cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2wenvc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of ()",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002423-250711103210423/datasets/export for details.
DOI: 10.15468/dl.y4rujp
title: Occurrence Download

description: A dataset containing 1531 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elsholtzia densa"
 ]
}

 The dataset includes 1531 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002425-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zj8dvv
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyprinus carpio",
 "Country is Algeria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002426-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27756177
title: Transitive prediction of small molecule function through alignment of high-content screening resources

description: # Datasets used in Transitive prediction of small molecule function through alignment of high-content screening resources 

This dataset supports the development of CLIP<sup>n</sup>, a contrastive-learning framework designed to align heterogeneous high-content screening (HCS) profile datasets.

***GitHub link:*** https://github.com/AltschulerWu-Lab/CLIPn

## Directory Structure

### Data Files
- **HCS_datasets.pkl**: Contains 13 high-content screening (HCS) datasets from multiple studies across 20 years.
- **Hypoxia.pkl**: Contains 8 profile datasets using different assays and treated under diverse hypoxia durations.
- **Expression.pkl**: Contains 2 transcriptional profile datasets and 6 image profile datasets for multimodal analysis.

### Folders
#### raw_profiles
##### HCS13/
- Contains raw data from 13 high-content screening (HCS) datasets. Each dataset includes meta and feature files. 

##### L1000/
- **CDRP_feature_exp.csv**: Raw L1000 expression data from the CDRP dataset.
- **CDRP_meta_exp.csv**: Metadata associated with the CDRP expression data.
- **LINCS_feature_exp.csv**: Raw L1000 expression data from the LINCS dataset.
- **LINCS_meta_exp.csv**: Metadata associated with the LINCS expression data.

##### RxRx3/
- **RxRx3_feature_final.csv**: Profile data from the RxRx3 dataset.
- **RxRx3_meta_final.csv**: Metadata from the RxRx3 dataset.

##### Uncharacterized_compounds/
- **NCI_cpnData.csv**: Feature data for uncharacterized compounds from the NCI dataset.
- **NCI_cpnInfo.csv**: Information about uncharacterized compounds in the NCI dataset.
- **Prestwick_UTSW_cpnData.csv**: Feature data for uncharacterized compounds from the Prestwick UTSW dataset.
- **Prestwick_UTSW_cpnInfo.csv**: Information about uncharacterized compounds from the Prestwick UTSW dataset.
DOI: 10.6084/m9.figshare.27756177.v1
title: Transitive prediction of small molecule function through alignment of high-content screening resources

description: # Datasets used in Transitive prediction of small molecule function through alignment of high-content screening resources 

This dataset supports the development of CLIP<sup>n</sup>, a contrastive-learning framework designed to align heterogeneous high-content screening (HCS) profile datasets.

***GitHub link:*** https://github.com/AltschulerWu-Lab/CLIPn

## Directory Structure

### Data Files
- **HCS_datasets.pkl**: Contains 13 high-content screening (HCS) datasets from multiple studies across 20 years.
- **Hypoxia.pkl**: Contains 8 profile datasets using different assays and treated under diverse hypoxia durations.
- **Expression.pkl**: Contains 2 transcriptional profile datasets and 6 image profile datasets for multimodal analysis.

### Folders
#### raw_profiles
##### HCS13/
- Contains raw data from 13 high-content screening (HCS) datasets. Each dataset includes meta and feature files. 

##### L1000/
- **CDRP_feature_exp.csv**: Raw L1000 expression data from the CDRP dataset.
- **CDRP_meta_exp.csv**: Metadata associated with the CDRP expression data.
- **LINCS_feature_exp.csv**: Raw L1000 expression data from the LINCS dataset.
- **LINCS_meta_exp.csv**: Metadata associated with the LINCS expression data.

##### RxRx3/
- **RxRx3_feature_final.csv**: Profile data from the RxRx3 dataset.
- **RxRx3_meta_final.csv**: Metadata from the RxRx3 dataset.

##### Uncharacterized_compounds/
- **NCI_cpnData.csv**: Feature data for uncharacterized compounds from the NCI dataset.
- **NCI_cpnInfo.csv**: Information about uncharacterized compounds in the NCI dataset.
- **Prestwick_UTSW_cpnData.csv**: Feature data for uncharacterized compounds from the Prestwick UTSW dataset.
- **Prestwick_UTSW_cpnInfo.csv**: Information about uncharacterized compounds from the Prestwick UTSW dataset.
DOI: 10.15468/dl.ts2jd3
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Badis badis badis"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002427-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15868266
title: Honnef Hirsch-Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.15868267
title: Honnef Hirsch-Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.6084/m9.figshare.27981239
title: Co-benefits for cropland yield, nitrogen emissions, and climate impact through multi-objective optimization agricultural manure solutions

description: Original meta-analysis data on the effects of manure substitution on yield, nitrogen emissions and soil health of different crops
DOI: 10.6084/m9.figshare.27981239.v1
title: Co-benefits for cropland yield, nitrogen emissions, and climate impact through multi-objective optimization agricultural manure solutions

description: Original meta-analysis data on the effects of manure substitution on yield, nitrogen emissions and soil health of different crops
DOI: 10.6084/m9.figshare.29099156
title: Host albumin metabolically unlocks an alternative oxylipin-mediated pathogenicity strategy of <i>Candida albicans</i>

description: Source data:
Source data file of all data used to generate the graphs in the manuscript

