Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
10,767
datasets available to search
ShareScore release 0.9.0
Dataset results
10,767 results for “Contribution”
Predator Contributions to Belowground Responses to Climate Warming at Harvard Forest 2014
Identifying the factors that control soil CO2 emissions will improve our ability to predict the magnitude of climate change-soil ecosystem feedbacks. Despite the integral role of invertebrates in belowground systems, they are excluded from climate change models. Soil invertebrates have consumptive and non-consumptive effects on microbes, whose respiration accounts for nearly half of soil CO2 emissions. By altering the behavior and abundance of invertebrates that interact with microbes, invertebrate predators may have indirect effects on soil respiration. We examined the effects of a generalist arthropod predator on belowground respiration under different warming scenarios. Based on research suggesting invertebrates may mediate soil CO2 emission responses to warming, we predicted that predator presence would result in increased emissions by negatively affecting these invertebrates. We altered the presence of wolf spiders (Pardosa spp.) in mesocosms containing a forest floor community. To simulate warming, we placed mesocosms of each treatment in ten open-top warming chambers ranging from 1.5 to 5.5° C above ambient at Harvard Forest, MA. As expected, CO2 emissions increased under warming and we found an interactive effect of predator presence and warming, though the effect was not consistent through time. The interaction between predator presence and warming was the inverse of our predictions: mesocosms with predators had lower respiration at higher levels of warming than those without predators. Carbon dioxide emissions were not significantly associated with microbial biomass. We did not find evidence of consumptive effects of predators on the invertebrate community, suggesting that predator presence mediates response of microbial respiration to warming through non-consumptive means. In our system we found a significant interaction between warming and predator presence that warrants further research into mechanism and generality of this pattern to other systems.
National contributions to climate change due to historical emissions of carbon dioxide, methane and nitrous oxide
<p>A complete description of the dataset is given by <a href="http://doi.org/10.1038/s41597-023-02041-1">Jones et al. (2023)</a>. Key information is provided below.</p> <p><strong>Background</strong></p> <p>A dataset describing the global warming response to national emissions CO<sub>2</sub>, CH<sub>4</sub> and N<sub>2</sub>O from fossil and land use sources during 1851-2021.</p> <p>National CO<sub>2 </sub>emissions data are collated from the Global Carbon Project (Andrew and Peters, 2024; Friedlingstein et al., 2024). </p> <p>National CH<sub>4</sub> and N<sub>2</sub>O emissions data are collated from PRIMAP-hist (HISTTP) (Gütschow et al., 2024).</p> <p>We construct a time series of cumulative CO2-equivalent emissions for each country, gas, and emissions source (fossil or land use). Emissions of CH<sub>4</sub> and N<sub>2</sub>O emissions are related to cumulative CO2-equivalent emissions using the Global Warming Potential (GWP*) approach, with best-estimates of the coefficients taken from the IPCC AR6 (Forster et al., 2021).</p> <p>Warming in response to cumulative CO2-equivalent emissions is estimated using the transient climate response to cumulative carbon emissions (TCRE) approach, with best-estimate value of TCRE taken from the IPCC AR6 (Forster et al., 2021, Canadell et al., 2021). 'Warming' is specifically the change in global mean surface temperature (GMST).</p> <p>The data files provide emissions, cumulative emissions and the GMST response by country, gas (CO<sub>2</sub>, CH<sub>4</sub>, N<sub>2</sub>O or 3-GHG total) and source (fossil emissions, land use emissions or the total).</p> <p><strong>Data records: overview</strong></p> <p>The data records include three comma separated values (.csv) files as described below.</p> <p>All files are in ‘long’ format with one value provided in the <em>Data</em> column for each combination of the categorical variables <em>Year, Country Name, Country ISO3 code, Gas, and Component</em> columns.</p> <p><em>Component</em> specifies fossil emissions, LULUCF emissions or total emissions of the gas.</p> <p><em>Gas</em> specifies CO<sub>2</sub>, CH<sub>4</sub>, N<sub>2</sub>O or the three-gas total (labelled 3-GHG).