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

description: A dataset containing 61910 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.75063 41.34149,-8.74519 41.33881,-8.71711 41.33194,-8.65423 41.31047,-8.61165 41.30008,-8.50208 41.31913,-8.4538 41.31118,-8.35601 41.33294,-8.32043 41.32555,-8.22427 41.33503,-8.17681 41.34654,-8.14851 41.36858,-8.16048 41.44879,-8.13893 41.52841,-8.06051 41.59785,-8.10809 41.6494,-8.16915 41.64147,-8.27183 41.61222,-8.34426 41.56553,-8.41742 41.55538,-8.43695 41.5443,-8.51241 41.5053,-8.59561 41.45697,-8.69043 41.4062,-8.72916 41.40641,-8.75063 41.34149))",
 "OccurrenceStatus is Present",
 "Year 2022-2025"
 ]
}

 The dataset includes 61910 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011534-251120083545085/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.30731603
title: Reproducibility Scripts for TCMLncDB: TCM and lncRNA Regulation in Cancer

description: This code repository contains all custom scripts and computational pipelines used to process raw data, perform analysis, and assemble the TCMLncDB integrated dataset.The provided code performs the following crucial steps:Data Processing and QC: Scripts like prepare_tpm_expression_data.R are used for pan-cancer TPM data preparation, while tumor_purity_estimation.R calculates tumor purity using the ESTIMATE algorithm, which is essential for accurate downstream analysis.Core Correlation Analysis: The lncRNA_PCG_correlation_analysis.R script calculates partial correlation coefficients between lncRNAs and PCGs across tumors, with the calculation adjusted for tumor purity.TCM-lncRNA Prediction: The key script, TCM_lncRNA_enrichment.R, calculating the lncRES score to quantify the functional association between TCM and lncRNAs.Reproducibility Notes and File StructureThis repository shares the computational steps used to create the final database. A key note is that much of the provided code will not run immediately because the massive TCGA and GEO raw data files are not shared here due to size limitations.GEO Data: Users wishing to fully reproduce the pipeline must first download the raw GEO data files using the accession numbers provided in the input file: Supplementary_Table_S1_GEO_Datasets_List.xlsx.Workflow Guide: The file structure guides the user through the process, with code organized into processing, filtering, and core analysis steps.We have shared all code used to assemble the original integrated dataset, enabling full transparency and validation of the methodology.
DOI: 10.6084/m9.figshare.30731603.v1
title: Reproducibility Scripts for TCMLncDB: TCM and lncRNA Regulation in Cancer

description: This code repository contains all custom scripts and computational pipelines used to process raw data, perform analysis, and assemble the TCMLncDB integrated dataset.The provided code performs the following crucial steps:Data Processing and QC: Scripts like prepare_tpm_expression_data.R are used for pan-cancer TPM data preparation, while tumor_purity_estimation.R calculates tumor purity using the ESTIMATE algorithm, which is essential for accurate downstream analysis.Core Correlation Analysis: The lncRNA_PCG_correlation_analysis.R script calculates partial correlation coefficients between lncRNAs and PCGs across tumors, with the calculation adjusted for tumor purity.TCM-lncRNA Prediction: The key script, TCM_lncRNA_enrichment.R, calculating the lncRES score to quantify the functional association between TCM and lncRNAs.Reproducibility Notes and File StructureThis repository shares the computational steps used to create the final database. A key note is that much of the provided code will not run immediately because the massive TCGA and GEO raw data files are not shared here due to size limitations.GEO Data: Users wishing to fully reproduce the pipeline must first download the raw GEO data files using the accession numbers provided in the input file: Supplementary_Table_S1_GEO_Datasets_List.xlsx.Workflow Guide: The file structure guides the user through the process, with code organized into processing, filtering, and core analysis steps.We have shared all code used to assemble the original integrated dataset, enabling full transparency and validation of the methodology.
DOI: 10.6084/m9.figshare.30731603.v2
title: Reproducibility Scripts for TCMLncDB: TCM and lncRNA Regulation in Cancer

