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

description: A dataset containing 505 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is LiCSiC - Foraminifera Linosa Sicily Channel Collection"
 ]
}

 The dataset includes 505 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036706-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00010327.0
title: Available datapackage for study 'An Open-Label Extension of Study HGT-SAN-055 Evaluating Long Term Safety and Clinical Outcomes of Intrathecal Administration of rhHNS in Patients With Sanfilippo Syndrome Type A (MPS IIIA)'

description: Sanfilippo syndrome, or Mucopolysaccharidosis (MPS) III, is a rare lysosomal storage disease (LSD) caused by loss in activity of 1 of 9 enzymes necessary for degradation of the glycosaminoglycan (GAG) heparan sulfate (HS) in lysosomes. MPS IIIA results from deficiency of the enzyme heparan N-sulfatase (sulfamidase). In the absence of this enzyme, intermediates of the HS degradation process accumulate in the lysosomes of neurons and glial cells, with lesser accumulation outside the brain. MPS IIIA symptoms arise on average at 7 months of age, with the average age of diagnosis at 4.5 years for the majority of patients. Patients present a wide spectrum and severity of clinical symptoms. The central nervous system (CNS) is the most severely affected organ system in patients with MPS IIIA, evidenced by deficits in language development, motor skills, and intellectual development. In addition, there are abnormal behaviors including but not limited to aggression and excess motor activity/hyperactivity that contribute to disturbances in sleep.Overall, individuals with MPS IIIA have a marked developmental delay and significantly reduced lifespan to 15 years of age on average.The purpose of this study is to collect long term safety and tolerability data in patients with MPS IIIA who previously received rhHNS in study HGT-SAN-055 (NCT01155778).
DOI: 10.5281/zenodo.17098066
title: MuSL: Multimodal deep learning for generalizable prediction of synthetic lethality from sequence, transcriptomic, and network data

description: MuSL: Multimodal deep learning for generalizable prediction of synthetic lethality from sequence, transcriptomic, and network data


Model Architecture




The MuSL framework integrates multimodal biological data through a tri-branch deep learning architecture to predict synthetic lethal (SL) gene pairs. As illustrated in the figure above, the model jointly learns from transcriptomic images, statistical features, and protein interaction networks.

1. Feature Learning Pathways

MuSL processes input data through three complementary pathways:





Image-Based Expression Branch (CNN):



Transforms the transcriptome profiles of gene pairs into two-dimensional joint density distribution maps (32×3232×32 histograms).

Utilizes a Convolutional Neural Network (CNN) to automatically extract spatial features, capturing complex patterns such as functional decoupling and mutual exclusivity directly from raw data.





Statistical Feature Branch (MLP):



Extracts 35 handcrafted statistical features capturing explicit expression patterns (e.g., correlation, variation) from the same transcriptomic data.

Projects these features through a dedicated fully connected layer (MLP) to form a representation that complements the deep image features.





Graph-Based Network Branch (GNN):



Models the Protein-Protein Interaction (PPI) network using a Graph Neural Network (GNN).

Crucial Innovation: Initializes node features using ESM2 protein language model embeddings, integrating evolutionary and sequence-level priors to generate robust topological relationship features.




2. Adaptive Fusion & Prediction



Cross-Modal Integration: The framework employs a cross-attention and gating fusion mechanism to dynamically weight and integrate features from all three pathways (CNN, Statistics, and GNN) based on their contextual importance.

Multi-Head Prediction: Predictions are generated from both modality-specific heads and the final fused representation using four specialized classifiers.


3. Training Strategy



Composite Loss Function: The model optimizes a joint objective that combines:



Classification losses from all four prediction heads.

Contrastive learning components to enforce semantic alignment and improve cross-modal consistency.





 




Required Data Files

The following H5AD files need to be downloaded and placed in the processed_data/ directory:



a549_cell_line_imputed.h5ad - A549 cell line single-cell RNA-seq data

k562_cell_line_imputed.h5ad - K562 cell line single-cell RNA-seq data

tcga_all.h5ad - TCGA bulk RNA-seq data

protein_embeddings.pt - Embeddings from ESM2

all_emb_genept.pkl - Embeddings from GenePT
DOI: 10.5281/zenodo.17098065
title: MuSL: Multimodal deep learning for generalizable prediction of synthetic lethality from sequence, transcriptomic, and network data

description: MuSL: Multimodal deep learning for generalizable prediction of synthetic lethality from sequence, transcriptomic, and network data


Model Architecture




The MuSL framework integrates multimodal biological data through a tri-branch deep learning architecture to predict synthetic lethal (SL) gene pairs. As illustrated in the figure above, the model jointly learns from transcriptomic images, statistical features, and protein interaction networks.

1. Feature Learning Pathways

MuSL processes input data through three complementary pathways:





Image-Based Expression Branch (CNN):



Transforms the transcriptome profiles of gene pairs into two-dimensional joint density distribution maps (32×3232×32 histograms).

Utilizes a Convolutional Neural Network (CNN) to automatically extract spatial features, capturing complex patterns such as functional decoupling and mutual exclusivity directly from raw data.





