cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9pchcz
title: Occurrence Download

description: A dataset containing 2582 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligularia fischeri (Ledeb.) Turcz."
 ]
}

 The dataset includes 2582 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009328-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jbuwgy
title: Occurrence Download

description: A dataset containing 2187 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Picea jezoensis (Siebold & Zucc.) Carrière"
 ]
}

 The dataset includes 2187 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127031-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmsyrb
title: Occurrence Download

description: A dataset containing 355808 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Silene vulgaris (Moench) Garcke"
 ]
}

 The dataset includes 355808 records from 1705 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049349-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9y6sp
title: Occurrence Download

description: A dataset containing 1488 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 countrycode countrycode,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, countrycode, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, countrycode, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, countrycode, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, countrycode, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, countrycode, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, countrycode, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'US'
 AND occurrence.datasetkey = '4fa7b334-ce0d-4e88-aaae-2e0c138d049e'
 AND occurrence."month" = 1
 AND (occurrence."year" &gt;= 2023 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.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence.hascoordinate = TRUE)
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",
 occurrence.countrycode

 The dataset's 1488 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023954-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxerqa
title: Occurrence Download

description: A dataset containing 45703563 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Asplenium bulbiferum G.Forst., Asplenium ruta-muraria L., Asplenium scolopendrium L., Asplenium septentrionale (L.) Hoffm., Asplenium trichomanes L., Asplenium viride Huds., Aster alpinus L., Aster amellus L., Asteraceae, Pyrrocoma lanceolata (Hook.) Greene, Galatella linosyris (L.) Rchb.fil., Symphyotrichum novae-angliae (L.) G.L.Nesom, Symphyotrichum novi-belgii (L.) G.L.Nesom, Galatella sedifolia (L.) Greuter, Symphyotrichum squamatum (Spreng.) G.L.Nesom, Tripolium pannonicum (Jacq.) Dobrocz., Aster willkommii Sch.Bip., Symphyotrichum ×salignum (Willd.) G.L.Nesom, Asteriscus aquaticus (L.) Less., Lysimachia linum-stellatum L., Astragalus alpinus L., Astragalus norvegicus Weber, Astragalus ancistrocarpus Boiss. & Hausskn., Astragalus angustifolius Lam., Astragalus arenarius L., Astragalus asterias Steven, Astragalus australis (L.) Lam., Astragalus austriacus Jacq., Astragalus boeticus L., Astragalus cicer L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 45703563 records from 8964 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003417-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/28634
title: Chandra X-ray Observatory ObsId 28634

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.25574/28635
title: Chandra X-ray Observatory ObsId 28635

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.25574/28636
title: Chandra X-ray Observatory ObsId 28636

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.25574/28637
title: Chandra X-ray Observatory ObsId 28637

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.5281/zenodo.17087106
title: Lake Atitlan water quality 2010-2024

description: Field data were collected monthly from a pelagic point identified as Weiss G (14°42’23.182” N 91°11’13.901” W), close to the lake center and with a depth of 325 m. From 2009 to early 2017, temperature (ºC) and dissolved oxygen (mg L-1) were measured monthly using a YSI 51B and YSI 85 probe that measures to 60 m depth. Additional depths were sampled by raising water to the surface with a 2.2 L opaque Van Dorn bottle and immediately reading the temperature and dissolved oxygen. From early 2017 continuous measurements were made using a RBR maestro probe that reached the lake bottom.

We collected all samples for laboratory analyses with a 2.2 L opaque van Dorn bottle at 0, 5, 10, 15, 20, 30, 40, 60, 80, 100, 150, 200, 225, 250, 275, and 305 m depths, except for 2010 to 2013, when sampling was usually limited to 100 m maximum depth. For chemical analyses, we transferred samples to acid-washed 250 ml glass BOD bottles and kept them on ice in darkness until processed in the laboratory within the next 9 hours. We manually filtered samples within 9 h of collection using 25 mm diameter 0.7 µm glass fiber filters (Whatman GF/F) and then refrigerated the filtered samples at 4 ºC until analysis within 48 h of filtration. Nutrient concentrations were determined using the methods:

- Ammonia (NH4+–N µg L-1) concentrations with the phenate method (detection limit

(DL) = 3 µg L-1) (APHA, 2005)

- Nitrate plus nitrite (NO3-–N + NO2-–N µg L-1) concentrations with the hydrazine reduction method (DL = 2 µg L-1) (Kamphake et al., 1967)

- Soluble reactive phosphate (SRP) (PO4-3–P µg L-1) concentrations with the ascorbic acid reduction method (DL = 1 µg L-1) (Murphy and Riley, 1962)

- Total phosphorus (TP µg L-1) with the SRP method after digestion with the method 4500-P J (APHA 2005).

