cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/gc37xd7bw8
title: Data of agronomic yield-related traits of PFSP

description: Observed data of agronomic yield-related traits of PFSP across six planting locations in West Java, Indonesia
DOI: 10.17632/gc37xd7bw8.1
title: Data of agronomic yield-related traits of PFSP

description: Observed data of agronomic yield-related traits of PFSP across six planting locations in West Java, Indonesia
DOI: 10.3886/e115967v2
title: National Neighborhood Data Archive (NaNDA): Religious, Civic, and Social Organizations by Census Tract, United States, 2003-2017

description: This dataset contains
measures of the number and per capita density of select types of religious,
civic, and social organizations – such as churches, mosques, synagogues, ethnic
associations, and veterans’ associations – per United States census tract from
2003 through 2017. <br>
description: Religious, civic, and social organizations in all census tracts in the United States, including Puerto
Rico and the US Virgin Islands. Smallest Geographic Unit: census tract
DOI: 10.3886/e124721v1
title: National Neighborhood Data Archive (NaNDA): Religious, Civic, and Social Organizations by ZIP Code Tabulation Area, United States, 2003-2017

description: An updated version of this dataset can be found:<br><br>Melendez, Robert, Finlay, Jessica, Clarke, Philippa, Noppert, Grace, and Gypin, Lindsay. National Neighborhood Data Archive (NaNDA): Civic, Social, and Religious Organizations by Census Tract and ZCTA, United States, 1990-2021. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor], 2024-07-24. https://doi.org/10.3886/E207966V1<br>
description: Religious, civic, and social organizations in all
ZIP code tabulation areas in the United States, including Puerto Rico and the US Virgin Islands. Smallest Geographic Unit: ZIP code tabulation area
description: A ZIP code to ZCTA crosswalk must be used to combine this dataset with ZIP code geocoded data. Such a crosswalk is available on the UDS Mapper website at https://udsmapper.org/zip-code-to-zcta-crosswalk/. Sample code for merging the UDS Mapper crosswalk with NaNDA datasets is available on the NaNDA repository at https://www.openicpsr.org/openicpsr/project/120088/.
DOI: 10.3886/e207966
title: National Neighborhood Data Archive (NaNDA): Civic, Social, and Religious Organizations by Census Tract and ZCTA, United States, 1990-2021

description: This dataset contains measures of the number and density of
select types of civic, social, and religious organizations per United States
Census Tract or ZIP Code Tabulation Area (ZCTA) from 1990 through 2021. The
dataset includes four separate files for four different geographic areas (GIS
shapefiles from the United States Census Bureau). The four geographies include:
<br>Census Tract 2010Census Tract 2020ZIP Code Tabulation Area (ZCTA) 2010ZIP Code Tabulation Area (ZCTA) 2020 Information about which dataset to use can be found in the
Usage Notes section of the data documentation.<br>
DOI: 10.3886/e207966v1-179823
title: National Neighborhood Data Archive (NaNDA): Civic, Social, and Religious Organizations by Census Tract and ZCTA, United States, 1990-2021

description: This dataset contains measures of the number and density of
select types of civic, social, and religious organizations per United States
Census Tract or ZIP Code Tabulation Area (ZCTA) from 1990 through 2021. The
dataset includes four separate files for four different geographic areas (GIS
shapefiles from the United States Census Bureau). The four geographies include:
<br>Census Tract 2010Census Tract 2020ZIP Code Tabulation Area (ZCTA) 2010ZIP Code Tabulation Area (ZCTA) 2020 Information about which dataset to use can be found in the
Usage Notes section of the data documentation.<br>
DOI: 10.17632/d5x2y65g5w.1
title: Malignancies Developed in Dermatologic Patients with MMF, Translant Patients, and Dermatologic Patients without Immunosuppression

description: List of malignancies in dermatologic patients without immunosuppression, dermatologic patients on MMF, and transplant recipient patients.
DOI: 10.5281/zenodo.10215402
title: Chromosome-level genome assembly of Triticum turgidum var 'Kronos'

description:  
This data is made available under the Toronto Agreement. 
All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you agree to:

respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.
contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.
fully cite the prepublication data along with any applicable versioning details.
understand that this data as accessed is precompetitive and is not patentable in its present state.
This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). https://doi.org/10.1038/461168a
 

If you have questions about the use of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu
 
Summary of the datasets
We produced 526 Gbp of high-fidelity (HiFi) reads for Kronos. As Kronos typically self-pollinates in the field and its residual heterozygosity is low, these reads were assembled with hifiasm v0.19.5-r587 (-l0) to produce haplotype-collapsed assembly. Primary and associated contigs were concatenated into a single file. These contigs are in the files with the prefix 'Kronos.contigs'. 
The concatenated primary and associated contigs were further scaffolded with chromosome conformation capture sequencing (Hi-C) data. We used yahs v1.2a.2. The resulting 14 largest scaffolds were greater than 600 Mbp in size, representing 14 chromosomes (7 x AB). These scaffolds were renamed based on the similarity to the bread wheat reference genome from the IWGSC. After plasmid genomes were separated, the rest of the contigs or scaffolds, which were all smaller than 4 Mbp, were concatenated into a single sequenced named 'Un' (for unplaced). These sequences can be found in the files with the prefix 'Kronos.collapsed'. 
 

