cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.v5kcxk
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is 0c163d39-b67e-4bd9-a2f4-6344b67247f9",
 "TaxonKey is Scylaticus Loew, 1857"
 ]
}

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016179-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14074113
title: ClinVar_Re_predictions

description: Associated data for:

Single point mutations in disordered proteins: linking sequence, ensemble, and function

by Eduardo Flores, Nirbhik Acharya,Carlos Castaneda, and Shahar Sukenik.

https://chemrxiv.org/engage/chemrxiv/article-details/6758cd7af9980725cfa9eec8 

repository includes:



all_id_mappings.tsv: mapping of uniprot code to gene number

uniprotkb_proteome_UP000005640_2024_08_16.tsv: uniprot human proteome export including sequences

allClinvarMissense.csv - output of analysis. headers are:



upID - Uniprot ID

geneID - human genome gene ID

N_res  - number of residues 

N_disordered   - number of disordered residues (metapredict > 0.7)

N_ordered    - number of ordered residues varID (metapredict < 0.3)   

change  - string for mutation at protein level 

orig - original 3-letter AA   

pos  - mutation position 

mut - mutation 3-letter AA   

wtRe - Re of    mutRe    wtRe_local    mutRe_local    changeType    res_disorder    disease    signi



clinvar_20240917.vcf.gz - clinvar export used as input for this analysis

job.sub - HT Condor submission file for the analysis

wrapper.sh - Wrapper called for every job initiated by job.sub

parseClinvar.py - full analysis for every mutation. See wrapper.sh for details on calling this script.
DOI: 10.5281/zenodo.14074112
title: ClinVar_Re_predictions

description: Associated data for:

Single point mutations in disordered proteins: linking sequence, ensemble, and function

by Eduardo Flores, Nirbhik Acharya,Carlos Castaneda, and Shahar Sukenik.

Current Opinion in Structural Biology, 91, 2025, 102987

Publication: https://www.sciencedirect.com/science/article/pii/S0959440X25000053

See also analysis repo at: https://github.com/sukeniklab/ClinVar_Re_predictions

Files descriptions:



job.sub - HT Condor submission file for the analysis

wrapper.sh - Wrapper called for every job initiated by job.sub

parseClinvar.py - full analysis for every mutation. See wrapper.sh for details on calling this script.

allClinvarMissense.csv - output of analysis. headers are:



upID - Uniprot ID

geneID - human genome gene ID

N_res  - number of residues 

N_disordered   - number of disordered residues (metapredict > 0.7)

N_ordered    - number of ordered residues varID (metapredict < 0.3)   

change  - string for mutation at protein level 

orig - original 3-letter AA   

pos  - mutation position 

mut - mutation 3-letter AA   

wtRe - Re of    mutRe    wtRe_local    mutRe_local    changeType    res_disorder    disease    signi



data.tar.gz contains data used by parseClinvar.py.:



clinvar_20240917.vcf.gz - clinvar export used as input for this analysis

all_id_mappings.tsv: mapping of uniprot code to gene number

uniprotkb_proteome_UP000005640_2024_08_16.tsv: uniprot human proteome export including sequence
DOI: 10.5281/zenodo.14780486
title: ClinVar_Re_predictions

description: Associated data for:

Single point mutations in disordered proteins: linking sequence, ensemble, and function

by Eduardo Flores, Nirbhik Acharya,Carlos Castaneda, and Shahar Sukenik.

Current Opinion in Structural Biology, 91, 2025, 102987

Publication: https://www.sciencedirect.com/science/article/pii/S0959440X25000053

See also analysis repo at: https://github.com/sukeniklab/ClinVar_Re_predictions

Files descriptions:



job.sub - HT Condor submission file for the analysis

wrapper.sh - Wrapper called for every job initiated by job.sub

parseClinvar.py - full analysis for every mutation. See wrapper.sh for details on calling this script.

allClinvarMissense.csv - output of analysis. headers are:



upID - Uniprot ID

geneID - human genome gene ID

N_res  - number of residues 

N_disordered   - number of disordered residues (metapredict > 0.7)

N_ordered    - number of ordered residues varID (metapredict < 0.3)   

change  - string for mutation at protein level 

orig - original 3-letter AA   

pos  - mutation position 

mut - mutation 3-letter AA   

wtRe - Re of    mutRe    wtRe_local    mutRe_local    changeType    res_disorder    disease    signi



data.tar.gz contains data used by parseClinvar.py.:



clinvar_20240917.vcf.gz - clinvar export used as input for this analysis

all_id_mappings.tsv: mapping of uniprot code to gene number

uniprotkb_proteome_UP000005640_2024_08_16.tsv: uniprot human proteome export including sequence
DOI: 10.15468/dl.ky3b63
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Magnolia zoquepopolucae A.Vázquez)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016218-250127130748423/datasets/export for details.
DOI: 10.34740/kaggle/dsv/10672284
title: Metals Oxidation States from Molecules in CCDC
DOI: 10.5281/zenodo.14812424
title: Seafloor Data
DOI: 10.5281/zenodo.14812425
title: Seafloor Data
DOI: 10.15468/dl.4b7zy2
title: Occurrence Download

description: A dataset containing 3222 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample, Human Observation)",
 "Country is Canada",
 "OccurrenceStatus is Present",
 "TaxonKey is Myrmica rubra (Linnaeus, 1758)"
 ]
}

