cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17199596
title: Nichesphere tutorial data

description: Nichesphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting cell boundaries overlaps for each cell type pair in single cell spatial data (MERFISH , CODEX …).

It also offers the possibility to look at biological process based differential communication among differential co-localization domains based on Ligand-Receptor pairs expression data, such as results from CrossTalkeR [ref.].

In our first example on Differential co-localization and process based differential communication analysis, we will use data from the Myocardial Infarction atlas from Kuppe, C. et. Al., 2022 to find differential co-localization domains and underlying differential cell - cell communication networks related to ischemia:

Dataset:

FileName: heart_MI_ST_SC_23samples.h5muModalities: ST+scRNAseqPhenotypes: 'border', 'fibrotic', 'ischemic', 'myogenic', 'remote'Filtering: minimum 1500 cells per sample

Annotation (for scRNAseq modality, mudata['sc']):

- mudata.obs column: "cell_type": 11 

- mudata.obs column: "cell_subtype2" 33

Phenotype (in scRNAseq modality, mudata['sc']):

- mudata.obs column: "sampleType"

Phenotype based ID (in both modalities, mudata['sc'] and mudata['visium']):



mudata.obs column: "patient_region_id"


Database:

Filename: nichesphereDB_pmid.csv

Nichesphere fibrosis related database contains ligands related to the biological processes below:








Process



Database



Number of ligands





Collagens



Matrisome (PMID:36399478)



45





ECM affiliated



Matrisome (PMID:36399478)



129





ECM glycoproteins



Matrisome (PMID:36399478)



168





ECM regulators



Matrisome (PMID:36399478)



204





Proteoglycans



Matrisome (PMID:36399478)



36





SecretedFactors



Matrisome (PMID:36399478)



265





Chemokine



Cytosig (PMID:34594031)



42





Cytokine



Cytosig (PMID:34594031)



86





GrowthFactor



Cytosig (PMID:34594031)



130





Inhibitory



Cytosig (PMID:34594031)



36






Folders "coloc", "comm" and "preprocessing" contain the necessary data to run each related tutorial, including jupyter notebooks. The rest of data files are explained along the tutorials.
DOI: 10.15468/dl.7wahv3
title: Occurrence Download

description: A dataset containing 24894 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-6.0953 36.93439,-6.50549 36.77208,-6.23729 36.32215,-6.00064 36.08664,-5.31437 35.93988,-4.9594 36.46819,-5.44058 36.73416,-5.71667 36.92358,-6.0953 36.93439))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 24894 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015463-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z425tf
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aesculus parviflora",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 70 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015467-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/xzd6uw
title: PAN-00173313 - lead block weight

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00173313&lt;/p&gt;
description: Modified: 2025-09-25T13:20:58+02:00
DOI: 10.5281/zenodo.17200511
title: senate-committees

description: This is a hypergraph, where nodes are members of the US Senate, and hyperedges correspond to commitee memberships. The dataset is derived from Congressional data compiled by Charles Stewart and Jonathan Woon. Each node is labeled with political party affiliation.

Find the dataset details in AHORN.
DOI: 10.5281/zenodo.17200512
title: senate-committees

description: This is a hypergraph, where nodes are members of the US Senate, and hyperedges correspond to commitee memberships. The dataset is derived from Congressional data compiled by Charles Stewart and Jonathan Woon. Each node is labeled with political party affiliation.

Find the dataset details in AHORN.
DOI: 10.15468/dl.vtdd5s
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aesculus parviflora",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 431 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015468-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3pu796
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aesculus parviflora",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015469-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nff2w
title: Occurrence Download

description: A dataset containing 45090 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hierophis viridiflavus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 45090 records from 1208 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015471-250920141307145/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.30208123
title: Metagenomic assembled genomes (MAGs)

description: 5866 MAGs of Qinghai-Xizang Lake Sediment Genome (QXLSG) catalogue, compressed by lakes
DOI: 10.6084/m9.figshare.30208123.v1
title: Metagenomic assembled genomes (MAGs)

description: 5866 MAGs of Qinghai-Xizang Lake Sediment Genome (QXLSG) catalogue, compressed by lakes
DOI: 10.15468/dl.kdnnny
title: Occurrence Download

description: A dataset containing 6558 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhincodon typus"
 ]
}

 The dataset includes 6558 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015470-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epf64t
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cranichis nudilabia Pabst"
 ]
}

 The dataset includes 42 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150539-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ndlcyw
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phrynocephalus ornatus Boulenger, 1887",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "DatasetKey is Literary descriptions of Iranian lizards"
 ]
}