We plan to release additional data, such as annotations, as they become ready. If you have questions or suggestions about this dataset, please contact Ksenia Krasileva and Kyungyong Seong: s.kyungyong [at] berkeley.edu
 
Acknowledgement
This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726).
DOI: 10.5281/zenodo.14189805
title: Chromosome-level genome assembly of Triticum turgidum var 'Kronos'

description:  

This data is made available under the Toronto Agreement. 

All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you agree to:



respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.

not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.

contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.

fully cite the prepublication data along with any applicable versioning details.

understand that this data as accessed is precompetitive and is not patentable in its present state.


This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). https://doi.org/10.1038/461168a

 



If you have questions about the use of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu


 

Updates in Zenodo v3

 

This update includes the second version of gene annotations for Kronos. This version contains 71,357 genes, a slight increase compared to the first annotation set (69,808 genes). No low-quality genes are present in this dataset. When assessed against the Poale datasets, the v2 annotation shows 99.9% completeness, with only one fragmented gene and three missing genes. The improved quality stems from incorporating long-read transcripts generated for Triticum and numerous rounds of manual curation and examination that guided the development of (lots of) scripts for model selection at each locus. We are planning to release additional datasets based on this enhanced annotation, including EMS mutant remapping data, RNA-seq analyses, and NLR gene models. If there are other datasets you would find valuable, please let us know—we are happy to support the community's needs.

 

Acknowledgement

This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726).
DOI: 10.5281/zenodo.15539216
title: Chromosome-level genome assembly of Triticum turgidum var 'Kronos'

description:  

This data is made available under the Toronto Agreement. 

All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you agree to:



respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.

not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.

contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.

fully cite the prepublication data along with any applicable versioning details.

understand that this data as accessed is precompetitive and is not patentable in its present state.


This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). https://doi.org/10.1038/461168a

 



If you have questions about the use of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu


 

Updates in Zenodo v5

This update includes the last version of annotation (v2.1)! In this version, we manually curated 2,328 intraceullar immune receptor (NLR) loci and included 1,089 reliable NLR annotations. All existing NLR annotations eventually classified as low-confidence in manual curation were removed. Other non-NLR annotations remain identical. If you need all curated NLRs, please check out another respository that contains additional datasets (Chromosome-level genome assembly of Triticum turgidum var 'Kronos' additional datasets)

We provide functional annotations for all predicted genes. Kronos.v2.1.pep.eggnog.tsv comes from eggNOG-mapper and Kronos.v2.1.pep.fa.InterPro.tsv comes from InterProScan. 

 

Acknowledgement

This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726). Please, feel free to reach out to us regarding this datasets.
DOI: 10.17632/d5x2y65g5w.2
title: Malignancies Developed in Dermatologic Patients with MMF, Translant Patients, and Dermatologic Patients without Immunosuppression

description: List of malignancies in dermatologic patients without immunosuppression, dermatologic patients on MMF, and transplant recipient patients.
DOI: 10.6084/m9.figshare.26049640
title: Quantifying and reducing the cost of tagging: Combining fluid dynamics and diving experiments to reduce impact from animal-borne tags

description: Data and code associated to manuscript submission
DOI: 10.15468/dl.p9sx4k
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Argentina anserina (L.) Rydb."
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078080-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.em7nfr
title: Occurrence Download

description: A dataset containing 2525 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nicotiana alata Link & Otto, Nicotiana alata subsp. grandiflora Comes, Nicotiana alata var. grandiflora Comes, Nicotiana alata f. rubella Moldenke, Nicotiana alata var. persica (Lindl.) Comes, Nicotiana tabacum var. alata Alef., Nicotiana alata x forgetiana, Nicotiana alata × forgetiana)"
 ]
}

 The dataset includes 2525 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078078-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2dd79c
title: CCDC 2216292: Experimental Crystal Structure Determination

description: Related Article: Isha Mishra, Reema L. Borkar, Bhaskaran Shankar, Malaichamy Sathiyendiran|2024|J.Organomet.Chem.|1014|123199|doi:10.1016/j.jorganchem.2024.123199
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hk80c
title: CCDC 2310492: Experimental Crystal Structure Determination

description: Related Article: Isha Mishra, Reema L. Borkar, Bhaskaran Shankar, Malaichamy Sathiyendiran|2024|J.Organomet.Chem.|1014|123199|doi:10.1016/j.jorganchem.2024.123199
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jr25k
title: CCDC 2345868: Experimental Crystal Structure Determination

description: Related Article: Junichiro Hirano, Sayaka Miyoshi, Eiji Yashima, Tomoyuki Ikai, Hiroshi Shinokubo, Norihito Fukui|2024|Chem.Commun.|60|6035|doi:10.1039/D4CC01573H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jv58v
title: CCDC 2348847: Experimental Crystal Structure Determination

