cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14047723
title: Patch-level UNI feature embeddings from colorectal cancer whole slide images (WSIs) in the SurGen dataset

description: This dataset contains UNI patch embeddings derived from the SurGen cohort's whole slide images (WSIs), focused on colorectal cancer cases. Each WSI was processed into 224x224 pixel tissue patches, extracted at a scale of 1.0 microns per pixel (MPP). A 1024-dimensional embedding was computed for each patch using the UNI foundation model[1]. This dataset allows for rapid downstream analysis of tasks such as biomarker prediction, survival analysis, tumour grading, and prognostic modelling. The SurGen dataset, comprising both primary colorectal and metastatic cases, offers a valuable resource for computational pathology research.

Each Zarr file within the dataset contains an array of patch-level features and a corresponding array of coordinates, enabling the retrieval of specific feature locations as needed.

Embeddings are provided in a zip archive and intended for reuse in research focused on digital pathology, tumour genomics, and oncology. For cohort ground truth labels please see the link below.

Access the original dataset: https://doi.org/10.6019/S-BIAD1285

GitHub for more info: https://github.com/CraigMyles/SurGen-Dataset

[1] Chen, R.J., Ding, T., Lu, M.Y., Williamson, D.F.K., et al. Towards a general-purpose foundation model for computational pathology. Nat Med (2024). https://doi.org/10.1038/s41591-024-02857-3
DOI: 10.15468/dl.dyqtge
title: Occurrence Download

description: A dataset containing 68695 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "TaxonKey is Cyanopica cyanus (Pallas, 1776)"
 ]
}

 The dataset includes 68695 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047822-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpwvp2
title: Occurrence Download

description: A dataset containing 11403661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11403661 records from 4486 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047821-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qwy962
title: Occurrence Download

description: A dataset containing 179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Veronica argute-serrata Regel & Schmalh.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 179 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045654-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vy09ag
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Strengeriana antioquensis von Prahl, 1987"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035823-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7642p
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is UCBG TAPIR Provider"
 ]
}

 The dataset includes 97 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115780-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zb3wgn
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Foudia sechellarum E.Newton, 1867"
 ]
}

 The dataset includes 408 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060588-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6k2a6h
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acanthomysis aspera Ii, 1964)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045655-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.segto1
title: Occurrence Download

description: A dataset containing 348321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arrhenatherum elatius (L.) P.Beauv. ex J.Presl & C.Presl",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 348321 records from 327 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035824-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unw9b6
title: Occurrence Download

description: A dataset containing 11171 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eristalis intricaria (Linnaeus, 1758)"
 ]
}

 The dataset includes 11171 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0120492-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nvrpn
title: Occurrence Download

description: A dataset containing 2153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32496433333334 65.07073733333334, 69.37031999999999 65.07073733333334, 69.37031999999999 82.15736799999999, 35.32496433333334 82.15736799999999, 35.32496433333334 65.07073733333334))",
 "EventDate is 2015-07-01,2015-07-31"
 ]
}

 The dataset includes 2153 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060624-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q842fq
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is SD - SD Herbarium, San Diego Natural History Museum"
 ]
}

 The dataset includes 123 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115762-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wweg75
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hypolobocera rotundilobata Rodríguez, 1994"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035838-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnxa7p
title: Occurrence Download

description: A dataset containing 977 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trichopsis vittata (Cuvier, 1831)"
 ]
}

 The dataset includes 977 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003418-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gt11y
title: Occurrence Download

description: A dataset containing 234937 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Mexico",
 "Country is El Salvador",
 "Country is Ecuador",
 "Country is Peru",
 "Country is Bolivia (Plurinational State of)",
 "Country is Colombia",
 "Country is French Guiana",
 "Country is Guyana",
 "Country is Argentina",
 "Country is Brazil",
 "Country is Costa Rica",
 "Country is Dominican Republic",
 "Country is Jamaica",
 "Country is Venezuela (Bolivarian Republic of)",
 "Country is Paraguay",
 "Country is Uruguay",
 "Country is Chile",
 "Country is Honduras",
 "Country is Panama",
 "Country is Nicaragua",
 "Country is Guatemala",
 "Country is Belize",
 "Country is Suriname",
 "Country is Haiti"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Phyllostomidae"
 ]
}

 The dataset includes 234937 records from 232 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035826-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a3kcnj
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is SMNS Herpetologie"
 ]
}

 The dataset includes 122 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115763-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cdpv8
title: Occurrence Download

description: A dataset containing 1037 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monoplex pilearis (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 1037 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060533-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqda7c
title: Occurrence Download

description: A dataset containing 5752982 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5752982 records from 972 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097814-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1176873.10fu
title: SH1176873.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176876.10fu
title: SH1176876.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176882.10fu
title: SH1176882.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176889.10fu
title: SH1176889.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176909.10fu
title: SH1176909.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176915.10fu
title: SH1176915.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.umgtub
title: Occurrence Download

description: A dataset containing 172 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothriechis nigroviridis"
 ]
}

 The dataset includes 172 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002746-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1176919.10fu
title: SH1176919.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176920.10fu
title: SH1176920.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176926.10fu
title: SH1176926.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1176927.10fu
title: SH1176927.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.