cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.v3h5zn
title: Occurrence Download

description: A dataset containing 430 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mustelus californicus Gill, 1864"
 ]
}

 The dataset includes 430 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012641-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xfkeia
title: Occurrence Download

description: A dataset containing 12052 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "Year 1960-2019",
 "HasCoordinate is true",
 "TaxonKey is Plebejus argus (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12052 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004517-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdspxs
title: Occurrence Download

description: A dataset containing 371 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.89495 16.98349,-96.92997 16.88942,-96.93066 16.88873,-96.89083 16.83792,-96.83315 16.83792,-96.78097 16.87912,-96.77341 16.93474,-96.78028 16.9883,-96.87984 17.00752,-96.95194 16.99379,-96.92516 16.92856,-96.90456 16.95946,-96.89495 16.98349))",
 "HasCoordinate is true",
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 371 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008559-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zbuc4c
title: Occurrence Download

description: A dataset containing 138258 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mirounga leonina (Linnaeus, 1758)"
 ]
}

 The dataset includes 138258 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012633-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9cc8pw
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is NT",
 "TaxonKey is Narcissus cuatrecasasii Fern.Casas, M.Laínz & Ruíz Rejón"
 ]
}

 The dataset includes 148 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079483-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxhtgs
title: Occurrence Download

description: A dataset containing 1357658 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Acer negundo L., Ailanthus altissima (Mill.) Swingle, Amaranthus retroflexus L., Ambrosia artemisiifolia L., Galinsoga parviflora Cav., Helianthus tuberosus L., Heracleum mantegazzianum Sommier & Levier, Impatiens glandulifera Royle, Impatiens parviflora DC., Lupinus polyphyllus Lindl., Lycium barbarum L., Pinus strobus L., Prunus serotina Ehrh., Reynoutria ×bohemica Chrtek & Chrtková, Reynoutria japonica Houtt., Reynoutria sachalinensis (F.Schmidt) Nakai, Robinia pseudoacacia L., Rudbeckia laciniata L., Solidago canadensis L., Solidago gigantea Aiton)"
 ]
}

 The dataset includes 1357658 records from 1646 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082482-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17395128
title: Data supporting "Genetic and Microbial Mechanisms Linking Oral and Gastrointestinal Diseases: Evidence from Integrative Multi-Omics Analyses"

description: This dataset supports the manuscript entitled “Genetic and Microbial Mechanisms Linking Oral and Gastrointestinal Diseases: Evidence from Integrative Multi-Omics Analyses,” submitted to Gut Microbes.

The repository contains processed data and analysis scripts generated during the study, which investigated the shared genetic architecture and microbial mediation between oral and gastrointestinal diseases using genome-wide association studies, pleiotropy mapping, transcriptome- and proteome-wide integration, and bidirectional Mendelian randomization analyses.

Contents include:





Harmonized GWAS summary statistics for oral and gastrointestinal traits.




Pleiotropy and colocalization results (PLACO and FUMA analyses).




Mendelian randomization and microbial mediation scripts and outputs.




Multi-omics integration results (TWAS/PWAS).




Data underlying main and supplementary figures.



Primary GWAS data were obtained from the UK Biobank and the Million Veteran Program under their data access policies. All derived summary data and scripts are freely available for reuse and further analysis.

Citation: Zhang R, Gao Y, Zhong W, Duan X, He Y, Ye Q. Data supporting “Genetic and Microbial Mechanisms Linking Oral and Gastrointestinal Diseases: Evidence from Integrative Multi-Omics Analyses.” Zenodo. 2025. DOI: 10.5281/zenodo.17395128].