 The dataset includes 36 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003810-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7m2xuq
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cranichis tenuis Rchb.f."
 ]
}

 The dataset includes 29 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150556-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mki0s7
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rumex sellowianus Rech.fil."
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003810-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3w7c69
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cranichis picta Rchb.f."
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150542-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.et9uwm
title: Occurrence Download

description: A dataset containing 3796039 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "PublishingCountry is Mexico",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 3796039 records from 354 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003810-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3pn2rn
title: Occurrence Download

description: A dataset containing 280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is 2cd829bb-b713-433d-99cf-64bef11e5b3e",
 "TaxonKey is Canis Linnaeus, 1758"
 ]
}

 The dataset includes 280 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150547-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.o6bjdi
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum heterodoxum Dunal"
 ]
}

 The dataset includes 337 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003810-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z24499
title: Occurrence Download

description: A dataset containing 4628 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craspedia variabilis J.Everett & Doust"
 ]
}

 The dataset includes 4628 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150598-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.loeqnk
title: Occurrence Download

description: A dataset containing 16886 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex diandra Schrank"
 ]
}

 The dataset includes 16886 records from 170 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-150316153013904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.th2zm6
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150555-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnamuo
title: Occurrence Download

description: A dataset containing 1503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Month is greater than or equal to January",
 "Country is United States of America",
 "TaxonKey is Diplopoda"
 ]
}

 The dataset includes 1503 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sap7we
title: Occurrence Download

description: A dataset containing 137 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cranichis subumbellata A.Rich. & Galeotti"
 ]
}

 The dataset includes 137 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150553-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f315ni
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "DecimalLatitude is greater than 41.4088616047421",
 "DecimalLatitude is less than 41.9270004101303",
 "DecimalLongitude is greater than -91.7001004930835",
 "DecimalLongitude is less than -91.0033973538803"
 ]
}

 The dataset includes 148 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-171025204727650/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f8cncy
title: Occurrence Download

description: A dataset containing 274 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craspedia costiniana J.Everett & J.Thomps."
 ]
}

 The dataset includes 274 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150581-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98dk1d
title: Occurrence Download

description: A dataset containing 189 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spilogale pygmaea Thomas, 1898"
 ]
}

 The dataset includes 189 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hppgla
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum ptycanthum Dunal"
 ]
}

 The dataset includes 85 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003811-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mtyyhd
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craspedorhachis rhodesiana Rendle"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150605-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nsh7n
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craspedorhachis africana Benth."
 ]
}

 The dataset includes 186 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150601-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.madx4f
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asplenium cariocanum Brade",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdyetd
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crassocephalum bauchiense (Hutch.) Milne-Redh."
 ]
}

 The dataset includes 74 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150606-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umcpv9
title: Occurrence Download

description: A dataset containing 90189 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is African Mammalia"
 ]
}

 The dataset includes 90189 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jjfl7
title: Occurrence Download

description: A dataset containing 405 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Passiflora ambigua Hemsl. ex Hook.fil."
 ]
}

 The dataset includes 405 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8v9283
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cranichis werffii Garay"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150561-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sku4hu
title: Occurrence Download

description: A dataset containing 356 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craniolaria integrifolia Cham."
 ]
}

 The dataset includes 356 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150564-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.okujc1
title: Occurrence Download

description: A dataset containing 876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago sativa",
 "Country is Russian Federation"
 ]
}

 The dataset includes 876 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-150811131857512/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lpvbl5
title: Occurrence Download

description: A dataset containing 334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pteronotus davyi Gray, 1838",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-93 7,-93 17,-78 17,-78 7,-93 7))"
 ]
}

 The dataset includes 334 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-150831095807960/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fh4fx8
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craniospermum canescens DC."
 ]
}

 The dataset includes 20 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150565-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.an4eej
title: Occurrence Download

description: A dataset containing 3906374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 3906374 records from 581 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ghgc2p
title: Occurrence Download

description: A dataset containing 165 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craniolaria annua L."
 ]
}

 The dataset includes 165 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150562-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v5zwka
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is United States of America",
 "Country is Mexico"
 ]
 },
 "TaxonKey is Asclepias texana A.Heller"
 ]
}

 The dataset includes 186 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003812-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mjrb4
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craniolaria argentina Speg."
 ]
}

 The dataset includes 28 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150563-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d39k3a
title: Occurrence Download

description: A dataset containing 533 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craspedia canens J.Everett & Doust"
 ]
}

 The dataset includes 533 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150579-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.