cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29578388
title: source code and processed datasets of EMO

description: Non-coding mutations play a critical role in regulating gene expression, yet predicting their effects across diverse tissues and cell types remains a challenge. Here, we present EMO, a transformer-based model that integrates DNA sequence with chromatin accessibility data (ATAC-seq) to predict the regulatory impact of non-coding single nucleotide polymorphisms (SNPs) on gene expression. A key component of EMO is its ability to incorporate personalized functional genomic profiles, enabling individual-level and disease-contextual predictions, and addressing critical limitations of current approaches. EMO generalizes across tissues and cell types by modeling both short- and long-range regulatory interactions and capturing dynamic gene expression changes associated with disease progression. In benchmark evaluations, the pretraining-based EMO framework outperformed existing models, with fine-tuning small-sample tissues enhancing the model's ability to fit target tissues. In single-cell contexts, EMO accurately identified cell-type-specific regulatory patterns and successfully captured the effects of disease-associated SNPs in conditions, linking genetic variation to disease-relevant pathways.
DOI: 10.6084/m9.figshare.29578388.v3
title: source code and processed datasets of EMO

description: Non-coding mutations play a critical role in regulating gene expression, yet predicting their effects across diverse tissues and cell types remains a challenge. Here, we present EMO, a transformer-based model that integrates DNA sequence with chromatin accessibility data (ATAC-seq) to predict the regulatory impact of non-coding single nucleotide polymorphisms (SNPs) on gene expression. A key component of EMO is its ability to incorporate personalized functional genomic profiles, enabling individual-level and disease-contextual predictions, and addressing critical limitations of current approaches. EMO generalizes across tissues and cell types by modeling both short- and long-range regulatory interactions and capturing dynamic gene expression changes associated with disease progression. In benchmark evaluations, the pretraining-based EMO framework outperformed existing models, with fine-tuning small-sample tissues enhancing the model's ability to fit target tissues. In single-cell contexts, EMO accurately identified cell-type-specific regulatory patterns and successfully captured the effects of disease-associated SNPs in conditions, linking genetic variation to disease-relevant pathways.
DOI: 10.6084/m9.figshare.29578388.v2
title: source code for EMO

description: Non-coding mutations play a critical role in regulating gene expression, yet predicting their effects across diverse tissues and cell types remains a challenge. Here, we present EMO, a transformer-based model that integrates DNA sequence with chromatin accessibility data (ATAC-seq) to predict the regulatory impact of non-coding single nucleotide polymorphisms (SNPs) on gene expression. A key component of EMO is its ability to incorporate personalized functional genomic profiles, enabling individual-level and disease-contextual predictions, and addressing critical limitations of current approaches. EMO generalizes across tissues and cell types by modeling both short- and long-range regulatory interactions and capturing dynamic gene expression changes associated with disease progression. In benchmark evaluations, the pretraining-based EMO framework outperformed existing models, with fine-tuning small-sample tissues enhancing the model's ability to fit target tissues. In single-cell contexts, EMO accurately identified cell-type-specific regulatory patterns and successfully captured the effects of disease-associated SNPs in conditions, linking genetic variation to disease-relevant pathways.
DOI: 10.5281/zenodo.16316328
title: Supplementary Materials associated with paper 'A comparative molecular study of rhizostome jellyfishes (Cnidaria, Scyphozoa, Rhizostomeae) from Japan reveals dominant Symbiodiniaceae associations with many and variable cassiosome production'

description: This is a repository for supporting figures associated with paper 'A comparative molecular study of rhizostome jellyfishes (Cnidaria, Scyphozoa, Rhizostomeae) from Japan reveals dominant Symbiodiniaceae associations with many and variable cassiosome production'
DOI: 10.15468/dl.uy56st
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neonotonia wightii",
 "Country is Tonga",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028365-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ptnfkv
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neonotonia wightii",
 "Country is Niue",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028364-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qaa9na
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neonotonia wightii",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 124 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028366-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4v3k67
title: Occurrence Download

description: A dataset listing the 263 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((27.22409 -24.53756,27.2401 -24.52885,27.24034 -24.53201,27.2432 -24.53383,27.2462 -24.53319,27.24779 -24.53099,27.2521 -24.53084,27.25382 -24.52718,27.25052 -24.52414,27.25061 -24.52022,27.24669 -24.51841,27.24303 -24.52168,27.23828 -24.52158,27.23663 -24.52557,27.24017 -24.52871,27.22409 -24.53756),(27.24518 -24.52598,27.24409 -24.52653,27.24463 -24.52509,27.24638 -24.52579,27.24432 -24.52655,27.24518 -24.52598))",
 "Geometry POLYGON((27.17959 -24.5731,27.31496 -24.5731,27.31496 -24.48533,27.17959 -24.48533,27.17959 -24.5731))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 263 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028357-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12544789
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.sfb8br
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oryctolagus cuniculus",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 129 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028367-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16318968
title: fullwcom

description: with commu
DOI: 10.15468/dl.6drqqq
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corylopsis platypetala"
 ]
}