</p> <p><em>Country ISO3 codes</em> are specifically the unique ISO 3166-1 alpha-3 codes of each country.</p> <p><strong>Data records: specifics</strong></p> <p>Data are provided relative to 2 reference years (denoted <em>ref_year </em>below): 1850 and 1991. 1850 is a mutual first year of data spanning all input datasets. 1991 is relevant because the United Nations Framework Convention on Climate Change was operationalised in 1992.</p> <p><em>EMISSIONS_ANNUAL_{ref_year-20}-2023.csv:</em> <em>Data </em>includes annual emissions of CO<sub>2</sub> (Pg CO<sub>2</sub> year<sup>-1</sup>), CH<sub>4</sub> (Tg CH<sub>4</sub> year<sup>-1</sup>) and N<sub>2</sub>O (Tg N<sub>2</sub>O year<sup>-1</sup>) during the period <em>ref_year-20 </em>to 2023. The <em>Data</em> column provides values for every combination of the categorical variables. Data are provided from <em>ref_year-20</em> because these data are required to calculate GWP* for CH<sub>4</sub>.</p> <p><em>EMISSIONS_CUMULATIVE_CO2e100_{ref_year+1}-2023.csv: Data </em>includes the cumulative CO<sub>2</sub> equivalent emissions in units Pg CO<sub>2</sub>-e<sub>100</sub> during the period <em>ref_year+1</em> to 2023 (i.e. since the reference year). The <em>Data</em> column provides values for every combination of the categorical variables. </p> <p><em>GMST_response_{ref_year+1}-2023.csv:</em> <em>Data</em> includes the change in global mean surface temperature (GMST) due to emissions of the three gases in units °C during the period <em>ref_year+1</em> to 2023 (i.e. since the reference year). The <em>Data</em> column provides values for every combination of the categorical variables. </p> <p><strong>Accompanying Code</strong></p> <p>Code is available at: <a href="https://github.com/jonesmattw/National_Warming_Contributions">https://github.com/jonesmattw/National_Warming_Contributions</a> .</p> <p>The code requires Input.zip to run (see README at the GitHub link).</p> <p><strong>Further info: Country Groupings</strong></p> <p>We also provide estimates of the contributions of various country groupings as defined by the UNFCCC:</p> <ul> <li>Annex I countries (number of countries, n = 42)</li> <li>Annex II countries (n = 23)</li> <li>economies in transition (EITs; n = 15)</li> <li>the least developed countries (LDCs; n = 47)</li> <li>the like-minded developing countries (LMDC; n = 24).</li> </ul> <p>And other country groupings:</p> <ul> <li>the organisation for economic co-operation and development (OECD; n = 38)</li> <li>the European Union (EU27 post-Brexit)</li> <li>the Brazil, South Africa, India and China (BASIC) group.</li> </ul> <p>See COUNTRY_GROUPINGS.xlsx for the lists of countries in each group.</p>
Dominant contribution of Asgard archaea to eukaryogenesis (2024) Tobiasson, V., Koonin, E. PROCESSED DATA AND METADATA
<h1>Main data deposit for "Dominant contribution of Asgard archaea to eukaryogenesis". </h1> <p>Victor Tobiasson, Jacob Luo, Yuri I Wolf, Eugene V Koonin</p> <p>Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA</p> <p><strong>The Origin of eukaryotes is one of the key problems in evolutionary biology. The demonstration that the Last Eukaryotic Common Ancestor (LECA) already contained the mitochondrion, an endosymbiotic organelle derived from an alphaproteobacterium, and the discovery of Asgard archaea, the closest archaeal relatives of eukaryotes inform and constrain evolutionary scenarios of eukaryogenesis. We undertook a comprehensive analysis of the origins of the core eukaryotic genes tracing to the LECA within a rigorous statistical framework centered around evolutionary hypotheses testing using constrained phylogenetic trees. The results reveal dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways. A limited contribution from Alphaproteobacteria was identified, primarily relating to the energy transformation systems and Fe-S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without consistent trends. These findings suggest a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard ancestor, followed by the capture of the Alphaproteobacterial endosymbiont, and augmented by numerous but sporadic horizontal acquisition of genes from other bacteria both before and after endosymbiosis. </strong></p> <div> <div> <div>Version 0.3, updated 180325</div> <div> </div> <div> </div> <div>Main data repository for:</div> <div>Dominant contribution of Asgard archaea to eukaryogenesis (2024) </div> <div>Tobiasson, V., Koonin, E.