cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rcrc7g
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((93.19256 22.78502,112.83593 22.78502,112.83593 44.19123,93.19256 44.19123,93.19256 22.78502))",
 "TaxonKey is Populus kangdingensis Z.Wang & S.L.Tung"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033674-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c5z3p5
title: Occurrence Download

description: A dataset containing 1498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Colombia, Ecuador)",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1498 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033675-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/qohgjz
title: House Incumbent Google Star Ratings

description: Data on Google reviews for office locations for US House members in potentially competitive districts.
DOI: 10.15468/dl.dhsbpu
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX.25_1",
 "TaxonKey is Tephritidae"
 ]
}

 The dataset includes 31 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033676-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6q6qqj
title: Occurrence Download

description: A dataset containing 12743 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leopardus pardalis (Linnaeus, 1758)"
 ]
}

 The dataset includes 12743 records from 373 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033677-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.86u7ud
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX.26_1",
 "TaxonKey is Mephitidae"
 ]
}

 The dataset includes 155 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033678-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/etwvpg
title: Appendix for: Constitutional Conventions in Central Europe: Insights from Experts

description: Appendix with a semi-structured questionnaire
DOI: 10.7910/dvn/e6nafi
title: Replication Data for:

description: The data set contains python code and reproduction data for the paper
DOI: 10.7910/dvn/8o1e8u
title: Phased plan for the implementation of the time-resolving magnetic recoil spectrometer on the National Ignition Facility (NIF)

description: The time-resolving magnetic recoil spectrometer (MRSt) is a transformative diagnostic that will be used to measure the time-resolved neutron spectrum from an inertial confinement fusion implosion at the National Ignition Facility (NIF). It uses a CD foil on the outside of the hohlraum to convert fusion neutrons to recoil deuterons. An ion-optical system positioned outside the NIF target chamber energy-disperses and focuses forward-scattered deuterons. A pulse-dilation drift tube (PDDT) subsequently dilates, un-skews, and detects the signal. While the foil and ion-optical system have been designed, the PDDT requires more development before it can be implemented. Therefore, a phased plan is presented that first uses the foil and ion-optical systems with detectors that can be implemented immediately—namely CR-39 and hDISC streak cameras. These detectors will allow the MRSt to be commissioned in an intermediate stage and begin collecting data on a reduced timescale, while the PDDT is developed in parallel. A CR-39 detector will be used in phase 1 for the measurement of the time-integrated neutron spectra with excellent energy-resolution, necessary for the energy calibration of the system. Streak cameras will be used in phase 2 for measurement of the time-resolved spectrum with limited spectral coverage, which is sufficient to diagnose the time-resolved ion temperature. Simulations are presented that predict the performance of the streak camera detector, indicating that it will achieve excellent burn history measurements at current yields, and good time-resolved ion-temperature measurements at yields above 3 × 10^17. The PDDT will be used for optimal efficiency and resolution in phase 3.
description: PSFC REPORT PSFC/JA-22-16<br><br>This work was supported, in part, by the U.S. Department of Energy NNSA MIT Center-of-Excellence under Contract No. DE-NA0003868 and Lawrence Livermore National Laboratory under Contract No. B635598.<br><br>If this record does not contain the full text, then the manuscript has been embargoed by the publisher thus restricting open access for 12 to 24 months after publication.
DOI: 10.15468/dl.82r4qc
title: Occurrence Download

description: A dataset containing 603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX.6_1",
 "TaxonKey is Mephitidae"
 ]
}

 The dataset includes 603 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033679-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.2541239
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: These two combined bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted for the purpose of using the "assignTaxonomy" command within the DADA2 pipeline.


	RefSeq+RDP: This database contains 14676 bacterial & 660 archaea full 16S rRNA gene sequences.  It was compiled in 14/05/2018 from predominantly the NCBI RefSeq 16S rrna database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database (https://rdp.cme.msu.edu/misc/resources.jsp).
	Genome Taxonomy Database (GTDB): our dada2 formatted GTDB reference sequence set contains 20486 bacteria and 1073 archaea full 16S rRNA gene sequences. The database was downloaded from (http://gtdb.ecogenomic.org/downloads) on 20/11/2018.


The formatting to DADA2 format of the databases was done using a locally written python 2.7 script. The script takes as input a taxonomy .txt file and a fasta file as provided by the core databases creators and then these two files are matched according to a unique sequence identifier available in both files. Then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence ID be it NCBI/RDP or GTDB ID to the species entry. We see this as an important QC step to highlight the issues/confidence associated with short read taxonomy assignment at the more finer rank levels.
description: Python script can be provided on request.
description: {"references": ["Parks, D. H., et al. (2018). \"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.\" Nature Biotechnology.", "Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42(Database issue):D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]", "NCBI 16S RefSeq Nucleotide sequence records: https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D"]}
DOI: 10.5281/zenodo.3188334
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: These two combined bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted for the purpose of using the "assignTaxonomy" command within the DADA2 pipeline.