Suplementary data 1:
Transcriptional profiling dataset of Candida albicans SC5314 infecting A-431 cells in the presence or absence of human serum albumin at 5 mg/mL. Data is from RNA sequencing was performed at 0.5 h, 3 h, and 24 h of infection.

Suplementary data 2:
Metabolome dataset of Candida albicans cells (intracellular metabolome) when grown in the presence or absence of human serum albumin at 5 mg/mL. Data is from 3 h, and 24 h of timepoints.

Suplementary data 3:
Metabolome dataset of Candida albicans supernatants (exometabolome) when grown in the presence or absence of human serum albumin at 5 mg/mL. Data is from a 24 h timepoint.
DOI: 10.6084/m9.figshare.29099156.v1
title: Host albumin metabolically unlocks an alternative oxylipin-mediated pathogenicity strategy of <i>Candida albicans</i>

description: Source data:
Source data file of all data used to generate the graphs in the manuscript

Suplementary data 1:
Transcriptional profiling dataset of Candida albicans SC5314 infecting A-431 cells in the presence or absence of human serum albumin at 5 mg/mL. Data is from RNA sequencing was performed at 0.5 h, 3 h, and 24 h of infection.

Suplementary data 2:
Metabolome dataset of Candida albicans cells (intracellular metabolome) when grown in the presence or absence of human serum albumin at 5 mg/mL. Data is from 3 h, and 24 h of timepoints.

Suplementary data 3:
Metabolome dataset of Candida albicans supernatants (exometabolome) when grown in the presence or absence of human serum albumin at 5 mg/mL. Data is from a 24 h timepoint.
DOI: 10.15468/dl.xq38qm
title: Occurrence Download

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

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002430-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7e8a39
title: Occurrence Download

description: A dataset containing 382 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elsholtzia pilosa"
 ]
}

 The dataset includes 382 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002429-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28408385
title: A taxonomically reliable DNA barcode reference library for North Sea macrobenthos

description: The dataset includes the GEANS reference library (including the sequences), details on the 4,005 barcodes produced (and their associated photos) or validated, the North Sea species list, the list of species targeted for barcoding in GEANS as well as the NJ trees for each phylum.
DOI: 10.6084/m9.figshare.28408385.v1
title: A taxonomically reliable DNA barcode reference library for North Sea macrobenthos

description: The dataset includes the GEANS reference library (including the sequences), details on the 4,005 barcodes produced (and their associated photos) or validated, the North Sea species list, the list of species targeted for barcoding in GEANS as well as the NJ trees for each phylum.
DOI: 10.15468/dl.jetttj
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bagarius lica"
 ]
}

 The dataset includes 22 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002431-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15868286
title: Hönningen Sprudel-Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.15868287
title: Hönningen Sprudel-Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.ys9b5f
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia affinis",
 "Country is Algeria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002434-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ydenfk
title: Occurrence Download

description: A dataset containing 676 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Embelia angustifolia"
 ]
}

 The dataset includes 676 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002433-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d55z2a
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bagarius yarrelli"
 ]
}

 The dataset includes 161 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002435-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15868300
title: Hooksiel Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.15868301
title: Hooksiel Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.5nmj4y
title: Occurrence Download

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

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002436-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epxvw2
title: Occurrence Download

description: A dataset containing 166336 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepomis macrochirus)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 166336 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002428-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhvcjb
title: Occurrence Download

description: A dataset containing 2369 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Embelia ribes"
 ]
}

 The dataset includes 2369 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002437-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kn9jc
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AAI7678"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002438-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15868318
title: Hopsten Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.5281/zenodo.15868319
title: Hopsten Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.rqtgxz
title: Occurrence Download

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

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002439-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eaxrnj
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Leptobarbus hoevenii)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 41 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002440-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ysd75
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADX8351"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002442-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmgqww
title: Occurrence Download

description: A dataset containing 2797 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Embothrium coccineum"
 ]
}

 The dataset includes 2797 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002441-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15868337
title: Horn /L. Apotheke (ca. 1924/1947)

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963 [Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).