</div> <div> </div> <div>Contains all final parsed data from the main Eukaryogenesis project </div> <div>investigating the evolutionary ancetries of eukaryotic protein families. </div> <div> </div> <div>Currently (non-static) available at: </div> <div>https://www.biorxiv.org/content/10.1101/2024.10.14.618318v2</div> <div>https://assets-eu.researchsquare.com/files/rs-5352492/v1/2f9c68ae-cf3e-420a-8d29-867b6fb1a878.pdf</div> <div> </div> <div>All code used to generate the data present within this repository available at: </div> <div>https://github.com/VictorTobiasson/eukgen </div> <div> </div> <div> </div> <div>### General information</div> <div> </div> <div>To identify associations between prokaryotic and eukaryotic protein families, separate</div> <div>hidden Markov model (HMM) databases for prokaryotes and eukaryotes were constructed </div> <div>using a custom, cascaded, sequence-to-profile clustering pipeline, implemented using </div> <div>mmseqs2, followed by a multistep data-reduction and multiple sequence alignment (MSA) </div> <div>procedure to generate HMM profiles using hhsuite. </div> <div> </div> <div>A prokaryotic database of 37 million protein sequences was curated from prokaryotic </div> <div>genomes obtained from the NCBI GenBank in November 2023 and supplemented with proteins </div> <div>extracted from 146 Asgard genome assemblies. To avoid inclusion of genes present only </div> <div>within a narrow subset of species, possibly resulting from horizontal transfer from </div> <div>eukaryotes post LECA, we reconstructed the “soft-core” pangenome for each of the 26 </div> <div>curated prokaryotic taxonomic classes. These pangenomes include only those genes that </div> <div>are present in at least 67% of the families within each class of Bacteria and Archaea. </div> <div>The initial eukaryotic database consisted of 30 million protein sequences from 993 </div> <div>species taken from EukprotV3 and cleaned using mmseqs2 to remove likely prokaryotic </div> <div>contaminants. </div> <div> </div> <div>Both databases were clustered and MSAs constructed for all non, singleton clusters </div> <div>and HMM profiles created. The resulting eukaryotic HMM dataset was queried against </div> <div>the prokaryotic dataset using hhblits to identify sets of homologous protein sequences. </div> <div>Each eukaryotic cluster and all its significant prokaryotic hits constituted an individual</div> <div> sequence set, hereinafter referred to as an Eukaryotic/Prokaryotic Orthologous Cluster </div> <div>(EPOC). The EPOCs constitute groups of homologous proteins from eukaryotes and prokaryotes </div> <div>(each EPOC contains a unique set of eukaryotic proteins, but some clusters of prokaryotic </div> <div>proteins can be present in multiple EPOCs) that were used for phylogenetic tree </div> <div>construction, annotation, and evolutionary hypothesis testing. </div> <div> </div> <div>To infer the most likely prokaryotic ancestry of the eukaryotic proteins in each EPOC, </div> <div>rather than relying on the tree topology directly, we employed a probabilistic approach </div> <div>for evolutionary hypothesis testing using constraint trees. We exhaustively sampled all </div> <div>arrangements of likely sister clades and obtained Expected Likelihood Weights (ELW) for </div> <div>the set of possible sister clade models. As the ELW metric is analogous to model selection </div> <div>confidence, here we take it to be proportional to the probability of a sampled prokaryotic </div> <div>clade to be the true sister group of the given eukaryotic clade among a set of competing </div> <div>sister clades. For each EPOC, our analysis dynamically accounts for long branch outliers </div> <div>and is robust to phylogenetically non-homogenous clades. This analysis is further capable </div> <div>of resolving eukaryotic paraphyly, treating each eukaryotic clade within a EPOC as a </div> <div>single datapoint for downstream analysis. Our resulting data contains EPOCs annotated </div> <div>using profiles generated from KEGG Orthology Groups (KOGs), each with an MSA generated </div> <div>using muscle5, a maximum likelihood tree inferred using IQtree2 and associated ELW values </div> <div>for all candidate prokaryotic sister phyla. The analysis of prokaryotic ancestry was </div> <div>performed only for those eukaryotic clades that included more than 5 distinct taxonomic </div> <div>labels, with at least one coming from Amorphea and one from Diaphoretickes, the two </div> <div>expansive eukaryotic clades considered to represent either the first or the second </div> <div>bifurcation in the evolution of eukaryotes. Thus, these clades likely represent genes </div> <div>mapping back to the LECA.