Statistical Feature Branch (MLP):



Extracts 35 handcrafted statistical features capturing explicit expression patterns (e.g., correlation, variation) from the same transcriptomic data.

Projects these features through a dedicated fully connected layer (MLP) to form a representation that complements the deep image features.





Graph-Based Network Branch (GNN):



Models the Protein-Protein Interaction (PPI) network using a Graph Neural Network (GNN).

Crucial Innovation: Initializes node features using ESM2 protein language model embeddings, integrating evolutionary and sequence-level priors to generate robust topological relationship features.




2. Adaptive Fusion & Prediction



Cross-Modal Integration: The framework employs a cross-attention and gating fusion mechanism to dynamically weight and integrate features from all three pathways (CNN, Statistics, and GNN) based on their contextual importance.

Multi-Head Prediction: Predictions are generated from both modality-specific heads and the final fused representation using four specialized classifiers.


3. Training Strategy



Composite Loss Function: The model optimizes a joint objective that combines:



Classification losses from all four prediction heads.

Contrastive learning components to enforce semantic alignment and improve cross-modal consistency.





 




Required Data Files

The following H5AD files need to be downloaded and placed in the processed_data/ directory:



a549_cell_line_imputed.h5ad - A549 cell line single-cell RNA-seq data

k562_cell_line_imputed.h5ad - K562 cell line single-cell RNA-seq data

tcga_all.h5ad - TCGA bulk RNA-seq data

protein_embeddings.pt - Embeddings from ESM2

all_emb_genept.pkl - Embeddings from GenePT
DOI: 10.34740/kaggle/dsv/14055452
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.25934/pr00010329.0
title: Available datapackage for study 'An Open-Label Extension of Study HGT-SAN-093 Evaluating the Safety and Efficacy Study of HGT-1410 (Recombinant Human Heparan N Sulfatase) Administration Via an Intrathecal Drug Delivery Device in Pediatric Patients With Mucopolysaccharidosis Type IIIA Disease'

description: This extension study will allow participants to continue receiving treatment with HGT-1410 and to initiate treatment in patients who received no-treatment in Study HGT-SAN-093, and will evaluate the long-term safety and efficacy of the study drug.
DOI: 10.25934/pr00010328.0
title: Available datapackage for study 'A Randomized, Controlled, Open-label, Multicenter, Phase IIb Safety and Efficacy Study of rhHNS (Recombinant Human Heparan N Sulfatase) Administration Via an Intrathecal Drug Delivery Device in Pediatric Patients With Early Stage Mucopolysaccharidosis Type IIIA Disease'

description: Sanfilippo syndrome Type A, or Mucopolysaccharidosis (MPS) IIIA, is a rare lysosomal storage disease caused by deficiency of the enzyme heparan N-sulfatase (sulfamidase). In the absence of this enzyme, there is an accumulation of the glycosaminoglycan, heparan sulfate, resulting in progressive neurodegeneration. Symptoms are usually first noted in the 1st or 2nd year of life, although definitive diagnosis is often delayed, with an average age of diagnosis of 4.5 years. The disease is characterized by developmental delays initially, followed by neurological developmental arrest, then regression. These developmental deficits are typically associated with severe behavioral disturbances. Patients have a significantly reduced lifespan, with few surviving beyond the 2nd or 3rd decade.The purpose of this study is to evaluate the safety and efficacy of recombinant human heparan-N-sulfatase (rhHNS) in pediatric patients with Early Stage Mucopolysaccharidosis Type III A Disease.
DOI: 10.15468/dl.fu4dcm
title: Occurrence Download

description: A dataset containing 2261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Konosirus punctatus"
 ]
}

 The dataset includes 2261 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036707-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.delphi.dz6j.imle
title: DELPHI simulation data xs_hzha03pyth6156hcnn_e205_m85.0_ka0_1l_e1
DOI: 10.7483/opendata.delphi.7pho.rn8m
title: DELPHI simulation data xs_hzha03pyth6156hattbb_e206.5_m90_m95_ca0_1l_e1
DOI: 10.7483/opendata.delphi.oq0v.gsvi
title: DELPHI simulation data xs_hzha03pyth6156hcmm_e206.5_m40.0_ra0_1l_u1
DOI: 10.7483/opendata.delphi.8fva.pgbk
title: DELPHI simulation data xs_hzha03pyth6156hcmm_e206.5_m55.0_ca0_1l_u1
DOI: 10.7483/opendata.delphi.xpj0.iz2c
title: DELPHI simulation data xs_hzha03pyth6156hattbb_e206.5_m90_m90_ca0_1l_e1
DOI: 10.7483/opendata.delphi.oroi.yjfg
title: DELPHI simulation data xs_hzha03pyth6156hcee_e206.5_m55.0_la0_1l_u1
DOI: 10.7483/opendata.delphi.16jt.pouo
title: DELPHI simulation data xs_hzha03pyth6156hcnn_e206.5_m77.5_ka0_1l_e1
DOI: 10.15468/dl.yf9k7r
title: Occurrence Download

description: A dataset containing 528 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neritina cariosa (Wood, 1828), Neritina clenchi (H.D.Russell, 1940), Neritina granosa G.B.Sowerby I, 1825, Neritina usnea (Röding, 1798))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 528 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0206458-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j725ng
title: Occurrence Download

description: A dataset containing 71560 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((1.8796086666666671 65.07073733333334, 35.924964333333335 65.07073733333334, 35.924964333333335 82.15736799999999, 1.8796086666666671 82.15736799999999, 1.8796086666666671 65.07073733333334))",
 "EventDate is 2015-05-01,2015-05-31"
 ]
}