	RefSeq+RDP: This database contains 14676 bacterial & 660 archaea full 16S rRNA gene sequences.  It was compiled in 14/05/2018 from predominantly the NCBI RefSeq 16S rrna database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database (https://rdp.cme.msu.edu/misc/resources.jsp).
	Genome Taxonomy Database (GTDB): our dada2 formatted GTDB reference sequence set contains 20486 bacteria and 1073 archaea full 16S rRNA gene sequences. The database was downloaded from (http://gtdb.ecogenomic.org/downloads) on 20/11/2018.


The formatting to DADA2 format of the databases was done using a locally written python 2.7 script. The script takes as input a taxonomy .txt file and a fasta file as provided by the core databases creators and then these two files are matched according to a unique sequence identifier available in both files. Then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence ID be it NCBI/RDP or GTDB ID to the species entry. We see this as an important QC step to highlight the issues/confidence associated with short read taxonomy assignment at the more finer rank levels.
description: The RefSeq+RDP database was updated due to a quotation mark bug that was wrongly placed in front of some of the species names. A file with all the affected species names has been uploaded to review. This shouldn't affect any assignments but might have caused some issues reading into R.  

Python script can be provided on request.
description: {"references": ["Parks, D. H., et al. (2018). \"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.\" Nature Biotechnology.", "Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42(Database issue):D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]", "NCBI 16S RefSeq Nucleotide sequence records: https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D"]}
DOI: 10.5281/zenodo.3951383
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: These two combined bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted for the purpose of using the "assignTaxonomy" command within the DADA2 pipeline. RefSeq+RDP: This database contains 14676 bacterial & 660 archaea full 16S rRNA gene sequences. It was compiled in 14/05/2018 from predominantly the NCBI RefSeq 16S rrna database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database (https://rdp.cme.msu.edu/misc/resources.jsp). Genome Taxonomy Database (GTDB): The new version of our dada2 formatted GTDB reference sequences now contains 21965 bacteria and 1126 archaea full 16S rRNA gene sequences. If you wonder why there are fewer species with 16S rRNA, that is because some metagenomics assembled genomes (MAGs) lack the 16S gene and thus cannot be extracted. The database was downloaded from https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/ on 19/07/2020. Please read the release notes and file descriptions. The formatting to DADA2 format of the databases was done using a simple awk bash scripts. The script takes as input a fasta file as provided by the core databases creators and then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence ID be it NCBI/RDP or GTDB ID to the species entry. We see this as an important QC step to highlight the issues/confidence associated with short read taxonomy assignment at the more finer rank levels.
description: The RefSeq+RDP database was updated due to a quotation mark bug that was wrongly placed in front of some of the species names. A file with all the affected species names has been uploaded to review. This shouldn't affect any assignments but might have caused some issues reading into R. The GTDB was updated due to a new release with taxonomy changes has been made available. The core GTDB team advises that everyone using the GTDB to convert to the release 95. I have also formatted all the 16S rRNA sequences in the GTDBr95 that have passed QC. If anyone finds a need for them I can share outside of here because I do not want to confuse anyone. awk script can be provided on request.
description: {"references": ["Parks, D. H., et al. (2018). \"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.\" Nature Biotechnology.", "Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42(Database issue):D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]", "NCBI 16S RefSeq Nucleotide sequence records: https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D"]}
DOI: 10.5281/zenodo.4361892
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: This Version was primarily updated because we have recently updated the RefSeq+RDP database and also included mitochondrial and eukaryotic 16S rRNA sequences. Also because I decided to include the required formats to be able to use the addSpecies command in DADA2. This command searches the database at 100% identity and has the flexibility to either get best hit or multiple hits to your amplicon. I recommend it if you are using a single or 2 region amplicons of the 16S rRNA gene. These two combined bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted for the purpose of using the "assignTaxonomy" command within the DADA2 pipeline. The data was converted to suite DADA2 format by Alishum Ali. RefSeq+RDP: This database contains 22433 bacterial, 1055 archaea and 99 eukaryotic full lengths16S rRNA gene sequences. It was compiled by <strong>Paul Greenfield </strong>on the <strong>06/11/2020</strong> from predominantly the NCBI RefSeq 16S rRNA database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database (https://rdp.cme.msu.edu/misc/resources.jsp). Genome Taxonomy Database (GTDB): The new version of our dada2 formatted GTDB reference sequences now contains 21965 bacteria and 1126 archaea full 16S rRNA gene sequences. If you wonder why there are fewer species with 16S rRNA, that is because some metagenomics assembled genomes (MAGs) lack the 16S gene and thus cannot be extracted. The database was downloaded from https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/ on 19/07/2020. Please read the release notes and file descriptions. The formatting to DADA2 was done using a simple awk bash scripts. The script takes as input a fasta file and a tab-delimited taxonomy file (slightly edited to remove special characters) and then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence ID be it NCBI/RDP or GTDB ID to the species entry (but replaced the "." with an " _". We see this as an important QC step to highlight the issues/confidence associated with short read taxonomy assignment at the finer rank levels. Also, this update includes two other files that you can use with the assignTaxonomy and addSpecies commands in DADA2.
description: Bash script can be provided on request.
description: {"references": ["Parks, D. H., et al. (2018). \"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.\" Nature Biotechnology.", "Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42(Database issue):D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]", "NCBI 16S RefSeq Nucleotide sequence records: https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D"]}
DOI: 10.5281/zenodo.13984843
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 220.  Please read this post for the stats on the updates. https://gtdb.ecogenomic.org/stats/r220 . 

