cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ttf3rc
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gentianella umbellata (M.Bieb.) Holub"
 ]
}

 The dataset includes 168 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0226593-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m65pm3
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Androsace minor (Hand.-Mazz.) C.M.Hu & Y.C.Yang",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 31 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0262830-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.htjpau
title: Occurrence Download

description: A dataset containing 185 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hesperolinon clevelandii (Greene) Small"
 ]
}

 The dataset includes 185 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241730-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.67ex37
title: Occurrence Download

description: A dataset containing 5937 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sardina pilchardus (Walbaum, 1792)",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLongitude is greater than -180"
 ]
}

 The dataset includes 5937 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0235969-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7f53fu
title: Occurrence Download

description: A dataset containing 1136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Glossophaga E.Geoffroy, 1818"
 ]
}

 The dataset includes 1136 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241734-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bb29yp
title: Occurrence Download

description: A dataset containing 34444 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Rodentia"
 ]
}

 The dataset includes 34444 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249066-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uf9hg3
title: Occurrence Download

description: A dataset containing 84530 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asparagus officinalis L."
 ]
}

 The dataset includes 84530 records from 955 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240110-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.axv83d
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Genista teretifolia Willk."
 ]
}

 The dataset includes 625 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022965-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14844636
title: Dataset of AlphaFold 3 and RoseTTAFold2NA Structures for Analysing the Capabilities of These Programmes in Predicting the Spacing and Orientation Preferences of Two Transcription Factors

description: Description:This dataset contains a collection of predicted TF‑TF–DNA complex structures generated using two state‑of‑the‑art artificial intelligence programmes: RoseTTAFold2NA and AlphaFold 3. The structures were predicted as part of a study aimed at evaluating the capability of these models to capture the spacing and orientation preferences in TF‑TF–DNA interactions, as derived from CAP‑SELEX experimental data. This repository is accompanied by an associated Zenodo repository [https://doi.org/10.5281/zenodo.14846538] containing the code used for analysing these data. The code repository was automatically copied by Zenodo from this GitHub repository

Background and Rationale:Transcription factors bind to specific DNA sequences to regulate gene expression. Experimental approaches such as CAP‑SELEX have enabled the characterisation of binding preferences by providing enriched k‑mer motifs and information on preferred spatial arrangements between TF binding sites. In this study, 119 position weight matrix (PWM) models, obtained from CAP‑SELEX experiments, were used to define the preferred DNA sequences for pairs of transcription factors (e.g. PAX2 and ELK3).

Dataset Content:A total of 1,620 PDB files were generated for each program, resulting in 3,240 predicted structures overall. The sequences used as input for AlphaFold 3 were identical to those used for RoseTTAFold2NA. For each PWM model, multiple competitive DNA sequences were generated to probe different spatial and orientational configurations.

Methodology:The prediction pipeline involved the following key steps:



Derivation of Input Sequences: Based on CAP‑SELEX data, two key k‑mers were identified for each TF. Multiple DNA sequences were constructed by varying the spacing (e.g. ±1 or ±2 nucleotides) and the orientation (e.g. swapping positions or using reverse complements) between the two k‑mers.

Structure Prediction: The generated sequences were used as input for RoseTTAFold2NA and AlphaFold 3, resulting in a set of predicted TF‑TF–DNA complex structures.

Analysis: The predicted structures were analysed by comparing the number of contacts in the region corresponding to the preferred DNA versus the competitive DNA. A contact was defined as a pair of atoms (one from an amino acid and one from a nucleic acid) whose minimum distance is less than the threshold of 0.45 nm.


