cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.em76dm
title: Occurrence Download

description: A dataset containing 116512 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Loxia pytyopsittacus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 116512 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011778-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syn3ab
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maeotias inexspectata",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011804-250802193616735/datasets/export for details.
DOI: 10.5281/zenodo.16740756
title: Dataset for: Magmatic volatile flux drives non-eruptive volcano-tectonic seismicity at Mount St. Helens, USA from 2008-2023

description: Full earthquake catalog for Mount St. Helens 2008 to 2024. Video S1 is included here. Please see the Supporting Information file for header descriptions.
DOI: 10.15468/dl.5krk2c
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea quamoclit",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 52 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011805-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qcfg9
title: Occurrence Download

description: A dataset containing 425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Veronica longifolia",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 425 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011806-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nyzf26
title: Occurrence Download

description: A dataset containing 5332 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Loxops coccineus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 5332 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011807-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9r6w6m
title: Occurrence Download

description: A dataset containing 2660 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyclothone pallida"
 ]
}

 The dataset includes 2660 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011808-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3v98jm
title: Occurrence Download

description: A dataset containing 272 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centaurea virgata",
 "Geometry POLYGON ((26.04335 1.226334, 135.0263 1.226334, 135.0263 55.38525, 26.04335 55.38525, 26.04335 1.226334))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 272 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011809-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzxgst
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bryconamericus lassorum)",
 "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/0011810-250802193616735/datasets/export for details.
DOI: 10.15468/dl.wz7xbs
title: Occurrence Download

description: A dataset containing 5009 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lurocalis rufiventris)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 5009 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011811-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8uyhfc
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Loxops ochraceus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011812-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7t3nq
title: Occurrence Download

description: A dataset containing 79281 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 (Sphyrapicus thyroideus)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 79281 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011787-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vaedu7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudolysimachion longifolium",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011813-250802193616735/datasets/export for details.
DOI: 10.5281/zenodo.16730944
title: HBV splicing project: transcriptomes, genomic references, and AI models for splice site prediction

description: This archive supports the study "Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models" (Lim CS, Brown CM. 2025. BioRxiv. https://doi.org/10.1101/2025.07.28.667110). It provides the following contents needed to reconstitute the full project structure of the HBV_splicing_paper_2025 GitHub repository.

Contents



data/: Processed HBV transcriptomes from liver biopsies and cultured cells

ref/: Reference genomes and annotations for human and HBV

src/: Source code, pretrained models, and checkpoints for:



SpliceBERT (LLM framework)

OpenSpliceAI (convolutional neural network)

IPSA (splicing metric calculation)




These directories are intended to be unzipped into the root of the GitHub repository to reproduce the complete project structure. Metadata for these files is maintained in the GitHub repository.

 

License Summary

This archive includes code and AI models under the following licenses:



src/SpliceBERT/: BSD 3-Clause

src/OpenSpliceAI/: GNU GPLv3

src/IPSA/: GNU GPLv2
DOI: 10.5281/zenodo.16730945
title: HBV splicing project: transcriptomes, genomic references, and AI models for splice site prediction

description: This archive supports the study "Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models" (Lim CS, Brown CM. 2025. BioRxiv. https://doi.org/10.1101/2025.07.28.667110). It provides the following contents needed to reconstitute the full project structure of the HBV_splicing_paper_2025 GitHub repository.

Contents



data/: Processed HBV transcriptomes from liver biopsies and cultured cells

ref/: Reference genomes and annotations for human and HBV

src/: Source code, pretrained models, and checkpoints for:



SpliceBERT (LLM framework)

OpenSpliceAI (convolutional neural network)

IPSA (splicing metric calculation)




These directories are intended to be unzipped into the root of the GitHub repository to reproduce the complete project structure. Metadata for these files is maintained in the GitHub repository.

