cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7096148
title: TrypTag: Genome-wide subcellular protein localisation in Trypanosoma brucei.

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen Trypanosoma brucei by endogenous tagging with mNeonGreen (mNG). This master deposition includes scripts, code and primer sequences used to build the TrypTag database, provided in the master directory structure. It does not include any microscopy data, which are spread over multiple Zenodo DOIs. Instead, raw and processed data directories include an index to each DOI.
description: Corrected DOI indexing to point to latest version rather than original upload, to better allow for any technical corrections in the future.
DOI: 10.5281/zenodo.7418745
title: TrypTag: Genome-wide subcellular protein localisation in Trypanosoma brucei.

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen Trypanosoma brucei by endogenous tagging with mNeonGreen (mNG). This master deposition includes a summary of the localisations, scripts, code and primer sequences used to build the TrypTag database, provided in the master directory structure. It does not include any microscopy data, which are spread over multiple Zenodo DOIs. Instead, this deposition and the raw and processed data directories include an index to each DOI.
description: Corrected DOI indexing to point to latest version rather than original upload, to better allow for any technical corrections in the future.
DOI: 10.5281/zenodo.7441744
title: TrypTag: Genome-wide subcellular protein localisation in Trypanosoma brucei.

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <em>Trypanosoma brucei</em> by endogenous tagging with mNeonGreen (mNG). This master deposition includes a summary of the localisations, scripts, code and primer sequences used to build the TrypTag database, provided in the master directory structure. It does not include any microscopy data, which are spread over multiple Zenodo DOIs. Instead, this deposition and the raw and processed data directories include an index linking gene IDs to each Zenodo DOI. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington <em>et al.</em> 2023 <em>Nature Microbiology </em>(doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this Zenodo deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean <em>et al.</em> 2016 <em>Trends in Parasitology</em> (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday <em>et al.</em> 2019 <em>Molecular and Biochemical Parasitology</em> (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to <em>Leishmania</em>.
description: Add recommended TrypTag citation information.
DOI: 10.5281/zenodo.7716544
title: TrypTag: Genome-wide subcellular protein localisation in Trypanosoma brucei.

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <em>Trypanosoma brucei</em> by endogenous tagging with mNeonGreen (mNG). This master deposition includes a summary of the localisations, scripts, code and primer sequences used to build the TrypTag database, provided in the master directory structure. It does not include any microscopy data, which are spread over multiple Zenodo DOIs. Instead, this deposition and the raw and processed data directories include an index linking gene IDs to each Zenodo DOI. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington <em>et al.</em> 2023 <em>Nature Microbiology </em>(doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this Zenodo deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean <em>et al.</em> 2016 <em>Trends in Parasitology</em> (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday <em>et al.</em> 2019 <em>Molecular and Biochemical Parasitology</em> (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to <em>Leishmania</em>.
description: Add recommended TrypTag citation information.
DOI: 10.5281/zenodo.7716836
title: TrypTag: Genome-wide subcellular protein localisation in Trypanosoma brucei.

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <em>Trypanosoma brucei</em> by endogenous tagging with mNeonGreen (mNG). This master deposition includes a summary of the localisations, scripts, code and primer sequences used to build the TrypTag database, provided in the master directory structure. It does not include any microscopy data, which are spread over multiple Zenodo DOIs. Instead, this deposition and the raw and processed data directories include an index linking gene IDs to each Zenodo DOI. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington <em>et al.</em> 2023 <em>Nature Microbiology </em>(doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this Zenodo deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean <em>et al.</em> 2016 <em>Trends in Parasitology</em> (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday <em>et al.</em> 2019 <em>Molecular and Biochemical Parasitology</em> (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to <em>Leishmania</em>.
description: V1115_210180807 to V1115_20180807 plate ID corrections.
DOI: 10.34740/kaggle/dsv/5142976
title: SPR X-Ray Age and Gender Dataset
DOI: 10.6084/m9.figshare.22081055
title: Description of data used in the tool, complete table

description: Table of variables description used in the "Data Integration Dashboard for Assessing and Planning Agricultural Interventions: a case in Senegal" paper
DOI: 10.6084/m9.figshare.22081055.v2
title: Description of data used in the tool, complete table

description: Table of variables description used in the "Data Integration Dashboard for Assessing and Planning Agricultural Interventions: a case in Senegal" paper
DOI: 10.6084/m9.figshare.22081055.v1
title: Description of data used in the tool, complete table

description: Table of variables description used in the "Data Integration Dashboard for Assessing and Planning Agricultural Interventions: a case in Senegal" paper
DOI: 10.17909/a4hr-v053
title: Data from HST Survey of the Orion Nebula Cluster ACS/Visible Bands. IV. Star formation in the ONC