 The dataset includes 224 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028369-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdgtq8
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (IND.3_1, IND.4_1, IND.24_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Spelaeornis reptatus"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028372-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxm5zk
title: Occurrence Download

description: A dataset containing 17561 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Falco tinnunculus"
 ]
}

 The dataset includes 17561 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028370-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/4.fd
title: ChildLens: An Egocentric Video Dataset for Activity Analysis in Children

description: ChildLens is an egocentric video and audio dataset capturing naturalistic everyday experiences in children aged 3–5 years. It contains 109 hours of recordings from 62 children in their home environment, collected using a 140° wide-lens camera with a microphone embedded in a child-friendly vest. The dataset includes detailed annotations with five location classes (livingroom, playroom, bathroom, hallway, and other) and 14 activity classes, covering audio-only (child talking, singing/humming, listening to music/audiobook, other person talking, overheard speech), video-only (watching something, drawing, crafting things, dancing, playing with object), and multimodal activities (playing without object, reading book, making music, pretend play).
The recordings, captured from chest height, offer a rich perspective on children’s daily interactions and behaviors. The dataset is designed to support research in developmental psychology, computer vision, and audio analysis.
DOI: 10.15468/dl.rf9h2z
title: Occurrence Download

description: A dataset containing 997 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ossaea marginata"
 ]
}

 The dataset includes 997 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028371-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/dans-28g-f5cg
title: Pachten hoeven Meierij van 's-Hertogenbosch 1590-1750

description: &lt;p&gt;Pachten, ten dele in geld en ten dele in natura, verschuldigd door de pachters van de boerderijen van twee charitatieve instellingen in 's-Hertogenbosch uit de periode 1590-1750. De boerderijen lagen verspreid over oostelijk Noord-Brabant.&lt;/p&gt;
description: &lt;p&gt;Voor informatie over context van en correlatie tussen de databestanden, zie de beschrijving in 'Pachten THG toelichting' onder Data files.&lt;/p&gt;
DOI: 10.15468/dl.dcqjcb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Bufo bufo)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028373-250717081556266/datasets/export for details.
DOI: 10.15468/dl.bvwyxj
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Bufo bufo)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028374-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8tk2aj
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Costus villosissimus"
 ]
}

 The dataset includes 549 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028376-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhs96k
title: Occurrence Download

description: A dataset containing 184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Foeniculum vulgare",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 184 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028379-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60507/fk2/5ds0jz/xbz9ve
title: Victoria_cruziana_VB03.tar.gz
DOI: 10.60507/fk2/5ds0jz/xu0fgi
title: README_Victoria_cruziana.txt
DOI: 10.60507/fk2/5ds0jz
title: Genome sequence and annotation of Victoria cruziana

description: The genome of a &lt;i&gt;Victoria cruziana&lt;/i&gt; plant was sequenced with nanopore long reads. The genome sequence was assembled with Verkko2, scaffolding was conducted with CPhasing and the gene models were predicted by BRAKER3 and GeMoMa. The functional annotation was predicted based on sequence similarity to well characterized Arabidopsis thaliana sequences.
DOI: 10.15468/dl.5r3bsw
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Foeniculum vulgare",
 "Country is Brazil",
 "HasCoordinate is true"
 ]
}

 The dataset includes 419 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028380-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mp2dkw
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Castanopsis ferox"
 ]
}

 The dataset includes 61 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028378-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s75qf5
title: Occurrence Download

description: A dataset containing 1767 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Costus afer"
 ]
}

 The dataset includes 1767 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028377-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/11478119
title: Balochi Language to English Translation Dataset
DOI: 10.5287/ora-yxaqpvgjv-1
title: Manipulation of skyrmion motion by magnetic field gradients

description: Full size CCD camera videos for https://www.nature.com/articles/s41467-018-04563-4
DOI: 10.5287/ora-yxaqpvgjv-2
title: Manipulation of skyrmion motion by magnetic field gradients

description: Full size CCD camera videos for https://www.nature.com/articles/s41467-018-04563-4
DOI: 10.5281/zenodo.10854757
title: TCRBuilder2+ predictions of the Observed T-cell receptor Space (OTS)

description: TCRBuilder2+ predictions of over 1.5 million TCR structures from the Observed T-cell receptor Space database. 