By linking experimental CAP‑SELEX data with high‑accuracy structural predictions, this resource facilitates a deeper understanding of the molecular mechanisms underlying transcriptional regulation and provides a valuable resource for improving existing methods as well as serving as a dataset for further methodological development.
DOI: 10.5281/zenodo.14844637
title: Dataset of AlphaFold 3 and RoseTTAFold2NA Structures for Analysing the Capabilities of These Programmes in Predicting the Spacing and Orientation Preferences of Two Transcription Factors

description: Description:This dataset contains a collection of predicted TF‑TF–DNA complex structures generated using two state‑of‑the‑art artificial intelligence programmes: RoseTTAFold2NA and AlphaFold 3. The structures were predicted as part of a study aimed at evaluating the capability of these models to capture the spacing and orientation preferences in TF‑TF–DNA interactions, as derived from CAP‑SELEX experimental data. This repository is accompanied by an associated Zenodo repository [https://doi.org/10.5281/zenodo.14846538] containing the code used for analysing these data. The code repository was automatically copied by Zenodo from this GitHub repository

Background and Rationale:Transcription factors bind to specific DNA sequences to regulate gene expression. Experimental approaches such as CAP‑SELEX have enabled the characterisation of binding preferences by providing enriched k‑mer motifs and information on preferred spatial arrangements between TF binding sites. In this study, 119 position weight matrix (PWM) models, obtained from CAP‑SELEX experiments, were used to define the preferred DNA sequences for pairs of transcription factors (e.g. PAX2 and ELK3).

Dataset Content:A total of 1,620 PDB files were generated for each program, resulting in 3,240 predicted structures overall. The sequences used as input for AlphaFold 3 were identical to those used for RoseTTAFold2NA. For each PWM model, multiple competitive DNA sequences were generated to probe different spatial and orientational configurations.

Methodology:The prediction pipeline involved the following key steps:



Derivation of Input Sequences: Based on CAP‑SELEX data, two key k‑mers were identified for each TF. Multiple DNA sequences were constructed by varying the spacing (e.g. ±1 or ±2 nucleotides) and the orientation (e.g. swapping positions or using reverse complements) between the two k‑mers.

Structure Prediction: The generated sequences were used as input for RoseTTAFold2NA and AlphaFold 3, resulting in a set of predicted TF‑TF–DNA complex structures.

Analysis: The predicted structures were analysed by comparing the number of contacts in the region corresponding to the preferred DNA versus the competitive DNA. A contact was defined as a pair of atoms (one from an amino acid and one from a nucleic acid) whose minimum distance is less than the threshold of 0.45 nm.


By linking experimental CAP‑SELEX data with high‑accuracy structural predictions, this resource facilitates a deeper understanding of the molecular mechanisms underlying transcriptional regulation and provides a valuable resource for improving existing methods as well as serving as a dataset for further methodological development.
DOI: 10.15468/dl.7ka355
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 {
 "or" : [
 "Country is Angola",
 "Country is Bahrain",
 "Country is Benin",
 "Country is Cameroon",
 "Country is Comoros",
 "Country is Congo",
 "Country is Congo, Democratic Republic of the",
 "Country is Côte d’Ivoire",
 "Country is Djibouti",
 "Country is Egypt",
 "Country is Eritrea",
 "Country is Equatorial Guinea",
 "Country is Gabon",
 "Country is Gambia",
 "Country is Ghana",
 "Country is Guinea",
 "Country is Guinea-Bissau",
 "Country is Iran (Islamic Republic of)",
 "Country is Iraq",
 "Country is Jordan",
 "Country is Kenya",
 "Country is Kuwait",
 "Country is Liberia",
 "Country is Madagascar",
 "Country is Mauritania",
 "Country is Mauritius",
 "Country is Mozambique",
 "Country is Nigeria",
 "Country is Oman",
 "Country is Qatar",
 "Country is Réunion",
 "Country is Saudi Arabia",
 "Country is Senegal",
 "Country is Seychelles",
 "Country is Sierra Leone",
 "Country is Somalia",
 "Country is South Africa",
 "Country is South Sudan",
 "Country is Sudan",
 "Country is Tanzania, United Republic of",
 "Country is Togo",
 "Country is United Arab Emirates",
 "Country is Yemen",
 "Country is Zambia",
 "Country is Zimbabwe"
 ]
 },
 "TaxonKey is Rhizophora stylosa Griffith",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (VAGRANT)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 {
 "not" : {
 "DegreeOfEstablishment" : [
 "is one of (CULTIVATED)"
 ]
 }
 },
 "DegreeOfEstablishment is null"
 ]
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022967-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5n9err
title: Occurrence Download

description: A dataset containing 13403 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (South America, North America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Paullinia L.",
 "Year 1995-2025"
 ]
}