When concentrations were below DL, we used one-half of the DL value for statistical analysis.

All recipients, as well as all glassware used, were washed with a 0.1N HCl solution, and rinsed three times with demineralized water. Acid washing followed by a triple rinse was repeated before each sample collection.

 

Basic scripts for data analysis are included.
DOI: 10.25574/28638
title: Chandra X-ray Observatory ObsId 28638

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.5281/zenodo.18673028
title: Lake Atitlan water quality 2010-2024

description: Field data were collected monthly from a pelagic point identified as Weiss G (14°42’23.182” N 91°11’13.901” W), close to the lake center and with a depth of 325 m. From 2009 to early 2017, temperature (ºC) and dissolved oxygen (mg L-1) were measured monthly using a YSI 51B and YSI 85 probe that measures to 60 m depth. Additional depths were sampled by raising water to the surface with a 2.2 L opaque Van Dorn bottle and immediately reading the temperature and dissolved oxygen. From early 2017 continuous measurements were made using a RBR maestro probe that reached the lake bottom.

We collected all samples for laboratory analyses with a 2.2 L opaque van Dorn bottle at 0, 5, 10, 15, 20, 30, 40, 60, 80, 100, 150, 200, 225, 250, 275, and 305 m depths, except for 2010 to 2013, when sampling was usually limited to 100 m maximum depth. For chemical analyses, we transferred samples to acid-washed 250 ml glass BOD bottles and kept them on ice in darkness until processed in the laboratory within the next 9 hours. We manually filtered samples within 9 h of collection using 25 mm diameter 0.7 µm glass fiber filters (Whatman GF/F) and then refrigerated the filtered samples at 4 ºC until analysis within 48 h of filtration. Nutrient concentrations were determined using the methods:

- Ammonia (NH4+–N µg L-1) concentrations with the phenate method (detection limit

(DL) = 3 µg L-1) (APHA, 2005)

- Nitrate plus nitrite (NO3-–N + NO2-–N µg L-1) concentrations with the hydrazine reduction method (DL = 2 µg L-1) (Kamphake et al., 1967)

- Soluble reactive phosphate (SRP) (PO4-3–P µg L-1) concentrations with the ascorbic acid reduction method (DL = 1 µg L-1) (Murphy and Riley, 1962)

- Total phosphorus (TP µg L-1) with the SRP method after digestion with the method 4500-P J (APHA 2005).

When concentrations were below DL, we used one-half of the DL value for statistical analysis.

All recipients, as well as all glassware used, were washed with a 0.1N HCl solution, and rinsed three times with demineralized water. Acid washing followed by a triple rinse was repeated before each sample collection.

 

Basic scripts for data analysis are included.
DOI: 10.25574/28639
title: Chandra X-ray Observatory ObsId 28639

description: Magnifying the First Black Holes: Chandra and JWST Observations of Abell 370
DOI: 10.15468/dl.kh3uwg
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Isothecium holtii)",
 "Country is one of (Norway)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1986",
 "Year is less than or equal to 2025",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "not" : {
 "BasisOfRecord" : [
 "is Machine Observation"
 ]
 }
 }
 ]
}

 The dataset includes 335 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024822-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ukfsgh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Isopterygiopsis alpicola)",
 "Country is one of (Norway)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1986",
 "Year is less than or equal to 2025",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "not" : {
 "BasisOfRecord" : [
 "is Machine Observation"
 ]
 }
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024821-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.du66mc
title: Occurrence Download

description: A dataset containing 2240 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ludwigia erecta",
 {
 "or" : [
 "Year 1990-2025",
 "Year 1990-2025"
 ]
 }
 ]
}

 The dataset includes 2240 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002720-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pp5jmx
title: Occurrence Download

description: A dataset containing 59918847 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "StateProvince is Ontario"
 ]
}

 The dataset includes 59918847 records from 1033 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002670-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abfg9u
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia artemisiifolia",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 61 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002722-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ejz88
title: Occurrence Download

description: A dataset containing 9741 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Erigeron canadensis",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9741 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002724-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q88t8b
title: Occurrence Download

description: A dataset containing 3308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia artemisiifolia",
 "Country is Korea, Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3308 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002723-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tzpdhh
title: Occurrence Download

description: A dataset containing 229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bomarea multiflora",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 229 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002725-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16050715
title: Data set and Main analysis code for SREP-24-02212A

description: For Manuscript (SREP-24-02212A) 

Title "Association between prenatal ambient particulate matter and childhood asthma is modified by community safety and child sex" consist main dataset for R (.RData) used and the code for main analysis in the manuscript.

