cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17715905
title: human_disease_schaefer

description: Human disease dataset annoted in Schaefer et al. 2024

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/human_disease_schaefer_single_no_caption](https://huggingface.co/datasets/jo-mengr/human_disease_schaefer_single_no_caption)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/human_disease/rnaseq._.samples.h5ad)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.15468/dl.p5gkg6
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Apodemus peninsulae, Arctictis binturong, Arctogalidia trivirgata, Arctonyx albogularis, Arctonyx collaris, Arielulus circumdatus, Arielulus societatis, Aselliscus dongbacanus, Aselliscus stoliczkanus, Atherurus macrourus, Axis axis, Balionycteris maculata, Balionycteris seimundi, Bandicota bengalensis, Bandicota indica, Bandicota savilei, Barbastella darjelingensis, Barbastella leucomelas, Belomys pearsonii, Berylmys berdmorei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 1969"
 ]
}

 The dataset includes 198 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037033-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17715395
title: human_pancreas_luecken

description: Pancreas dataset with complex batch effects (different assays) from Luecken et. al

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/human_pancreas_luecken_single_no_caption](https://huggingface.co/datasets/jo-mengr/human_pancreas_luecken_single_no_caption)- **Raw Data Source**: [Download](https://figshare.com/ndownloader/files/24539828)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.5281/zenodo.17715396
title: human_pancreas_luecken

description: Pancreas dataset with complex batch effects (different assays) from Luecken et. al

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/human_pancreas_luecken_single_no_caption](https://huggingface.co/datasets/jo-mengr/human_pancreas_luecken_single_no_caption)- **Raw Data Source**: [Download](https://figshare.com/ndownloader/files/24539828)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.15468/dl.64vadc
title: Occurrence Download

description: A dataset containing 971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is one of (Adenocalymma adenophorum (Sandwith) L.G.Lohmann, Adenocalymma albiflorum (Salzm. ex DC.) B.M.Gomes & L.H.Fonseca, Adenocalymma allamandiflorum (Bureau ex K.Schum.) L.G.Lohmann, Adenocalymma apurense (Kunth) Sandwith, Adenocalymma biternatum (A.Samp.) L.G.Lohmann, Adenocalymma bracteolatum DC., Adenocalymma bracteosum (DC.) L.G.Lohmann, Adenocalymma calcareum Udulutsch & P.Dias, Adenocalymma cidii (A.H.Gentry ex Hauk) L.G.Lohmann, Adenocalymma cladotrichum (Sandwith) L.G.Lohmann)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 971 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037034-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y6j22e
title: Occurrence Download

description: A dataset containing 52073 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Limosa limosa, Limosa limosa melanuroides, Limosa limosa islandica, Navicula limosa limosa, Pinanga limosa limosa, Navicula limosa limosa, Limosa limosa bohaii, Heteranthera limosa limosa, Limosa limosa limosa, Dendronina limosa limosa)"
 ]
}

 The dataset includes 52073 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037002-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17827890
title: GloSED - Global standardised soil eukaryome dataset

description: Global Standardised Soil Eukaryome Dataset (GloSED)

Dataset description

The GloSED dataset is a metabarcoding-based dataset encompassing the entire spectrum of soil eukaryotes collected and analysed using standardized protocols.

Key characteristics

- Sampling sites: 4,147 globally distributed locations across 121 countries  - Taxonomic scope: Complete soil eukaryome including fungi, protists, animals, and plants  - Operational taxonomic units: 988,824 curated OTUs  - Sequencing technology: PacBio long-read sequencing of full-length ITS  

Data collection and processing

- Standardized sampling design: 50x50 m plots  - Soil cores: 40 cores per plot (5 cm diameter x 5 cm depth), pooled by volume  - DNA extraction: PowerMax Soil DNA Isolation kit (Qiagen) with FavorPrep cleanup  - Primers: universal eukaryotic primers ITS9mun/ITS4ngsUni  - Processing: NextITS v.1.0.0 workflow (DOI: 10.5281/zenodo.15074882)  - Taxonomic annotation: EUKARYOME v.1.9.4 database (DOI: 10.1093/database/baae043)  