 The dataset includes 13403 records from 279 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022966-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qz8tt4
title: Occurrence Download

description: A dataset listing the 249 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Observation, Material sample, Specimen, Occurrence evidence)",
 "Country is Canada",
 "Geometry POLYGON((-73.52306 45.35615,-73.54144 45.35155,-73.56641 45.34161,-73.57207 45.31909,-73.56029 45.29953,-73.53578 45.28395,-73.49902 45.29224,-73.48111 45.31279,-73.49337 45.34393,-73.52306 45.35615))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 249 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022952-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14839696
title: unimpeded: rlcdm bao.sdss_dr16+bicep_keck_2018

description: cosmological model:rlcdm, dataset:bao.sdss_dr16+bicep_keck_2018
DOI: 10.5281/zenodo.14839697
title: unimpeded: rlcdm bao.sdss_dr16+bicep_keck_2018

description: cosmological model:rlcdm, dataset:bao.sdss_dr16+bicep_keck_2018
DOI: 10.3886/icpsr38971.v1
title: A Two-State Examination of Varied Measurement Strategies for Juvenile Reoffending, Florida and Oregon, 2012-2017
title: Version 1

description: Past research indicates that there is wide variation in the measurement of juvenile recidivism across state juvenile justice systems. As such, concerns have been raised that cross-agency differences in the definition and measurement of juvenile recidivism may hamper the generalizability of knowledge as well as comparisons across jurisdictions. Yet it is unclear whether measurement choices do impact the conclusions of studies of juvenile recidivism. These data were collected to answer questions about the impact of measurement variation on the rates and predictors of juvenile recidivism. The first sample included 104,354 unique spells of Florida Department of Juvenile Justice supervision, including 48,616 diversion spells, 43,799 probation spells, and 11,939 residential commitment spells that ended between July 1, 2012 and June 30, 2016. The second sample used data from the Oregon Youth authority and featured 2,743 unique spells of supervision, including 1,616 probation spells and 1,127 parole spells that ended between July 1, 2012 and June 30, 2016. The data include a variety of operationalizations of juvenile recidivism that vary in terms of the type of system contact captured, the follow-up length used, and whether the measure includes adult criminal justice system information. The data also include information on youths' demographic characteristics, delinquency history, and risk and protective factors. Contextual data from the American Community Survey and Uniform Crime Reports are also included.
description: The sample for the Florida data is archival data on a release cohort of all youth who completed Florida Department of Juvenile Justice programs between July 1, 2012 and June 30, 2017. For the Oregon data, the sample is all probation and parole youth with open cases between July 1, 2012 through June 30, 2016.
description: Datasets: 
DS0: Study-Level Files
DS1: Florida Data
DS2: Oregon Data
description: All youth released from the custody (i.e., residential placement, diversion, probation, or parole) of the Florida Department of Juvenile Justice or between July 1, 2012 and June 30, 2017. All probation and parole youth with open cases under the Oregon Youth Authority between July 1, 2012 through June 30, 2016.
description: record abstracts
DOI: 10.15468/dl.3jxde5
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 {
 "or" : [
 "Country is Angola",
 "Country is Bahrain",
 "Country is Benin",
 "Country is Cameroon",
 "Country is Comoros",
 "Country is Congo",
 "Country is Congo, Democratic Republic of the",
 "Country is Côte d’Ivoire",
 "Country is Djibouti",
 "Country is Egypt",
 "Country is Eritrea",
 "Country is Equatorial Guinea",
 "Country is Gabon",
 "Country is Gambia",
 "Country is Ghana",
 "Country is Guinea",
 "Country is Guinea-Bissau",
 "Country is Iran (Islamic Republic of)",
 "Country is Iraq",
 "Country is Jordan",
 "Country is Kenya",
 "Country is Kuwait",
 "Country is Liberia",
 "Country is Madagascar",
 "Country is Mauritania",
 "Country is Mauritius",
 "Country is Mozambique",
 "Country is Nigeria",
 "Country is Oman",
 "Country is Qatar",
 "Country is Réunion",
 "Country is Saudi Arabia",
 "Country is Senegal",
 "Country is Seychelles",
 "Country is Sierra Leone",
 "Country is Somalia",
 "Country is South Africa",
 "Country is South Sudan",
 "Country is Sudan",
 "Country is Tanzania, United Republic of",
 "Country is Togo",
 "Country is United Arab Emirates",
 "Country is Yemen",
 "Country is Zambia",
 "Country is Zimbabwe"
 ]
 },
 "TaxonKey is Sonneratia alba Sm.",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (VAGRANT)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 {
 "not" : {
 "DegreeOfEstablishment" : [
 "is one of (CULTIVATED)"
 ]
 }
 },
 "DegreeOfEstablishment is null"
 ]
 }
 ]
}

