cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7nj2f4
title: Occurrence Download

description: A dataset containing 50276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Betula humilis Schrank, Betula nana L.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 50276 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0232877-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kdrzh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coleophora anatipennella (Hübner, 1796)",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is United States of America",
 "Country is United States",
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0369350-210914110416597/datasets/export for details.
DOI: 10.15468/dl.tgv7ax
title: Occurrence Download

description: A dataset containing 42036 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-104.85354 23.29196,-104.02919 23.29196,-104.02919 23.78146,-104.85354 23.78146,-104.85354 23.29196))"
 ]
}

 The dataset includes 42036 records from 223 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026801-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.114672
title: MONASTÈRES COPTES_nb_1967_00539

description: Référence : nb_1967_00539<br />Site : Esna<br />Secteur : Deir el-Fakhoury<br />Type : photographie<br />
DOI: 10.15468/dl.hhcypi
title: Occurrence Download

description: A dataset containing 1359 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anopterus glandulosus Labill.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1359 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041154-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.114671
title: MONASTÈRES COPTES_nb_1967_00538

description: Référence : nb_1967_00538<br />Site : Esna<br />Secteur : Deir el-Fakhoury; Salles ruinées sud et ouest<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.114670
title: MONASTÈRES COPTES_nb_1967_00537

description: Référence : nb_1967_00537<br />Site : Esna<br />Secteur : Deir el-Fakhoury; Toiture<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.114669
title: MONASTÈRES COPTES_nb_1967_00536

description: Référence : nb_1967_00536<br />Site : Esna<br />Secteur : Deir el-Fakhoury; Enceinte extérieure<br />Type : photographie<br />
DOI: 10.15468/dl.nafjhq
title: Occurrence Download

description: A dataset containing 13844 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thunbergia alata Bojer ex Sims"
 ]
}

 The dataset includes 13844 records from 399 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028771-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8hygwq
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pasimachus purpuratus (Putzeys, 1845)"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026795-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trftsv
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is Planktic foraminifera abundance of Hole 84-566"
 ]
}

 The dataset includes 63 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019190-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9c4pf7
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arma chinensis (Fallou, 1881) Fallou, 1881"
 ]
}

 The dataset includes 77 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036291-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mx3wkv
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neopilinida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005471-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxv2eh
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ONCFS Réseau Ours brun - Ours 2009 présence Régulière Mailles 10km LAEA Réseau Ours brun ONCFS"
 ]
}

 The dataset includes 45 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025618-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.chm7j9
title: Occurrence Download

description: A dataset containing 319686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Cirsium arvense (L.) Scop."
 ]
}

 The dataset includes 319686 records from 468 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109845-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebz33b
title: Occurrence Download

description: A dataset containing 232 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma taylori Brandon, Maruska & Rumph, 1982"
 ]
}

 The dataset includes 232 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0309715-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gv0s6p
title: Occurrence Download

description: A dataset containing 48224 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Amphibia",
 "TaxonKey is Aves",
 "TaxonKey is Insecta",
 "TaxonKey is Reptilia",
 "TaxonKey is Mammalia",
 "TaxonKey is Chilopoda",
 "TaxonKey is Diplopoda",
 "TaxonKey is Arachnida"
 ]
 },
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "HasCoordinate is true",
 "DecimalLongitude is greater than or equal to 10.000000",
 "DecimalLongitude is less than 15.000000",
 "DecimalLatitude is greater than or equal to -25.000000",
 "DecimalLatitude is less than -20.000000",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2018"
 ]
}

 The dataset includes 48224 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001264-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phss6k
title: Occurrence Download

description: A dataset containing 20521 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Veronica urticifolia Jacq."
 ]
}

 The dataset includes 20521 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109878-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v9nuud
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Drilonius Kiesenwetter, 1874",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0312259-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yftxsv
title: Occurrence Download

description: A dataset containing 1248 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aethopyga ignicauda (Hodgson, 1836)"
 ]
}

 The dataset includes 1248 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001264-180920211646547/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzs4wb
title: Occurrence Download

description: A dataset containing 997 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glyptina J.L.LeConte, 1859"
 ]
}

 The dataset includes 997 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109916-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2axy9
title: Occurrence Download

description: A dataset containing 467 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oplurus cuvieri (Gray, 1831)"
 ]
}

 The dataset includes 467 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0286373-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l44edy
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lonicera vegeta Rehder"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001264-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.114668
title: MONASTÈRES COPTES_nb_1967_00535

description: Référence : nb_1967_00535<br />Site : Esna<br />Secteur : Deir el-Fakhoury; Enceinte extérieure<br />Type : photographie<br />
DOI: 10.15468/dl.m4bmae
title: Occurrence Download

description: A dataset containing 6737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hypopomidae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 6737 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015976-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-19040
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.25549/pcra-c14-19048
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.25549/pcra-c14-19056
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.25549/pcra-c14-19050
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.25549/pcra-c14-19061
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.25549/pcra-c14-19063
title: Minute book no. 15, PMU, AoG GB, OMC, May 1946 - Mar. 1948

description: [description english/roman)] Assemblies of God [AoG] OMC minute book No. 15 including OMC annual statement, 57 pages of index followed by 203 pages of minutes. All matters relating to AOG OMC council member appointments, decisions, policy and missionary personnel issues.
DOI: 10.15468/dl.f9f4kj
title: Occurrence Download

description: A dataset listing the 1302743391 species recorded in GBIF matching the query:
{ }

 The dataset's 1302743391 records were derived from 23724 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005327-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.96dpcv
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria japonica Houtt.",
 "Country is Austria",
 "GadmGid is AUT.9_1"
 ]
}