License: CC-BY 4.0Contact: Dr. Rui Zhang (2020283020180@whu.edu.cn)
DOI: 10.15468/dl.7ffver
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nigidius lewisi Boileau, 1905",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0209059-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb98hz
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.35042 44.59452,-79.2398 44.59716,-79.25547 44.69124,-79.29648 44.70976,-79.31897 44.69455,-79.35042 44.59452))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EX, CR, EW, EN, VU, NT)",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 1600-2023"
 ]
}

 The dataset includes 72 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0259814-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsaqfb
title: Occurrence Download

description: A dataset containing 1706 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glechoma hederacea subsp. grandis (A.Gray) H.Hara",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1706 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186630-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxue3s
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothrocophias microphthalmus (Cope, 1875)"
 ]
}

 The dataset includes 163 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0259798-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j95jap
title: Occurrence Download

description: A dataset containing 566 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lythrum anceps (Koehne) Makino",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 566 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186628-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhe7qu
title: Occurrence Download

description: A dataset containing 624 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lathrocasis tenerrima (A.Gray) L.A.Johnson"
 ]
}

 The dataset includes 624 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004439-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wn87r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kopsia flavida Blume",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0202050-220831081235567/datasets/export for details.
DOI: 10.15468/dl.t69kzc
title: Occurrence Download

description: A dataset containing 409 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Japan",
 "TaxonKey is Ursus thibetanus G"
 ]
}

 The dataset includes 409 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008843-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j7nj3f
title: Occurrence Download

description: A dataset containing 20180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caryophyllaceae",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 20180 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186629-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awk6ea
title: Occurrence Download

description: A dataset containing 1155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Cameroon, Congo, Democratic Republic of the, Gabon, Congo)",
 "TaxonKey is Casearia Jacq."
 ]
}

 The dataset includes 1155 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275098-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bp2ph8
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oxalis triangularis A.St.-Hil.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186636-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n3j645
title: Occurrence Download

description: A dataset containing 1843 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Glyptemys muhlenbergii (Schoepff, 1801))"
 ]
}

 The dataset includes 1843 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275100-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sc966x
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parambassis siamensis (Fowler, 1937)",
 "TaxonKey is Parambassis siamensis (Fowler, 1937)",
 "TaxonKey is Esomus metallicus Ahl, 1923",
 "Year is greater than 0"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275096-220831081235567/datasets/export for details.
DOI: 10.15468/dl.ybzh2r
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Epilobium fauriei Lév.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0206123-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbkmmx
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Türkiye",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polygala supina Schreb."
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275097-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z85ghp
title: Occurrence Download

description: A dataset containing 369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Occurrence evidence)",
 "Continent is Asia",
 "Country is India",
 "GadmGid is IND.1_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 369 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208272-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjnsfu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parambassis siamensis (Fowler, 1937)",
 "TaxonKey is Pristolepis fasciata (Bleeker, 1851)",
 "TaxonKey is Esomus metallicus Ahl, 1923",
 "Year is greater than 0"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275099-220831081235567/datasets/export for details.
DOI: 10.15468/dl.7etmcn
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cotula coronopifolia L."
 ]
}

 The dataset includes 31 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208879-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gc9d4x
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chimonanthus praecox (L.) Link",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 43 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186635-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n6amg5
title: Occurrence Download

description: A dataset containing 289 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tulipa kolpakowskiana"
 ]
}

 The dataset includes 289 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015462-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.strhya
title: Occurrence Download

description: A dataset containing 137586 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is one of (Lichen Herbarium (H): Lichen exsiccatae, Lichen collection (NMTG-LICHEN) of Naturmuseum Thurgau, Lichen diversity in forests, Lichen herbarium (H): Type specimens of lichen-forming fungi, Lichen herbarium, UiB, Lichen herbarium, NMBU, Lichen specimen database of Faurie collection, CLU Lichen Herbarium, Lichen diversity in grasslands, LISU Lichen collection)"
 ]
}

 The dataset includes 137586 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015447-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y2pxqa
title: Occurrence Download

description: A dataset containing 11970 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Herpestes ichneumon)",
 "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 11970 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015465-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.szcm8d
title: Occurrence Download

description: A dataset containing 11970 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Herpestes ichneumon)",
 "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 11970 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015464-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yv2sv5
title: Occurrence Download

description: A dataset containing 11970 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Herpestes ichneumon)",
 "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 11970 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015466-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15790388
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.