</div> <div> </div> <div>For further details please see main publication or contact</div> <div>victor.tobiasson@nih.gov</div> <div>eugene.koonin@nih.gov</div> <div> </div> <div> </div> <div>### Included files</div> <div> </div> <div>Unless otherwise stated all files contained are tab separated and utf-8 encoded </div> <div>with the first row containing header information. </div> <div>All data entries encoding lists are “|” (pipe) separated. </div> <div>Fields without data values are filled with string entries of “none”.</div> <div> </div> <div>--- Databases ---</div> <div>euk72_ep.tar.gz</div> <div>prok2311_as.tar.gz</div> <div>Prok2311As_final_clusters.tsv</div> <div>Euk72Ep_final_clusters.tsv</div> <div>prok2311_as.hmmDB.tar.gz</div> <div>euk72_ep.hmmDB.tar.gz</div> <div> </div> <div>--- Annotation and Curation ---</div> <div>NCBI_taxonomy_species_addendum.tsv</div> <div>NCBI_taxonomy_class_addendum.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>KEGG_category_mapping.tsv</div> <div>KEGG_metadata.tsv</div> <div> </div> <div>--- EPOC data ---</div> <div>EPOC_data.tar.gz</div> <div>EPOC_annotation_KEGG.tsv</div> <div>EPOC_data.tsv</div> <div>EPOC_data.pangenomes_s10.tsv</div> <div>EPOC_data.pangenomes_s25.tsv</div> <div>EPOC_data.pangenomes_s67.tsv</div> <div>EPOC_data.GTDB.tsv</div> <div> </div> <div># euk72_ep.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files </div> <div>constituting the initial eukaryotic mmseqs2 database with taxonomy annotation. </div> <div>Constructed from a pre-selected list of 72 eukaryotic proteomes downloaded from </div> <div>NCBI as well as a “clean” version of Eukprot, lacking highly prokaryotic-like </div> <div>contaminant sequences. </div> <div> </div> <div># prok2311_as.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files constituting the </div> <div>initial prokaryotic mmseqs2 database with taxonomy annotation. Constructed from </div> <div>47545 complete genomes retrieved from NCBI in November 2023. </div> <div> </div> <div># prok2311_as.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from prok2311_as non--singleton clusters, contains 26286 profiles.</div> <div> </div> <div># euk72_ep.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from euk72_ep non-singleton clusters, contains 1631704 profiles.</div> <div> </div> <div># NCBI_taxonomy_species_addendum.tsv</div> <div>Taxonomy mapping file with manually curated ‘class’ level annotation for poorly </div> <div>annotated species. </div> <div> </div> <div>taxid: NCBI taxid</div> <div>proposed_class_id: Manually assigned NCBI taxid</div> <div>proposed_class_label: NCBI class name</div> <div>org_name: NCBI organism name</div> <div> </div> <div># NCBI_taxonomy_class_addendum.tsv</div> <div>Class revision file mapping poorly populated class level entries to higher order </div> <div>manually curated labels. Also includes information for small classes with shallow </div> <div>taxonomy which are deleted from the EPOC analysis at the level of tree construction.</div> <div> </div> <div>taxid: NCBI taxid</div> <div>ncbi_class: NCBI taxid of rank corresponding to ‘class’ following manual </div> <div>amendment as per NCBI_taxonomy_species_addendum.tsv</div> <div>revised_class_id: Manually assigned NCBI taxid of rank corresponding to ‘class’</div> <div>revised_class_label: Proposed cleartext name of manually revised revised_class_id </div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Final taxonomy at NCBI rank ‘class’ following revisions for all sequences in Euk72Ep or </div> <div>Prok2311As. These taxonomic labels are used for EPOC tree annotation. </div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of manually revised NCBI rank ‘class’ identifier for annotation</div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Final taxonomy at GTDB rank ‘phylum’ transferred using marker genes from GTDB release 220</div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of assigne GTDB phylum</div> <div> </div> <div># Prok2311As_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation </div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># Euk72Ep_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation</div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># EPOC_data.tar.gz</div> <div>Gunzip-ed directory containing 16035 EPOC folders. Each folder is named corresponding </div> <div>to the eukaryotic cluster representative which generated its profile as an ID </div> <div>Matches