 The dataset includes 71560 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032787-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iopzbz
title: Occurrence Download

description: A dataset containing 5024 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Digitaria eriantha Steud."
 ]
}

 The dataset includes 5024 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028230-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z2eeb5
title: Occurrence Download

description: A dataset containing 2436 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.11235 -12.32927,-76.81709 -12.32927,-76.81709 -12.09707,-77.11235 -12.09707,-77.11235 -12.32927))",
 "HasGeospatialIssue is false",
 "TaxonKey is Charadrius vociferus Linnaeus, 1758"
 ]
}

 The dataset includes 2436 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002883-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.skzxtu
title: Occurrence Download

description: A dataset containing 2725 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hibiscus mutabilis L."
 ]
}

 The dataset includes 2725 records from 256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021219-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xe0cfy
title: Occurrence Download

description: A dataset containing 400112 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Austria",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 400112 records from 224 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028230-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uv5sm2
title: Occurrence Download

description: A dataset containing 129127 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is BMSM Bailey-Matthews National Shell Museum"
 ]
}

 The dataset includes 129127 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0153031-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdd3y3
title: Occurrence Download

description: A dataset containing 2399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Astronia Blume, Astronidium A.Gray, Beccarianthus Cogn., Tessmannianthus Markgr., Melastoma L., Dissochaeta Blume, Dalenia Korth., Creochiton Blume, Diplectria (Blume) Rchb., Pseudodissochaeta M.P.Nayar, Macrolenes Naudin)"
 ]
}

 The dataset includes 2399 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032761-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ws5mx
title: Occurrence Download

description: A dataset containing 327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polygala senega L.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 327 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177272-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xippnb
title: Occurrence Download

description: A dataset containing 138441 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1950-2018",
 "Geometry POLYGON((-11 34,25 34,25 70,-11 70,-11 34))",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Matricaria chamomilla L.",
 "TaxonKey is Matricaria inodora Lam.",
 "TaxonKey is Tripleurospermum inodorum (L.) Sch.-Bip",
 "TaxonKey is Matricaria perforata Mérat",
 "TaxonKey is Tripleurospermum perforatum (Mérat) M.Laínz",
 "TaxonKey is Tripleurospermum perforatum (Mérat) Wagenitz",
 "TaxonKey is Matricaria recutita L."
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 138441 records from 406 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028231-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrf44m
title: Occurrence Download

description: A dataset containing 90524 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Turdoides malcolmi (Sykes, 1832)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 90524 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032776-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pykj5l
title: Occurrence Download

description: A dataset containing 265462 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Tanzania, United Republic of",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 265462 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028231-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e6pbzz
title: Occurrence Download

description: A dataset containing 1217 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg."
 ]
}

 The dataset includes 1217 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0187370-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vwzluq
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is South Africa",
 "Country is Madagascar"
 ]
 },
 "TaxonKey is Senecio madagascariensis Poir."
 ]
}

 The dataset includes 349 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028231-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ca2v6b
title: Occurrence Download

description: A dataset containing 87012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aplonis panayensis (Scopoli, 1786)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 87012 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032754-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2twgvu
title: Occurrence Download

description: A dataset containing 674 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chamaeleo jacksonii Boulenger, 1896"
 ]
}

 The dataset includes 674 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0167874-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfasuy
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is South Africa",
 "Country is Madagascar"
 ]
 },
 "TaxonKey is Senecio madagascariensis Poir."
 ]
}

 The dataset includes 349 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028233-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gjfb5b
title: Occurrence Download

description: A dataset containing 208726 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Ranidae"
 ]
}

 The dataset includes 208726 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0203528-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/f1k-xtl-3jy
title: Indeterminatae-dicot

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.f2jf5j
title: Occurrence Download

description: A dataset containing 59022 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aphyllanthes monspeliensis L."
 ]
}

 The dataset includes 59022 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139063-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rz4xem
title: Occurrence Download

description: A dataset containing 5861 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhopalosiphum padi (Linnaeus, 1758)"
 ]
}

 The dataset includes 5861 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073723-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-34081
title: Correspondence book No.5 of Pentecostal Missionary Union [PMU], 1923-1925

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 5 including 57 pages of subject index; 2042 pages of PMU outgoing correspondence.
DOI: 10.15468/dl.saymvu
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Marchantia subintegra Mitt."
 ]
}

 The dataset includes 61 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323098-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.