 The dataset includes 42 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006038-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13909575
title: FSI-ROM-Predictor-Data
DOI: 10.15468/dl.67fpnx
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria japonica Houtt.",
 "Country is Luxembourg",
 "GadmGid is LUX.3.3.4_1"
 ]
}

 The dataset includes 112 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006039-241007104925546/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.27203055
title: <b>Soil moisture influences nectar robbing and plant fitness in a primrose species</b>

description: 1. Low soil moisture, a prominent indicator of a changing climate, has overarching impacts on plant reproduction both directly and indirectly by affecting the visitation rate of pollinators. However, the role of soil moisture in modifying the behaviors of species interacting with plants is less well explored, as are the mechanisms associated with those changes in behavior. If species behavior changes from mutualistic to antagonistic, low soil moisture has the potential to disrupt mutualisms, with plant fitness consequences.2. We investigated the effects and underlying mechanisms of soil moisture on the intensity of nectar robbing (a common behavioral interaction between plants and pollinators) in natural populations of <i>Primula florindae</i> on the southeast Tibetan Plateau. To understand the relationships between soil moisture and nectar robbing and the mechanisms involved, we explored within-population variation in nectar robbing, floral and nectar traits, and the diversity and evenness of the co-flowering plant community in areas with natural variation in soil moisture. We then used an experimental approach to test how nectar robbing affected male and female components of <i>P. florindae</i> reproduction.3. We found that plants growing in low moisture soil experienced higher nectar robbing. Low soil moisture was associated with reduced flower size, nectar production, and the diversity of nectariferous plants. However, the Partial Least Squares Path Model revealed that only flower size (an estimate of nectar accessibility) had a significant effect on intensity of nectar robbing, with low soil moisture triggering a morphological mismatch between flowers and the primary pollinators bumblebees, prompting them to shift to nectar robbing behaviors. Nectar robbing reduced all components of male and female plant reproduction explored by up to 45%.4. <i>Synthesis</i>: This study provides new insight into how soil moisture influences plant-animal interactions, changing the behavior of floral visitors from mutualism to antagonism, and highlights that future soil water availability caused by global climate change may not only directly affect plants but also indirectly affect plants through changes in species interactions.
DOI: 10.15468/dl.wme44j
title: Occurrence Download

description: A dataset containing 936 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ulmus parvifolia Jacq."
 ]
}

 The dataset includes 936 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006040-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bphfhm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reynoutria japonica Houtt.",
 "Geometry POLYGON((48.11 16.12, 48.11 16.62, 48.5 16.62, 48.5 16.12, 48.11 16.12))",
 "Year is 2020"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006041-241007104925546/datasets/export for details.
DOI: 10.15468/dl.c4ya23
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.57602 52.56087,-3.1961 52.56087,-3.1961 52.82081,-3.57602 52.82081,-3.57602 52.56087))",
 "OccurrenceStatus is Present",
 "TaxonKey is Ascomycota",
 "Year 2009-2009"
 ]
}

 The dataset includes 42 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006042-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13376043
title: Data for: Detection of oomycete pathogens in UK peat-free growing media and implications for plant health

description: This dataset on Zenodo accompanies the manuscript Frederickson-Matika et al. (2024), Detection of oomycete pathogens in UK peat-free growing media and implications for plant health.

There are two files:



metadata.tsv - plain text table as tab-separated variables

raw_data.tar.gz - compressed archive of 43 paired raw FASTQ files


This represents a subset of two complete Illumina MiSeq plates (in two dated folderes) run at the James Hutton Institute containing other environmental samples using the same protocol. Only the synthetic controls and peat-free samples are provided here.To repeat the analysis described in the paper, first install THAPBI PICT. See https://github.com/peterjc/thapbi-pict/ for instructions. At the time of the paper, v1.0.14 was the current release.

Next, decompress the raw data into a folder of paired gzipped FASTQ files. There is no need to decompress those:

    $ tar -zxvf raw_data.tar.gz    $ ls -1 plate_20220505/ plate_20230608/

If you wish, verify the checksums to confirm the data integrity:

    $ cd plate_20220505/
    $ md5sum -c MD5SUM.txt    $ cd ../plate_20230608/
    $ md5sum -c MD5SUM.txt    $ cd ..

Setup output directories:

   $ mkdir -p intermediate/ summary/

Run the THAPBI PICT pipeline:

   $ thapbi_pict pipeline -m 1s3g \          -i plate_*/ -o summary/peat-free \          -y plate_*/GBL*.fastq.gz \          -n plate_*/GBL*.fastq.gz \          -s intermediate/ \          -t metadata.tsv -u \          -x 9 -c 1,2,3,4,5,6,7,8

The options here are as follows:



-i - two input directories of paired raw FASTQ files.

-n - negative controls used to increase the absolute abundance threshold

-y - synthetic controls used to increase the fractional abundance threshold

-s - optional location to store intermediate files

-o - output stem for reports

-t - filename for tab-separated-variable metadata

-u - show unsequenced samples defined in the metadata

-x - which metadata column contains Illumina FASTQ filename stems

-c - which metadata columns to include in the report.


This assumes the following key default settings:



-a 100 (default absolite abundance threshold)

-f 0.001 (default fractional abundance threshold)

-d -(default provided ITS1 database).


With these settings, only synthetic sequences were found in the controls, and therefore the thresholds were not automatically increased any further.

Opening the output file summary/peat-free.ITS1.samples.1s3g.xlsx in Excel or similar should show you a table resembling Table 1 in the paper, but one row per sequencing sample, and additional columns with per-sample per-species read counts etc.