There has been no change to the RDP-RefSeq reference database please use previous versions.

If anyone has concerns with MAG extracted 16S rRNA gene contamination concerns, then I suggest that they contact the curators of GTDB themselves because it is outside of my role with these resources designed for DADA2 usage only. 

Another concern that was raised was the orientation of the DB sequences, to get past this problem please use the tryRC = TRUE argument in the assignTaxonomy command within DADA2, this will search your ASVs in the reverse complement as well.  

The bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted to use the "assignTaxonomy" command within the DADA2 pipeline. The data was converted to suite DADA2 format by Alishum Ali.



Genome Taxonomy Database (GTDB): The new version of our dada2 formatted GTDB reference sequences now contains 58102 bacteria and 3672 archaea full 16S rRNA gene sequences. If you wonder why there are fewer species with 16S rRNA, that is because some metagenomics-assembled genomes (MAGs) lack the 16S gene and thus cannot be extracted.  The database was downloaded from https://data.ace.uq.edu.au/public/gtdb/data/releases/ on 24/10/2024. Please read the release notes and file descriptions. 


The formatting to DADA2 was done using simple awk bash scripts. The script takes as input a fasta file and a tab-delimited taxonomy file (slightly edited to remove special characters) and then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence GTDB ID to the species entry (but replaced the "." with an " _". We see this as an important QC step to highlight the issues/confidence associated with short-read taxonomy assignment at the finer rank levels.

Also, this update includes two other files that you can use with the assignTaxonomy and addSpecies commands in DADA2.
description: Bash script can be provided on request.
DOI: 10.5281/zenodo.2541238
title: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

description: This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 220.  Please read this post for the stats on the updates. https://gtdb.ecogenomic.org/stats/r220 . 

There has been no change to the RDP-RefSeq reference database please use previous versions.

If anyone has concerns with MAG extracted 16S rRNA gene contamination concerns, then I suggest that they contact the curators of GTDB themselves because it is outside of my role with these resources designed for DADA2 usage only. 

Another concern that was raised was the orientation of the DB sequences, to get past this problem please use the tryRC = TRUE argument in the assignTaxonomy command within DADA2, this will search your ASVs in the reverse complement as well.  

The bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted to use the "assignTaxonomy" command within the DADA2 pipeline. The data was converted to suite DADA2 format by Alishum Ali.



Genome Taxonomy Database (GTDB): The new version of our dada2 formatted GTDB reference sequences now contains 58102 bacteria and 3672 archaea full 16S rRNA gene sequences. If you wonder why there are fewer species with 16S rRNA, that is because some metagenomics-assembled genomes (MAGs) lack the 16S gene and thus cannot be extracted.  The database was downloaded from https://data.ace.uq.edu.au/public/gtdb/data/releases/ on 24/10/2024. Please read the release notes and file descriptions. 


The formatting to DADA2 was done using simple awk bash scripts. The script takes as input a fasta file and a tab-delimited taxonomy file (slightly edited to remove special characters) and then it outputs a fasta file with all 7 taxonomy ranks separated by ";" as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence GTDB ID to the species entry (but replaced the "." with an " _". We see this as an important QC step to highlight the issues/confidence associated with short-read taxonomy assignment at the finer rank levels.

Also, this update includes two other files that you can use with the assignTaxonomy and addSpecies commands in DADA2.
description: Bash script can be provided on request.
DOI: 10.7910/dvn/ercou2
title: Data source and processing

description: Original data in submitted papers
DOI: 10.7910/dvn/rked0h
title: HM Cloud Properties

description: Cloud properties retrieved from the Himawari-8.
DOI: 10.7910/dvn/j3193r
title: Metaheuristics Results

description: Metaheuristics Results
DOI: 10.7910/dvn/vz2xab
title: Formation of the layered circulation in South China Sea with the mixing stimulated exchanging current through Luzon Strait

description: Formation of the layered circulation in South China Sea with the mixing stimulated exchanging current through Luzon Strait
DOI: 10.15468/dl.d4htcr
title: Occurrence Download

description: A dataset containing 8526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bruguiera Lam.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8526 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033680-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8h62vj
title: Occurrence Download

description: A dataset containing 4100268 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The New York Botanical Garden Herbarium (NY)"
 ]
}

 The dataset includes 4100268 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0228469-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pqepw9
title: Occurrence Download

description: A dataset listing the 1587 species recorded in GBIF matching the query:
{
 "and" : [
 "Year 1950-2000",
 "TaxonKey is Augochlora pura (Say, 1837)"
 ]
}

 The dataset's 1587 records were derived from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030860-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yg7srz
title: Occurrence Download

description: A dataset containing 1420 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is National Lamprey Survey of Scotland (2003-2005)"
 ]
}

 The dataset includes 1420 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006807-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.