 Data files and formats

Core data

- `GloSED__OTU_sequences.fasta.gz`: Quality-filtered representative sequences for all OTUs, FASTA format  - `GloSED__OTU_table.tsv.zip`: Sample-by-OTU abundance matrix (TSV format)  - `GloSED__Taxonomy.tsv.zip`: Complete taxonomic annotations with UNITE-based species hypotheses (TSV format)  

- `GloSED__OTU_table.parquet`: Columnar format of abundance data for efficient querying (Parquet format)  - `GloSED__Taxonomy.parquet`: Columnar format of taxonomic data (Parquet format)  

- `GloSED__phyloseq.RData`: phyloseq object for R-based analyses  - `GloSED__BIOM.biom`: BIOM v.2.1 format compatible with QIIME2  

Metadata files

- `GloSED__Sample_metadata.xlsx`: Sample metadata  - `DRI.json`: Data Reuse Information tag with ORCID identifiers  - `DRI.csv`: Tabular format mapping accession IDs 

- `Contributors.xlsx`: List of contributors

Data reuse information

This dataset includes Data Reuse Information (DRI) tags to support equitable data sharing (Hug et al., 2025). The DRI identifies creators who prefer to be contacted before reuse:

DRI: `{0000-0002-1635-1249, 0000-0003-2786-2690}`

Please contact these individuals prior to reuse of the data.

Related resources



Raw sequence data:



European Nucleotide Archive (ENA) project: PRJEB103811

Sample accessions: ERS27941879 - ERS27946063  

Sequence accessions: ERR15957609 - ERR15964175



Bioinformatics pipeline: NextITS

Reference databases: EUKARYOME, UNITE
DOI: 10.5281/zenodo.17827889
title: GloSED - Global standardised soil eukaryome dataset

description: Global Standardised Soil Eukaryome Dataset (GloSED)

Dataset description

The GloSED dataset is a metabarcoding-based dataset encompassing the entire spectrum of soil eukaryotes collected and analysed using standardized protocols.

Key characteristics

- Sampling sites: 4,147 globally distributed locations across 121 countries  - Taxonomic scope: Complete soil eukaryome including fungi, protists, animals, and plants  - Operational taxonomic units: 988,824 curated OTUs  - Sequencing technology: PacBio long-read sequencing of full-length ITS  

Data collection and processing

- Standardized sampling design: 50x50 m plots  - Soil cores: 40 cores per plot (5 cm diameter x 5 cm depth), pooled by volume  - DNA extraction: PowerMax Soil DNA Isolation kit (Qiagen) with FavorPrep cleanup  - Primers: universal eukaryotic primers ITS9mun/ITS4ngsUni  - Processing: NextITS v.1.0.0 workflow (DOI: 10.5281/zenodo.15074882)  - Taxonomic annotation: EUKARYOME v.1.9.4 database (DOI: 10.1093/database/baae043)  

 Data files and formats

Core data

- `GloSED__OTU_sequences.fasta.gz`: Quality-filtered representative sequences for all OTUs, FASTA format  - `GloSED__OTU_table.tsv.zip`: Sample-by-OTU abundance matrix (TSV format)  - `GloSED__Taxonomy.tsv.zip`: Complete taxonomic annotations with UNITE-based species hypotheses (TSV format)  

- `GloSED__OTU_table.parquet`: Columnar format of abundance data for efficient querying (Parquet format)  - `GloSED__Taxonomy.parquet`: Columnar format of taxonomic data (Parquet format)  

- `GloSED__phyloseq.RData`: phyloseq object for R-based analyses  - `GloSED__BIOM.biom`: BIOM v.2.1 format compatible with QIIME2  