description: We have performed a comprehensive study of the Orion Nebula Cluster (ONC) combining the photometric data obtained by the two \textit{HST} Treasury programs that targeted this region.
To consistently analyze the rich dataset obtained in a wide variety of filters, we adopted a Bayesian approach to fit the Spectral Energy Distribution of the sources, deriving mass, age, extinction, distance, and accretion for each source in the region. The resulting age distribution of the bona-fide cluster members strongly supports the idea  that  star  formation  in  the ONC is best described by a major episode of star formation that happened $\sim 1$ Myr ago. 
Our derived empirical IMF for this cluster, characterized as a broken power-law, appears mostly compatible with a Chabrier system IMFs for \Mstar $\leq 0.3$ \Msun, with a possible lack of low-mass/brown dwarf objects at the lowest masses.
Both the accretion luminosity (\Lacc) and mass accretion rates (\dMacc) are also best described by broken power-law relations.
This suggests that for the majority of young circumstellar disks in this cluster the excess emission may be dominated by X-ray-driven photoevaporation by the centrao star rather than external photoevaporation. If this is the case, the slopes of the power-law relations may be largely determined by the initial conditions set at the onset of the star formation process, which may be quite similar between regions that eventually form clusters of different sizes.
DOI: 10.17909/9aca-qz94
title: Data from HST Survey of the Orion Nebula Cluster ACS/Visible Bands. IV. Star formation in the ONC

description: We have performed a comprehensive study of the Orion Nebula Cluster (ONC) combining the photometric data obtained by the two \textit{HST} Treasury programs that targeted this region.
To consistently analyze the rich dataset obtained in a wide variety of filters, we adopted a Bayesian approach to fit the Spectral Energy Distribution of the sources, deriving mass, age, extinction, distance, and accretion for each source in the region. The resulting age distribution of the bona-fide cluster members strongly supports the idea  that  star  formation  in  the ONC is best described by a major episode of star formation that happened $\sim 1$ Myr ago. 
Our derived empirical IMF for this cluster, characterized as a broken power-law, appears mostly compatible with a Chabrier system IMFs for \Mstar $\leq 0.3$ \Msun, with a possible lack of low-mass/brown dwarf objects at the lowest masses.
Both the accretion luminosity (\Lacc) and mass accretion rates (\dMacc) are also best described by broken power-law relations.
This suggests that for the majority of young circumstellar disks in this cluster the excess emission may be dominated by X-ray-driven photoevaporation by the centrao star rather than external photoevaporation. If this is the case, the slopes of the power-law relations may be largely determined by the initial conditions set at the onset of the star formation process, which may be quite similar between regions that eventually form clusters of different sizes.
DOI: 10.13020/gneg-dv46
title: Supporting data for Intermolecular Forces Dictate Vibrational Energy Transfer in Plasmonic–Molecule Systems
DOI: 10.15151/esrf-es-1096965502
title: PROTEINS RELATED TO PATHOGENESIS OF DISEASES, VIRAL PROTEINS, CELL DIVISION, SIGNALLING AND CHROMATIN PROCESSES

description: Our BAG is composed of eight PIs at six different institutions in Italy and Austria. We focus on a large variety of human, bacterial, viral and synthetic protein targets and address diverse biological contexts by combining structural biology with biochemistry, biophysics, cellular and in vivo investigations.
DOI: 10.6073/pasta/8fb72cf42711a9e0fe4b84d3fb4abf01
title: Genome size influences grassland plant community responses to nutrients across diverse climate and species assemblages of the Northern hemisphere.

description: Genome size varies widely across angiosperms, impacting the nitrogen and phosphate demands of nuclei, the scaling effects on minimum cell size, and plant metabolic processes. To determine the ecological consequences of these nutrient and scaling effects, we combined genome size and species abundance data from replicated nutrient addition experiments in the Nutrient Network, encompassing 27 grassland communities distributed across a range of climates in the Northern hemisphere. We found that larger genome species (mostly C3 grasses and perennial forbs) became more abundant and decreased less in richness under combined nitrogen and phosphorus fertilisation, potentially indicating a release from nuclei nutrient constraints. Responses did not depend upon temperature or seasonal attributes but were strongest at sites with low precipitation, indicating that GS effects on water-use-efficiency modulates GS-nutrient interactions. Cumulatively our data indicate that genome size is a globally important predictor of a species success and grassland community structures.
DOI: 10.6075/j0028rr4
title: Heterogeneous Stock (HS) Rat Genotypes, Version 1. In Genotype data from: NIDA Center for GWAS in Outbred rats