description: This code repository contains all custom scripts and computational pipelines used to process raw data, perform analysis, and assemble the TCMLncDB integrated dataset.The provided code performs the following crucial steps:Data Processing and QC: Scripts like prepare_tpm_expression_data.R are used for pan-cancer TPM data preparation, while tumor_purity_estimation.R calculates tumor purity using the ESTIMATE algorithm, which is essential for accurate downstream analysis.Core Correlation Analysis: The lncRNA_PCG_correlation_analysis.R script calculates partial correlation coefficients between lncRNAs and PCGs across tumors, with the calculation adjusted for tumor purity.TCM-lncRNA Prediction: The key script, TCM_lncRNA_enrichment.R, calculating the lncRES score to quantify the functional association between TCM and lncRNAs.Reproducibility Notes and File StructureThis repository shares the computational steps used to create the final database. A key note is that much of the provided code will not run immediately because the massive TCGA and GEO raw data files are not shared here due to size limitations.GEO Data: Users wishing to fully reproduce the pipeline must first download the raw GEO data files using the accession numbers provided in the input file: Supplementary_Table_S1_GEO_Datasets_List.xlsx.Workflow Guide: The file structure guides the user through the process, with code organized into processing, filtering, and core analysis steps.We have shared all code used to assemble the original integrated dataset, enabling full transparency and validation of the methodology.
DOI: 10.5281/zenodo.17733340
title: Fundprotokoller fra Museum Odenses Privatsamlinger. OBM5006 C. Mikkelsens samling, OBM5007 P. Helweg Mikkelsens samling, Broholm samlingen og OBM5010 Ehlerts samling.

description: Fra 1860 og indtil et moderne journalnummersystem blev taget i anvendelse i 1972, blev alle genstande registreret i protokoller. De er stadig den væsentligste kilde til viden om de ældre dele af museets samlinger og de bruges derfor hele tiden som opslagsværker.

I dag sker dette kun sjældent ved at bladre i de tykke og for nogles vedkommende skrøbelige protokoller. De er blevet scannet i så høj opløsning, at de gamle snørklede tekster nogle gange er lettere at læse på skærmen end på papiret. Hidtil har det kun været museets personale, der har haft adgang til denne kolossale vidensbank, men nu er scanningerne lagt på hjemmesiden, så alle har mulighed for at gå på jagt i protokolteksterne ind og gøre spændende “fund” og få oplysninger om tidligere tiders ofte fantasifulde mere end realistiske tolkning af genstandene.
DOI: 10.5281/zenodo.17733341
title: Fundprotokoller fra Museum Odenses Privatsamlinger. OBM5006 C. Mikkelsens samling, OBM5007 P. Helweg Mikkelsens samling, Broholm samlingen og OBM5010 Ehlerts samling.

description: Fra 1860 og indtil et moderne journalnummersystem blev taget i anvendelse i 1972, blev alle genstande registreret i protokoller. De er stadig den væsentligste kilde til viden om de ældre dele af museets samlinger og de bruges derfor hele tiden som opslagsværker.

I dag sker dette kun sjældent ved at bladre i de tykke og for nogles vedkommende skrøbelige protokoller. De er blevet scannet i så høj opløsning, at de gamle snørklede tekster nogle gange er lettere at læse på skærmen end på papiret. Hidtil har det kun været museets personale, der har haft adgang til denne kolossale vidensbank, men nu er scanningerne lagt på hjemmesiden, så alle har mulighed for at gå på jagt i protokolteksterne ind og gøre spændende “fund” og få oplysninger om tidligere tiders ofte fantasifulde mere end realistiske tolkning af genstandene.
DOI: 10.15468/dl.w35rb6
title: Occurrence Download

description: A dataset containing 859146 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'AU'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2000 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 859146 records were derived from 1660 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011544-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnzn5x
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diploptera punctata (Eschscholtz, 1822)"
 ]
}

 The dataset includes 55 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014327-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcmzec
title: Occurrence Download

description: A dataset containing 820 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX.25_1",
 "TaxonKey is Felidae"
 ]
}