 The dataset includes 3222 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016220-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spgp3k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Magnolia zotictla A.Sánchez-Gonz., Gut.-Lozano & A.Vázquez)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016221-250127130748423/datasets/export for details.
DOI: 10.15468/dl.vpdh53
title: Occurrence Download

description: A dataset containing 48269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Athene cunicularia (Molina, 1782)"
 ]
}

 The dataset includes 48269 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016219-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69r6t4
title: Occurrence Download

description: A dataset listing the 864 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-81.83579 26.02085,-81.51649 26.02085,-81.51649 26.25946,-81.83579 26.25946,-81.83579 26.02085))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset's 864 records were derived from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016181-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m64k8r
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia biocellata Schltdl.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016222-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14808371
title: Annotation guidelines and data for complex known-item search requests for leisure domains

description: This dataset consists of the forum threads that have been annotated for known-item search. The post containing the search request and the post containing the correct answer have been marked, as well as the post where the original poster confirms the correct has been given. The guidelines explain the annotation process.

This dataset is used for and described in the ACM CHIIR 2025 paper entitled "Exploring the Zero-Shot Known-Item Retrieval\\ Capabilities of LLMs for Casual Leisure Information Needs".
DOI: 10.15468/dl.yg58jr
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia breedlovei W.R.Anderson)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016223-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.raepn8
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia glandulosa (Cav.) DC.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 36 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016225-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a69qut
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allophylus laxiflorus Gagnep."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016226-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14810309
title: PhD thesis Appendix SQL files

description: This release is the final version of the PhD Appendix that includes the SQL files and some instructions on how you can use them.
This version was released to get the Digital Object Identifier via Zenodo.
DOI: 10.5281/zenodo.14810310
title: PhD thesis Appendix SQL files

description: This release is the final version of the PhD Appendix that includes the SQL files and some instructions on how you can use them.
This version was released to get the Digital Object Identifier via Zenodo.
DOI: 10.6084/m9.figshare.28352600.v1
title: <b>Code of Great achievable whole-profile sequestration potential of mineral-associated organic carbon in Chinese croplands</b>

description: Mineral-associated organic carbon (MAOC), characterized by due to its relatively slow turnover rate, playis a critical role inpivotal for long-term soil organic carbon (SOC) sequestration, supporcontributing to soil health, climate change mitigation, and therefore food security. However, the depth vertical distributions of MAOC storage and its sequestration potential across soil depths remain poorly understood, especially at large spatial extents. Here, we report a national dataset of SOC and MAOC measurements across seven sequential depth layers down to 2 m atfrom 365 cropland sites in Chinese croplands (nonexcluding -paddy fields) across China, sampling seven sequential soil layers down to 2 m. Our findings We showreveal substantial spatial variability in that the depth distribution of MAOC concentration with depth, s varies widely across the sites, strongly being positively correlated withto depth-specific soil carbon- to- nitrogen ratios and fine mineral particle contents (clay and silt). WhileAveraging across the sites, MAOC is the dominatesnt SOC across all sampled depthsfraction at all depths, but its relative contribution dominance diminishes eclines in deeper layers, particularly below 1 m, probably due to reducedlimited microbial activities in deeper soi layerstherein. NotablyAdditionally, we find that current average MAOC stockslevels only constitute &lt;25% of their attainable maximum MAOC, with even larger deficits in subsoils (0.3-2 m) exhibiting even greaterwith higher deficits in high-clay and /silt regionscontent. Nationwideal-scale mapping estimates a totalthat the SOC stock in the 0–2 m depth of Chinese croplands is of 11.4 Gt (95% confidence interval: 6.8–16.2 Gt) in the 0–2 m depth of Chinese croplands, with &gt;75% of this stock residing belowin the 0.3–2 m layer and MAOC contributing 55% to the total SOC. We project that an aAdditional 4.7 and 13.4 Gt MAOC can be sequestered in the 0–0.3 and 0.3–2 m depths, respectively, if properly managed. These findings underscore the untapped substantial potential for whole-profile carbon sequestration viain the form of MAOC accumulation in Chinese croplands. Achieving this potential will require , emphasizing the need of novel agricultural management strategies tailored to enhance MAOC formation and stabilization across the entire soil profile, with implications for climate-smart land management and national carbon neutrality goalsto reach this potential.
DOI: 10.15468/dl.k5bhwc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia guatemalensis Nied.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016227-250127130748423/datasets/export for details.
DOI: 10.5281/zenodo.14812207
title: Nile Delta Palimpsestual River Network (PRN)

description: Nile Delta Palimpsestual-river-network (PRN)
CC-BY-SA-4.0 license

The data offered here was created as part of the PhD project Hinojosa-Baliño, I. (2022). Urban fluctuations in the north-central region of the Nile Delta: 4000 years of river and urban development in Egypt. [Doctoral, Durham University]. The these can be downloaded from Durham eTheses.