The data is completely de-identified and no personal identifiable information is included.
DOI: 10.5281/zenodo.16050716
title: Data set and Main analysis code for SREP-24-02212A

description: For Manuscript (SREP-24-02212A) 

Title "Association between prenatal ambient particulate matter and childhood asthma is modified by community safety and child sex" consist main dataset for R (.RData) used and the code for main analysis in the manuscript.

The data is completely de-identified and no personal identifiable information is included.
DOI: 10.15468/dl.ttuarn
title: Occurrence Download

description: A dataset containing 296602 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Trifolium medium"
 ]
}

 The dataset includes 296602 records from 1002 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002605-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fiuib4
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019916-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gf974d
title: Occurrence Download

description: A dataset containing 3126 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 one of (Achillea tomentosa L.)"
 ]
}

 The dataset includes 3126 records from 126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071992-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gp48ma
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129201-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hq8zxn
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020791-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fj8rx
title: Occurrence Download

description: A dataset containing 134308448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta",
 "Year 2000-2020"
 ]
}

 The dataset includes 134308448 records from 3843 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139535-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39yq2u
title: Occurrence Download

description: A dataset containing 21637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (France, Switzerland, Belgium, Netherlands, Spain, Andorra, Portugal, Italy, Luxembourg)",
 "TaxonKey is Gryllotalpa"
 ]
}

 The dataset includes 21637 records from 588 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021360-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/browneg-ouc11399922x
title: #186a, UPI continued Interview, 1976-12-30

description: #186a, UPI continued Interview, 1976-12-30. Gift of Edmund G. Brown, Jr., 1985, 2019, and 2023. Transcript was created by WhisperAI.
DOI: 10.25549/browneg-ouc113999278
title: Audiovisual material, posters and other material added to the collection from accession no. 2023-011

description: The Edmund G. Brown, Jr. papers comprise the papers of Jerry Brown during his tenure as California Secretary of State (1971-1975) and his first two terms as the Governor of California (1975-1983). Over the course of his career, Jerry Brown has served as the California Secretary of State (1971-1975), the 34th Governor of California (1975-1983), the Mayor of Oakland (1999-2007), the Attorney General of California (2007-2011), and the 39th Governor of California (2011-2019).
DOI: 10.5281/zenodo.17550873
title: PCNE v2.0.0 validation

description:  

This repository contains all the data used to validate PCNE v2.0.0 (https://github.com/riccabolla/PCNE), and is to be used with scripts provided at https://github.com/riccabolla/PCNE_paper_script.

 

1. Real_data:



Real_data_reads: it contains filtered reads*

Real_data_assembly: it contains assembled genomes generated using reads in the previous folder

Platon_real_data: it contains the platon's output generated


*Reads have been taken from this work: Xiang G, Zhao Z, Zhang S, et al. Porin deficiency or plasmid copy number increase mediated carbapenem-resistant Escherichia coli resistance evolution. Emerg Microbes Infect. 2024;13(1):2352432. doi:10.1080/22221751.2024.2352432

2. Simulated_dataset:



It containts the chromosome and plasmid fasta files

Sim_50x: it contains the simulated reads

Shovill_50x: it contains assemblies generated using the simulated reads

Mobsuite: it contains mobsuite's output generated

Platon: it contains platon's output generated


3. Case_study:



Case_study_reads: it contains filtered reads**

Case_study_assembly: it contains assemblies generated using reads in the previous folder

Case_study_mobsuite: it contains mobsuite's output generated

Case_study_abricate: it contains abricate's output generated


**Reads have been taken from this work: Jian, Z., Liu, Y., Wang, Z. et al. A nosocomial outbreak of colistin and carbapenem-resistant hypervirulent Klebsiella pneumoniae in a large teaching hospital. Sci Rep 14, 27744 (2024). https://doi.org/10.1038/s41598-024-79030-w