 The dataset includes 820 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181477-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hh5gx6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potamogeton lucens L.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136876-240321170329656/datasets/export for details.
DOI: 10.15468/dl.7rdyt3
title: Occurrence Download

description: A dataset containing 1630 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1630 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004215-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.922ana
title: Occurrence Download

description: A dataset containing 511 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus melilotoides Pall."
 ]
}

 The dataset includes 511 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0096961-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qfbsh9
title: Occurrence Download

description: A dataset containing 279965 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pipridae"
 ]
}

 The dataset includes 279965 records from 247 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014327-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bd6dvm
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hymenostegia bakeriana Hutch. & Dalziel"
 ]
}

 The dataset includes 49 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025885-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n6rqyu
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Gastropods of the mole burrows in the forest zone of Western Siberia"
 ]
}

 The dataset includes 163 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105289-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sbxcsd
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quiscalus lugubris lugubris"
 ]
}

 The dataset includes 181 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014326-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wtx8a
title: Occurrence Download

description: A dataset containing 3459 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bradypus variegatus Schinz, 1825",
 "Year 2019-2023"
 ]
}

 The dataset includes 3459 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136875-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eod40t
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clibadium erosum (Sw.) DC.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 36 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014328-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhjyrw
title: Occurrence Download

description: A dataset containing 647 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cleidion vieillardii Baill."
 ]
}

 The dataset includes 647 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004293-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8j7hz
title: Occurrence Download

description: A dataset containing 3770 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 Spizocorys starki (Shelley, 1902)"
 ]
}

 The dataset includes 3770 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004127-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tw6s4y
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Equus hemionus kulan (Groves & Mazák, 1967)"
 ]
}

 The dataset includes 42 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0143652-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r6x8c4
title: Occurrence Download

description: A dataset containing 851040 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-83.42064 42.02290,-82.54335 42.02290,-82.54335 42.37366,-83.42064 42.37366,-83.42064 42.02290))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 1961-2020"
 ]
}

 The dataset includes 851040 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0135391-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vffgbt
title: Occurrence Download

description: A dataset containing 1858 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 2000-2017",
 "Geometry POLYGON((-119.69432 43.42228,-118.4425 43.42228,-118.4425 44.72829,-119.69432 44.72829,-119.69432 43.42228))",
 "DatasetKey is EOD – eBird Observation Dataset",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Bubo virginianus (J.F.Gmelin, 1788)",
 "TaxonKey is Aquila chrysaetos (Linnaeus, 1758)",
 "TaxonKey is Falco sparverius Linnaeus, 1758",
 "TaxonKey is Buteo jamaicensis (Gmelin, 1788)"
 ]
 }
 ]
}

 The dataset includes 1858 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014328-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2c6ye
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cola zemagoana Kenfack & D.W.Thomas"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004182-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eh37v2
title: Occurrence Download

description: A dataset containing 3890 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Mexico",
 "Country is Puerto Rico",
 "Country is Cuba",
 "Country is Bahamas",
 "Country is Cayman Islands",
 "Country is Jamaica",
 "Country is Belize",
 "Country is Turks and Caicos Islands",
 "Country is Nicaragua"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Porites porites (Pallas, 1766)"
 ]
}

 The dataset includes 3890 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136502-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r0nmku
title: Occurrence Download

description: A dataset containing 119489 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apis mellifera Linnaeus, 1758"
 ]
}

 The dataset includes 119489 records from 568 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014329-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f3q6tc
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clutia sericea Müll.Arg."
 ]
}

 The dataset includes 7 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004249-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rlxczd
title: Occurrence Download

description: A dataset containing 1550 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eucalyptus globulus subsp. globulus",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 1550 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014330-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5gsrk
title: Occurrence Download

description: A dataset containing 4249 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulinus truncatus (Audouin, 1827)"
 ]
}

 The dataset includes 4249 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0197860-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2ctww
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acalypha virgata L."
 ]
}

 The dataset includes 53 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136878-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4a6a65
title: Occurrence Download

description: A dataset containing 1123 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 Ramphocelus passerinii costaricensis Cherrie, 1891"
 ]
}

 The dataset includes 1123 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004291-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.