description: Rat Genome assembly: Rnor_6.0 All software versions used to generate the data in this object are noted below and in the Methods section of the associated publication: • fastx_toolkit-0.0.14 • Cutadapt v1.9.1 • bwa-0.7.12 • picard-tools-1.141 • GATK IndelRealginer v3.5 • Beagle v4.1 • impute-2.3.2 • java openjdk version “1.8.0_191” • python 2 Demultiplexing was performed using fastx_toolkit. Barcode, adapter and quality trimming was performed using Cutadapt. The Rattus norvegicus genome assembly rn6 was used as the reference genome for read alignment with the BWA software. We then used GATK IndelRealginer to improve alignment quality by locally realigning reads around a reference set of known indels in 42 whole-genome sequenced inbred rat strains, including the eight HS progenitor strains. Variants were called, and genotype likelihoods were computed at variant sites using ANGSD, under the SAMtools model for genotype likelihoods (ANGSD-SAMtools). Beagle was used to improve the genotyping within the samples without the use of an external reference panel. We used a combination of existing sequencing and array genotyping data from the HS rat founder and other inbred laboratory rat strains (Hermsen et al. 2015) as reference panel for imputation. Imputation by IMPUTE2 was performed in 5Mb windows using the aforementioned reference panels and genetic maps.
description: This collection contains genotype data collected as part of the NIDA Center for GWAS in Outbred rats and more than 10 additional research projects that use N/NIH heterogeneous stock (HS) outbred rats. We obtain genotypes for DNA samples derived from rats that are phenotyped by different research projects. We use these genotypes to perform genome wide association studies (GWAS) and a number of related analyses.
DOI: 10.5281/zenodo.7707021
title: wikipathways-20230210-gmt-Bos_taurus.gmt

description: See GMT file for Bos taurus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707022
title: wikipathways-20230210-gmt-Bos_taurus.gmt

description: See GMT file for Bos taurus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707051
title: wikipathways-20230210-gmt-Sus_scrofa.gmt

description: See GMT file for Sus scrofa pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707052
title: wikipathways-20230210-gmt-Sus_scrofa.gmt

description: See GMT file for Sus scrofa pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707047
title: wikipathways-20230210-gmt-Saccharomyces_cerevisiae.gmt

description: See GMT file for Saccharomyces cerevisiae pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707048
title: wikipathways-20230210-gmt-Saccharomyces_cerevisiae.gmt

description: See GMT file for Saccharomyces cerevisiae pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7719517
title: amazona_dufresniana_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.7719516
title: amazona_dufresniana_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.7707045
title: wikipathways-20230210-gmt-Rattus_norvegicus.gmt

description: See GMT file for Rattus norvegicus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707046
title: wikipathways-20230210-gmt-Rattus_norvegicus.gmt

description: See GMT file for Rattus norvegicus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.6084/m9.figshare.21200971
title: Socioeconomic Impact of COVID-19 during three pandemic waves

description: Provides in-depth data regarding diverse socio-economic impacts, mobility, and human behavioral changes due to COVID-19 across three identified pandemic phases. Data was gathered through a field survey. Useful for cross-impact analysis across time which depicts the evolution of socio-economic, mobility, and human behavioral changes over pandemic periods. This is also useful for policy decisions and implications. Further, this contains Survey instrument which was developed for the data collection under AI4COVID project (website: ai4covind.lk ) in Sri Lanka
DOI: 10.6084/m9.figshare.21200971.v6
title: Socioeconomic Impact of COVID-19 during three pandemic waves

description: Provides in-depth data regarding diverse socio-economic impacts, mobility, and human behavioral changes due to COVID-19 across three identified pandemic phases. Data was gathered through a field survey. Useful for cross-impact analysis across time which depicts the evolution of socio-economic, mobility, and human behavioral changes over pandemic periods. This is also useful for policy decisions and implications. Further, this contains Survey instrument which was developed for the data collection under AI4COVID project (website: ai4covind.lk ) in Sri Lanka
DOI: 10.6084/m9.figshare.21200971.v5
title: Socioeconomic Impact of COVID-19 during three pandemic phases

description: Provides in-depth data regarding diverse socio-economic impacts, mobility, and human behavioral changes due to COVID-19 across three identified pandemic phases. Data was gathered through a field survey. Useful for cross-impact analysis across time which depicts the evolution of socio-economic, mobility, and human behavioral changes over pandemic periods. This is also useful for policy decisions and implications. Further, this contains Survey instrument which was developed for the data collection under AI4COVID project (website: ai4covind.lk ) in Sri Lanka
DOI: 10.5281/zenodo.7707043
title: wikipathways-20230210-gmt-Populus_trichocarpa.gmt

description: See GMT file for Populus trichocarpa pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707044
title: wikipathways-20230210-gmt-Populus_trichocarpa.gmt

description: See GMT file for Populus trichocarpa pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707042
title: wikipathways-20230210-gmt-Pan_troglodytes.gmt

description: See GMT file for Pan troglodytes pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707041
title: wikipathways-20230210-gmt-Pan_troglodytes.gmt

description: See GMT file for Pan troglodytes pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707039
title: wikipathways-20230210-gmt-Mus_musculus.gmt

description: See GMT file for Mus musculus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707040
title: wikipathways-20230210-gmt-Mus_musculus.gmt

description: See GMT file for Mus musculus pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707035
title: wikipathways-20230210-gmt-Homo_sapiens.gmt

description: See GMT file for Homo sapiens pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}
DOI: 10.5281/zenodo.7707036
title: wikipathways-20230210-gmt-Homo_sapiens.gmt

description: See GMT file for Homo sapiens pathways for all released versions.
description: {"references": ["Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. PMID: 18651794; PMCID: PMC2475545."]}