Metadata files

- `GloSED__Sample_metadata.xlsx`: Sample metadata  - `DRI.json`: Data Reuse Information tag with ORCID identifiers  - `DRI.csv`: Tabular format mapping accession IDs 

- `Contributors.xlsx`: List of contributors

Data reuse information

This dataset includes Data Reuse Information (DRI) tags to support equitable data sharing (Hug et al., 2025). The DRI identifies creators who prefer to be contacted before reuse:

DRI: `{0000-0002-1635-1249, 0000-0003-2786-2690}`

Please contact these individuals prior to reuse of the data.

Related resources



Raw sequence data:



European Nucleotide Archive (ENA) project: PRJEB103811

Sample accessions: ERS27941879 - ERS27946063  

Sequence accessions: ERR15957609 - ERR15964175



Bioinformatics pipeline: NextITS

Reference databases: EUKARYOME, UNITE
DOI: 10.5281/zenodo.17721690
title: cxg_pseudo_bulk_full_train

description: CellxGene pseudo bulk dataset with 350k samples. Annotated with natural language descriptions obtained in CellWhisperer Study.

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation](https://huggingface.co/datasets/jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/cellxgene_census/full_data.h5ad)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.5281/zenodo.17721691
title: cxg_pseudo_bulk_full_train

description: CellxGene pseudo bulk dataset with 350k samples. Annotated with natural language descriptions obtained in CellWhisperer Study.

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation](https://huggingface.co/datasets/jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/cellxgene_census/full_data.h5ad)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.6084/m9.figshare.30818498
title: MERS-CoV Population Vulnerability Meta-Analysis: Host, Geographic, and Temporal Patterns from 1,807 Global Sequences

description: This dataset provides a structured meta-analysis of Middle East respiratory syndrome coronavirus (MERS-CoV) sequences to assess population-level vulnerability and pandemic potential. It includes:equence-submissions-list.csv: Curated metadata for 1,807 MERS-CoV sequences (751 human, 678 camel) from NCBI, with host, country, and collection year.protein-metadata.acc: Accession list of structural protein sequences.merscov_population_vulnerability_summary.txt: Summary statistics showing geographic concentration (70% of human cases in Saudi Arabia), temporal decline in cases since 2015, and lack of sustained human-to-human transmission.This resource supports risk assessment of MERS-CoV’s zoonotic constraint and low pandemic potential. All data are released under CC-BY-4.0 for reuse in public health modeling and genomic surveillance.*equence-submissions-list.csv is actually Sequence, a typo, but file name was not corrected because it now is part of few high throughput data processing pipeline, and any name change will render out processing pipelines erroneous.Study by: TahirHB@Hotmail.Com<br><br>
DOI: 10.6084/m9.figshare.30818498.v1
title: MERS-CoV Population Vulnerability Meta-Analysis: Host, Geographic, and Temporal Patterns from 1,807 Global Sequences

description: This dataset provides a structured meta-analysis of Middle East respiratory syndrome coronavirus (MERS-CoV) sequences to assess population-level vulnerability and pandemic potential. It includes:equence-submissions-list.csv: Curated metadata for 1,807 MERS-CoV sequences (751 human, 678 camel) from NCBI, with host, country, and collection year.protein-metadata.acc: Accession list of structural protein sequences.merscov_population_vulnerability_summary.txt: Summary statistics showing geographic concentration (70% of human cases in Saudi Arabia), temporal decline in cases since 2015, and lack of sustained human-to-human transmission.This resource supports risk assessment of MERS-CoV’s zoonotic constraint and low pandemic potential. All data are released under CC-BY-4.0 for reuse in public health modeling and genomic surveillance.*equence-submissions-list.csv is actually Sequence, a typo, but file name was not corrected because it now is part of few high throughput data processing pipeline, and any name change will render out processing pipelines erroneous.Study by: TahirHB@Hotmail.Com<br><br>
DOI: 10.5281/zenodo.17853127
title: Source data for Figure 1 and Supplementary Figures 1-3 of DRAP3R manuscript