 The dataset includes 227 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022968-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wj3tnh
title: Occurrence Download

description: A dataset containing 22847981 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Cardinalis cardinalis (Linnaeus, 1758)"
 ]
}

 The dataset includes 22847981 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022956-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27x5av
title: Occurrence Download

description: A dataset containing 787636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lupinus polyphyllus Lindl., Festuca rubra L., Achillea millefolium L., Trisetum flavescens (L.) P.Beauv., Primula veris L., Gentiana pneumonanthe L., Arnica montana L., Pulsatilla vulgaris Mill., Dactylorhiza incarnata (L.) Soó, Gymnadenia conopsea (L.) R.Br., Leontodon hispidus L., Scabiosa columbaria L., Campanula rotundifolia L., Helianthemum nummularium (L.) Mill., Leucanthemum vulgare Lam., Anthoxanthum odoratum L., Filipendula ulmaria (L.) Maxim., Ranunculus acris L., Lathyrus pratensis L., Galium verum L., Sanguisorba officinalis L., Lotus corniculatus L., Hypericum perforatum L., Orchis mascula (L.) L., Polygonum bistorta Garcke, Carlina vulgaris L.)",
 "Country is Sweden",
 "HasCoordinate is true",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 787636 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022960-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c1q743
title: Occurrence Download

description: A dataset containing 2867 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Ohio State University Fish Division (OSUM)",
 "TaxonKey is Cyprinella spiloptera (Cope, 1867)"
 ]
}

 The dataset includes 2867 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017586-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5gadr
title: Occurrence Download

description: A dataset containing 22241 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendragapus obscurus (Say, 1822)"
 ]
}

 The dataset includes 22241 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075361-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nvp2wq
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Papua New Guinea",
 "HasCoordinate is true",
 "TaxonKey is Paederina Bordoni, 1975",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 177 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009243-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcrjxd
title: Occurrence Download

description: A dataset containing 952409 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "Geometry POLYGON((-55.12939 -27.09825,-46.73584 -27.09825,-46.73584 -23.0393,-55.12939 -23.0393,-55.12939 -27.09825))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 952409 records from 577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017589-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8jbzek
title: Occurrence Download

description: A dataset containing 5868 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Ortalis guttata (Spix, 1825)"
 ]
}

 The dataset includes 5868 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063056-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bkavp4
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((67.44305 7.13198,138.28289 7.13198,138.28289 35.43276,67.44305 35.43276,67.44305 7.13198))",
 "HasCoordinate is true",
 "TaxonKey is Borreria latifolia (Aubl.) K.Schum.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009243-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.