 

License Summary

This archive includes code and AI models under the following licenses:



src/SpliceBERT/: BSD 3-Clause

src/OpenSpliceAI/: GNU GPLv3

src/IPSA/: GNU GPLv2
DOI: 10.15468/dl.hxjwfc
title: Occurrence Download

description: A dataset containing 18234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lurocalis semitorquatus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 18234 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011814-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7x7nj
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinanthus alectorolophus",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 64 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010509-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/c1q-y93-wwb
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wha-n5z-5cf
title: Pseudotriloculina linneiana (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ys5-j28-nv5
title: †Belemnitida

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l7z-56n-p4a
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yhb-5n3-d0j
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/29a-gdq-4lf
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vrk-7xk-ewm
title: Isurus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eq4-kmy-qr5
title: Pseudothurmannia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/td5-cfg-gcr
title: †Isocrinus (Isocrinus) von Meyer in Agassiz, 1836

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.jkrx7y
title: Occurrence Download

description: A dataset containing 1494823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 {
 "or" : [
 "Country is Norway",
 "Country is Svalbard and Jan Mayen"
 ]
 }
 ]
}

 The dataset includes 1494823 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021601-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/552-pgy-wyt
title: Orionina reticulata (Hartmann, 1956)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zml-r8m-5za
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/df9-zyw-4f0
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h3y-y2x-0kq
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zn0-f06-fwr
title: †Dominocythere Stoermer & Wienholz, 1967

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9qe-gas-qym
title: †Pseudothurmannia picteti Sarkar, 1955

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/br3-s4t-fpd
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/396-794-l05
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jzr-eqc-pf0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dng-g9z-qss
title: Ungulatella Cushman, 1931

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nyk-hk3-5gw
title: Duvalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qcr-ael-3gn
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/281-5kn-t7g
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/crj-xdk-z8g
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/frj-hr0-lxn
title: Siphonina pulchra Cushman, 1919

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jt5-kt2-20s
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z5a-ffm-94x
title: Pyramidulina comatula (Cushman, 1923)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/epq-9qx-c43
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vl0-kr1-4pc
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dty-0md-ed5
title: Textularia pseudogramen Chapman & Parr, 1937

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ecl-jv5-p9j
title: †Pilocrinus Jaekel, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ns0-mh1-559
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tvn-h81-dqj
title: Pseudothurmannia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wxr-mwa-6ps
title: Pseudothurmannia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qdq-sks-hgp
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tbh-75d-s0k
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5wj-sxd-hqc
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fd9-kn1-1g9
title: Pseudobelus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bxf-fh8-6qt
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xbn-bn4-ha0
title: Phyllopachyceras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/249-p84-80s
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.17358346
title: MainstreamBIO_MutualLearning_Dataset1_2025.10.15_v1

description: Data and insights collected through MainstreamBIO Mutual Learning workshops in each Multi-actor Innovation Platform.
DOI: 10.5281/zenodo.17358347
title: MainstreamBIO_MutualLearning_Dataset1_2025.10.15_v1

description: Data and insights collected through MainstreamBIO Mutual Learning workshops in each Multi-actor Innovation Platform.
DOI: 10.15468/dl.ttxnhx
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050652-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d2gm9h
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102243-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ojovq2
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033160-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.onmtqg
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003477-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6hjqb8
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002712-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aoab1c
title: Occurrence Download

description: A dataset containing 561852542 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is EOD – eBird Observation Dataset"
 ]
}

 The dataset includes 561852542 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002710-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iutml2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102247-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fqfyyx
title: Occurrence Download

description: A dataset containing 1101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pachycondyla stigma (Fabricius, 1804))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1101 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072489-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oaj681
title: Occurrence Download

description: A dataset containing 561852542 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is EOD – eBird Observation Dataset"
 ]
}

 The dataset includes 561852542 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002706-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bbuvww
title: Occurrence Download

description: A dataset containing 1536786432 species occurrences available in GBIF matching the query:
{ }

 The dataset includes 1536786432 records from 17852 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002756-171002173027117/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/11644863
title: Residential Activity Capture Dataset(RACD)
DOI: 10.15468/dl.rxwrvz
title: Occurrence Download

description: A dataset containing 5988 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 Adinandra Jack"
 ]
}

 The dataset includes 5988 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010660-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16636871
title: Youth Empowerment and Crime Reduction in Ekiti State, Nigeria