description: Related Article: Chenyang Zhao, Zujian Li, Lukang Ji, Hanxiao Wang, Guanghui Ouyang, Minghua Liu|2024|Chem.Commun.|60|6047|doi:10.1039/D4CC01810A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jx4tf
title: CCDC 2350755: Experimental Crystal Structure Determination

description: Related Article: Zi-Jian Jiang, Shan-Yuan Zhong, Yu-Hua Chen, Qing Liao, Mei-Jin Lin|2024|Dyes Pigm.|227|112158|doi:10.1016/j.dyepig.2024.112158
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25934/pr00009748
title: Causal inference in retrospective rheumatoid arthritis clinical studies

description: Our research project focuses on understanding the effects of various treatments on individuals with rheumatoid arthritis (RA), a chronic autoimmune condition that affects about 1% of people worldwide. RA leads to the immune system mistakenly attacking the body's joints, causing inflammation, pain, and potentially irreversible joint damage if not adequately treated. Treatment typically involves medications known as Disease Modifying Anti-Rheumatic Drugs (DMARDs),  which can significantly slow the disease's progression and prevent severe joint damage. However, finding the right medication or combination of medications can be a complex process, as what works best varies from person to person. Alongside DMARDs, other treatments (like steroids, immunosuppressant and Anti-tumor necrosis factor (TNF) drugs) are used to manage symptoms, especially during the early stages of the disease or flare-ups. Our study aims to delve deeper into how different treatments impact RA patients, considering other factors like age, sex, smoking status, and the presence of other health conditions, which can influence treatment effectiveness and patient outcomes.
Patients with RA often face additional health challenges, including a higher risk of cardiovascular disease, infections, and certain types of cancer. These comorbidities not only affect the overall health and mortality of RA patients but also complicate treatment decisions. Our research seeks to also understand these complexities better by exploring how various RA treatments interact with these comorbidities. By employing advanced statistical methods enhanced by the knowledge of cause-effect relationships between clinical variables, we aim to re-evaluate existing data and uncover new insights into the most effective treatment strategies. This approach will help us to tailor treatments more precisely to individual patient needs, improving their quality of life and potentially reducing the risk of severe joint damage and other health complications.
DOI: 10.5884/13172
title: CCGS Amundsen underway gas measurements, 2018-2019

description: Membrane inlet mass spectrometer (MIMS) and optode / gas tension device (GTD) gas systems were deployed on the CCGS Amundsen in 2018 and 2019. These autonomous sensors obtained measurements of dissolved O2, Ar, and N2 from the ship's underway seawater supply line at approximately 10-20 sec. intervals (<100 m spatial resolution). Raw and calibrated absolute gas concentrations, supersaturation anomalies, and gas ratios are reported. Data from the underway gas instrumentation were combined with hydrographic observations of surface and depth-resolved temperature and salinity (obtained by the Amundsen Science research group) collected via underway thermosalinograph (TSG) and Rosette-mounted conductivity-temperature-depth (CTD) instrumentation.
description: These underway, ship-based data, were collected using autonomous gas analyzers to observe spatial and temporal trends in surface dissolved gas (O2, Ar and N2) distributions throughout the waters of the pan-Canadian Arctic (including Labrador Sea, Davis Strait, Baffin Bay, and the Canadian Arctic Archipelago consisting of Lancaster Sound, Queen Maud Gulf, and the northern waters of Nares Strait and Kennedy Channel). Ultimately, these data will be combined with hydrographic observations to derive high spatial resolution estimates of surface waters net community production (i.e. photosynthesis minus respiration) over a multi-year period.
DOI: 10.15468/dl.3wxmpw
title: Occurrence Download

description: A dataset containing 9699 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "Country is Sri Lanka",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phalacrocorax fuscicollis Stephens, 1826",
 "Year 2020-2024"
 ]
}

 The dataset includes 9699 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078081-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkumk9
title: Occurrence Download

description: A dataset containing 651 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Incilius cavifrons (Firschein, 1950)"
 ]
}

 The dataset includes 651 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078083-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7emy9
title: Occurrence Download

description: A dataset containing 1063 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nicotiana sylvestris Speg.)"
 ]
}

 The dataset includes 1063 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078084-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fs7rxq
title: Occurrence Download

description: A dataset containing 1114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nigella sativa L., Nigella sativa var. hispidula Boiss., Nigella sativa var. brachyloba Boiss., Nigella sativa var. sativa, Nigella sativa var. citrina DC., Nigella sativa var. cretica (Mill.) DC., Nigella sativa var. indica (Roxb.) DC.)"
 ]
}

 The dataset includes 1114 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078085-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mub7rg
title: Occurrence Download

description: A dataset containing 371 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nothotsuga longibracteata (W.C.Cheng) H.H.Hu ex C.N.Page, Nothotsuga longibracteata (W.C.Cheng) H.H.Hu, Nothotsuga longibracteata subsp. fanjingshenensis Silba)"
 ]
}

 The dataset includes 371 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078086-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.72ycak
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Acentronura dendritica (Barbour, 1905)"
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078088-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.