranging from 1.5 to 2.2 Å. The ligand images (blobs) were interpolated from their calculated difference electron density map in a 3D grid-like bounding box, around their atomic positions, and stored in point clouds. These ligand grid representations were further processed to retrive the final ligands representation in 3D point clouds using a mask of the shape of the ligand. A grid spacing of 0.5 Å gave the best results. The density value of the grid points was used as feature. The labeling approach used the structure of the ligands to propose vocabularies of chemical classes based on the chemical atoms themselves and their cyclic substructures. These structure annotations were applied pointwise to the ligand 3D representations using an atomic sphere model. Four proposed vocabularies were validated by successfully training good performance deep learning models for the semantic segmentation of a stratified dataset from LigPCDS, using 78902 entries.

The four validated deep learning models are: (i) the LigandRegion, composed by generic atoms of any type; (ii) the AtomCycle, composed by generic atoms outside cycles and generic cycles; (iii) the AtomC347CA56, composed by generic atoms outside cycles, not aromatic cycles of size 3 to 7 and aromatic cycles of size 5 and 6; and (iv) the AtomSymbolGroups, composed by the atoms symbols with groupings. The mean accuracy of these models in their cross-validation was between 49.7% [-19.4,20.2] and 77.4% [-11.7,12.1] in terms of Intersection over Union (mIoU) metric and between 62.4% [-18.8,19.7] and 87.0% [-8.4,8.8] in F1-score (mF1), confidence interval between squared brackets. The models i, ii and iii and the used labeled representations in 3D point cloud are contained in the SP-based record; and model iv and its used labeled representations are contained in the AtomSymbol-based record.

The dataset and validated models may be used to tackle problems regarding known and unknown ligand building to drug discovery and fragment screening pipelines. 

The code used to create and validated the LigPCDS is available at the following repository: https://github.com/danielatrivella/np3_ligand

This repository also contains the NP³ Blob Label application for ligand building using the validated deep learning models from LigPCDS.
DOI: 10.5281/zenodo.7872577
title: LigPCDS: Labeled Dataset of X-ray Protein Ligand Images in 3D Point Cloud and Validated Deep Learning Models

description: The difference electron density from X-ray protein crystallography was used to create the first dataset of labeled ligand images in 3D point clouds, named LigPCDS. The dataset contain 244,226 entries of free organic ligands containing 3D representations labeled with two major labeling approaches: SP-based and AtomSymbol-based.

 

The data from free organic molecules (non-covalent ligands) was retrieved from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) in december 2019 with resolutions ranging from 1.5 to 2.2 Å. The ligand images (blobs) were interpolated from their calculated difference electron density map in a 3D grid-like bounding box, around their atomic positions, and stored in point clouds. These ligand grid representations were further processed to retrive the final ligands representation in 3D point clouds using a mask of the shape of the ligand. A grid spacing of 0.5 Å gave the best results. The density value of the grid points was used as feature. The labeling approach used the structure of the ligands to propose vocabularies of chemical classes based on the chemical atoms themselves and their cyclic substructures. These structure annotations were applied pointwise to the ligand 3D representations using an atomic sphere model. Four proposed vocabularies were validated by successfully training good performance deep learning models for the semantic segmentation of a stratified dataset from LigPCDS, using 78902 entries.

The four validated deep learning models are: (i) the LigandRegion, composed by generic atoms of any type; (ii) the AtomCycle, composed by generic atoms outside cycles and generic cycles; (iii) the AtomC347CA56, composed by generic atoms outside cycles, not aromatic cycles of size 3 to 7 and aromatic cycles of size 5 and 6; and (iv) the AtomSymbolGroups, composed by the atoms symbols with groupings. The mean accuracy of these models in their cross-validation was between 49.7% [-19.4,20.2] and 77.4% [-11.7,12.1] in terms of Intersection over Union (mIoU) metric and between 62.4% [-18.8,19.7] and 87.0% [-8.4,8.8] in F1-score (mF1), confidence interval between squared brackets. The models i, ii and iii and the used labeled representations in 3D point cloud are contained in the SP-based record; and model iv and its used labeled representations are contained in the AtomSymbol-based record.

The dataset and validated models may be used to tackle problems regarding known and unknown ligand building to drug discovery and fragment screening pipelines. 

The code used to create and validated the LigPCDS is available at the following repository: https://github.com/danielatrivella/np3_ligand

This repository also contains the NP³ Blob Label application for ligand building using the validated deep learning models from LigPCDS.
DOI: 10.15468/dl.chybav
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Poecilocharax weitzmani)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 134 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051163-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzdbcy
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Belize",
 "DatasetKey is one of (iNaturalist Research-grade Observations, NMNH Extant Specimen Records (USNM, US), Tropicos MO Specimen Data, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (Plantas vasculares), Royal Botanic Gardens, Kew - Herbarium Specimens, The New York Botanical Garden Herbarium (NY), Pl@ntNet automatically identified occurrences, Base de datos del Herbario CIQR de El Colegio de la Frontera Sur, unidad Chetumal, Natural History Museum (London) Collection Specimens, Tropicos Specimens Non-MO)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cordia sebestena"
 ]
}

 The dataset includes 116 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051164-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytuc9c
title: Occurrence Download

description: A dataset containing 174528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Colibri cyanotus"
 ]
}

 The dataset includes 174528 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051098-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5nad4
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ruta graveolens",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 56 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051169-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p5cmjw
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ruta graveolens",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051166-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9jnjs
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera suntui",
 "HasCoordinate is true"
 ]
}

 The dataset includes 81 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051168-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7982j
title: Occurrence Download

description: A dataset containing 16437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sorex vagrans"
 ]
}

 The dataset includes 16437 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051167-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhtmvk
title: Occurrence Download

description: A dataset containing 18291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Australia)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1940",
 "Year is less than or equal to 1940"
 ]
}

 The dataset includes 18291 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051140-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gntrwj
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ruta graveolens",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 247 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051170-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.