Data files are offered as Geopackages (GPKG) and the main files include Metadata in QMD format, but they should have their own Metadata embedded.

Contents



PRN (realistic). Palimpsestual river network with channel width represented with a realistic width based on different sources.

Spider network combined with PRN (lines). Palimpsestual reconstructed river network with approximate channel width, type of channel and potential speed that a boat could have achieved in that specific channel.

Lagoons. This is a polygon layer representing the boundaries of lakes in the Nile Delta. This is just a background layer.
DOI: 10.5281/zenodo.14812208
title: Nile Delta Palimpsestual River Network (PRN)

description: Nile Delta Palimpsestual-river-network (PRN)
CC-BY-SA-4.0 license

The data offered here was created as part of the PhD project Hinojosa-Baliño, I. (2022). Urban fluctuations in the north-central region of the Nile Delta: 4000 years of river and urban development in Egypt. [Doctoral, Durham University]. The these can be downloaded from Durham eTheses.

Data files are offered as Geopackages (GPKG) and the main files include Metadata in QMD format, but they should have their own Metadata embedded.

Contents



PRN (realistic). Palimpsestual river network with channel width represented with a realistic width based on different sources.

Spider network combined with PRN (lines). Palimpsestual reconstructed river network with approximate channel width, type of channel and potential speed that a boat could have achieved in that specific channel.

Lagoons. This is a polygon layer representing the boundaries of lakes in the Nile Delta. This is just a background layer.
DOI: 10.15468/dl.vmxm4e
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia lindeniana A.Juss.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016229-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e218041
title: Replication: Efficiency of Bus Priority Infrastructure

description: We use bus GPS data across 500 routes to estimate the impact of priority infrastructure on buses' speed and ridership in Chile. Almost 100 million bus trips allow us to leverage within-route variation in the proportion of the route in which buses travel along bus lanes or Bus Rapid Transit (BRT) corridors. Corridors increase bus speeds by 20\% at peak hours. Bus lanes, often seen as an equally effective but cheaper alternative to a BRT corridor, are, on average, ineffective. However, bus lanes achieve the same travel time savings as BRT corridors only when fully isolated from private vehicles, coupled with monitoring cameras and enforcement.
DOI: 10.3886/e218041v1
title: Replication: Efficiency of Bus Priority Infrastructure

description: We use bus GPS data across 500 routes to estimate the impact of priority infrastructure on buses' speed and ridership in Chile. Almost 100 million bus trips allow us to leverage within-route variation in the proportion of the route in which buses travel along bus lanes or Bus Rapid Transit (BRT) corridors. Corridors increase bus speeds by 20\% at peak hours. Bus lanes, often seen as an equally effective but cheaper alternative to a BRT corridor, are, on average, ineffective. However, bus lanes achieve the same travel time savings as BRT corridors only when fully isolated from private vehicles, coupled with monitoring cameras and enforcement.
DOI: 10.15468/dl.wvjf6f
title: Occurrence Download

description: A dataset containing 1455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.46.4_1",
 "Geometry POLYGON((-72.83022 44.52352,-72.83816 44.51884,-72.83141 44.51431,-72.82068 44.51318,-72.81373 44.51559,-72.80678 44.5221,-72.80797 44.52904,-72.81115 44.53527,-72.80757 44.54136,-72.80638 44.54618,-72.80876 44.55028,-72.81909 44.55,-72.82783 44.54773,-72.83399 44.54632,-72.83816 44.54221,-72.83499 44.53669,-72.82048 44.54123,-72.8196 44.53543,-72.82227 44.53386,-72.82045 44.52742,-72.82088 44.52556,-72.82505 44.52593,-72.83022 44.52352))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 1455 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016231-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4hs9zj
title: Occurrence Download

description: A dataset containing 1804 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Lessertia frutescens (L.) Goldblatt & J.C.Manning"
 ]
}

 The dataset includes 1804 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016232-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.utpmuj
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia nitida (Jacq.) Rich. ex A.Juss.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016233-250127130748423/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.25000367
title: Dynamic changes in histone lysine lactylation during meiosis prophase I in mouse spermatogenesis

description: These are raw ChIP-seq data for histone lactylation (H4K8la) in germ cells.
DOI: 10.15468/dl.5n6pq5
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 Rhododendron amundsenianum Hand.-Mazz."
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016234-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h98b68
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bunchosia palmeri S.Watson)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 77 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016235-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.