The dataset also contains the sequence files as a linked list contained in a text file. The index, i.e. row number of the amino acid sequence corresponds to the number in the TCR predictions filename.If you would like to pre-view this list without downloading the entire dataset, it is contained in this repository: https://github.com/npqst/TCRPredDab .

If you use TCRPredDab in your research please cite: 

Quast, N.P., et al. _T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity_. Commun Biol 8, 362 (2025). https://doi.org/10.1038/s42003-025-07708-6

and: 

Raybould,M.I.J. et al. _The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling_. Cell Reports Volume 43, Issue 9 (2024). https://doi.org/10.1016/j.celrep.2024.114704
DOI: 10.5281/zenodo.10854756
title: TCRBuilder2+ predictions of the Observed T-cell receptor Space (OTS)

description: TCRBuilder2+ predictions of over 1.5 million TCR structures from the Observed T-cell receptor Space database. 

The dataset also contains the sequence files as a linked list contained in a text file. The index, i.e. row number of the amino acid sequence corresponds to the number in the TCR predictions filename.If you would like to pre-view this list without downloading the entire dataset, it is contained in this repository: https://github.com/npqst/TCRPredDab .

If you use TCRPredDab in your research please cite: 

Quast, N.P., et al. _T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity_. Commun Biol 8, 362 (2025). https://doi.org/10.1038/s42003-025-07708-6

and: 

Raybould,M.I.J. et al. _The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling_. Cell Reports Volume 43, Issue 9 (2024). https://doi.org/10.1016/j.celrep.2024.114704
DOI: 10.15468/dl.b2ht3j
title: Occurrence Download

description: A dataset containing 287 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Philodendron edmundoi"
 ]
}

 The dataset includes 287 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002784-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vhha2c
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Aristida spegazzinii"
 ]
}

 The dataset includes 197 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002785-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fub85q
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chamaedorea alternans",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 74 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002786-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hjjaue
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "IsSequenced is true",
 "TaxonKey is Kappaphycus alvarezii"
 ]
}

 The dataset includes 156 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002787-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bjampt
title: Occurrence Download

description: A dataset listing the 227 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((7.7902 48.54235,7.78972 48.54847,7.78367 48.55374,7.77486 48.55412,7.76665 48.55057,7.76317 48.54403,7.76406 48.53636,7.76945 48.52828,7.77699 48.52809,7.78453 48.53034,7.7897 48.5362,7.7902 48.54235))",
 "PublishingCountry is France",
 "TaxonKey is Plantae",
 "Year 2016-2026"
 ]
}

 The dataset's 227 records were derived from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002750-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r4qx5g
title: Occurrence Download

description: A dataset containing 155829 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Observation, Human Observation)",
 "DatasetKey is one of (NABU|naturgucker, Observation.org, Nature data from around the World, International Barcode of Life project (iBOL), ArtenFinder, iNaturalist Research-grade Observations, Pl@ntNet automatically identified occurrences, Naturhistorisches Museum Mainz, Feldbeobachtungsdaten Pflanzen, Pl@ntNet observations, Monitoring data from the federal state Rhineland-Palatinate (Germany))",
 "Geometry POLYGON((7.60991 50.28339,7.57079 50.37532,7.52813 50.41373,7.48922 50.41309,7.43273 50.42394,7.38481 50.44893,7.34128 50.47801,7.29333 50.52544,7.26421 50.5688,7.20735 50.58664,7.17435 50.62284,7.09299 50.63307,6.98349 50.62542,6.89287 50.48412,6.89709 50.42465,6.93962 50.37765,7.04767 50.32812,7.16153 50.29695,7.29896 50.24901,7.37676 50.23851,7.43476 50.22996,7.47857 50.2308,7.53891 50.24604,7.59571 50.2537,7.60991 50.28339))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2005-2026"
 ]
}

 The dataset includes 155829 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002751-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.