description: Source data for Figure 1 and Supplementary Figures 1-3 in the manuscript entitled: Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing (DRAP3R)
DOI: 10.5281/zenodo.17853128
title: Source data for Figure 1 and Supplementary Figures 1-3 of DRAP3R manuscript

description: Source data for Figure 1 and Supplementary Figures 1-3 in the manuscript entitled: Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing (DRAP3R)
DOI: 10.15468/dl.9hhuja
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Notophyllum americanum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037035-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bd9d4n
title: Occurrence Download

description: A dataset containing 616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Berylmys bowersi, Berylmys mackenziei, Berylmys manipulus, Biswamoyopterus biswasi, Biswamoyopterus laoensis, Blarinella griselda, Blarinella quadraticauda, Blarinella wardi, Bos gaurus, Bos javanicus, Bos sauveli, Boselaphus tragocamelus, Budorcas taxicolor, Callosciurus caniceps, Callosciurus erythraeus, Callosciurus finlaysonii, Callosciurus inornatus, Callosciurus nigrovittatus, Callosciurus notatus, Callosciurus phayrei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 1969"
 ]
}

 The dataset includes 616 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037036-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17723522
title: cxg_pseudo_bulk_full_val

description: CellxGene pseudo bulk dataset with 350k samples. Annotated with natural language descriptions obtained in CellWhisperer Study.

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation](https://huggingface.co/datasets/jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/cellxgene_census/full_data.h5ad)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.5281/zenodo.17723523
title: cxg_pseudo_bulk_full_val

description: CellxGene pseudo bulk dataset with 350k samples. Annotated with natural language descriptions obtained in CellWhisperer Study.

## Processed AnnData Objects

This deposit contains processed AnnData objects (single-cell genomics data) that were processed using the `adata_hf_datasets` Python package. The files are in HDF5 (.h5ad) or Zarr format and contain preprocessed gene expression data along with computed embeddings.

### Available Embeddings (.obsm layers)

The AnnData objects contain the following embedding layers: `X_pca`, `X_scvi_fm`, `X_geneformer`, `X_gs10k`, `X_geneformer-v1`, `X_cw-geneformer`.

## Related Resources

- **HuggingFace Dataset**: [jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation](https://huggingface.co/datasets/jo-mengr/cxg_pseudo_bulk_full_multiplets_natural_language_annotation)- **Raw Data Source**: [Download](https://medical-epigenomics.org/papers/schaefer2024/data/datasets/cellxgene_census/full_data.h5ad)

## Package Information

These files were processed using the `adata_hf_datasets` package. For more information about the processing pipeline, please refer to the associated HuggingFace dataset repository.
DOI: 10.15468/dl.uh2w56
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Plan de gestion 2020 - 2024 du site du Vallon du Manas (64) mené par le CEN Nouvelle-Aquitaine-Observations faunistiques (inventaire) réalisées par le CEN Nouvelle-Aquitaine"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037037-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1jrvt3
title: Occurrence Download

description: A dataset containing 713236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arecaceae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 713236 records from 418 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030068-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a8sv6s
title: Occurrence Download

description: A dataset containing 5929 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Pinus canariensis C.Sm. ex DC.",
 "TaxonKey is Pinus canariensis f. brevifolia Kuntze",
 "TaxonKey is Pinus canariensis C.Sm.",
 "TaxonKey is Pinus canariensis f. canariensis"
 ]
}

 The dataset includes 5929 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059765-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfcxja
title: Occurrence Download

description: A dataset containing 184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taraxacum officinale Weber",
 "Country is Canada"
 ]
}

 The dataset includes 184 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053324-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3tyzwj
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphydryas gillettii (W.Barnes, 1897)"
 ]
}

 The dataset includes 161 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002243-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.