the tree_name field in EPOC_data_prok2311As.tsv</div> <div>contains the following files:</div> <div> </div> <div><EPOC_ID>.merged.fasta: sequences for all members of the EPOC</div> <div><EPOC_ID>.merged.fasta.leaf_mapping: tsv separated file containing taxonomy and tree reduction data</div> <div><EPOC_ID>.merged.fasta.muscle: main cropped MSA for tree generation </div> <div><EPOC_ID>.merged.fasta.muscle.iqtree: IQtree2 output from tree generation</div> <div><EPOC_ID>.merged.fasta.muscle.treefile.annot: annotated newick tree file with final tree</div> <div><EPOC_ID>.merged.tree_data.tsv: final parsed tree data with columns matching EPOC_data_prok2311As.tsv</div> <div> </div> <div>EPOCs with more than one possible eukaryotic sister phyla also contains </div> <div>a folder "constraint_analysis" with constraint tree information used for </div> <div>ELW value calculation. </div> <div> </div> <div># EPOC_data.tsv</div> <div>Main resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) </div> <div>based on pangenomes defined as including 10% of species per class. This is the main</div> <div>data to be used for genereting the core dataset and for data visualistation</div> <div>Contains information regarding tree breakdown, LCA membership and phylogenetic </div> <div>distances between all detected LCAs. Equivalent to the stacked dataframes from all </div> <div>EPOC directories in EPOC_data </div> <div> </div> <div>tree_name: unique index for each EPOC </div> <div>euk_clade_rep: unique index for each annotated eukaryotic clade within each tree_name</div> <div>euk_clade_size: number of original sequences represented by euk_clade_rep</div> <div>euk_clade_weight: metric for taxonomic purity for each euk_clade_rep</div> <div>euk_leaf_clade: boolean indicating whether euk_clade_rep contains a single leaf</div> <div>euk_LCA: lowest taxa spanning all members in euk_clade_rep</div> <div>euk_scope: list of all taxonomic classes in euk_clade_rep</div> <div>euk_scope_len: length of euk_scope list</div> <div>prok_clade_rep: unique index for each annotated prokaryotic clade for each euk_clade_rep</div> <div>prok_clade_size: number of original sequences represented by prok_clade_rep</div> <div>prok_clade_weight: metric for taxonomic purity for each prok_clade_rep</div> <div>prok_leaf_clade: boolean indicating whether prok_clade_rep contains a single leaf</div> <div>prok_taxa: lowest taxa spanning all members in prok_clade_rep</div> <div>dist: tree-distance from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>top_dist: graph-distance (node-distance) from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>raw_stem_length: tree-distance from lowest tree node containing the union of all members of prok_clade_rep and euk_clade_rep to the tree node containing all members of euk_clade_rep</div> <div>median_euk_leaf_dist: median value for all tree distances from the tree node containing all members of euk_clade_rep to the individual leaves</div> <div>stem_length: raw_stem_length/median_euk_leaf_dist</div> <div>logL: log likelihood of best constraint tree constructed</div> <div>deltaL: log likelihood difference between constraint tree for prok_clade_rep and best constraint tree constructed</div> <div>bp-RELL: validation metric from IQtree -trees, see iqtree.org</div> <div>bp-RELL_accept: as above</div> <div>p-KH: as above</div> <div>p-KH_accept: as above</div> <div>p-SH: as above</div> <div>p-SH_accept: as above</div> <div>c-ELW: as above</div> <div>c-ELW_accept: as above</div> <div>p-AU: as above</div> <div>p-AU_accept: as above</div> <div> </div> <div># EPOC_data.pangenomes_s10.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 10% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s25.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 25% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s67.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 67% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.GTDB.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>under revised taxonomy from GTDB based on data from Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.alpha_replicates.tsv</div> <div>Resulting data from 20 repetitions of Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>from a subset of Alphaproteobacterial-derived EPOCs. </div> <div>Identical file structure to EPOC_data.tsv with the addition of:</div> <div> </div> <div>rep: indicating technical replicate number, 0-19</div> <div> </div> <div># EPOC_annotation_KEGG.tsv</div> <div>Parsed HHblits output of HMM profiles generated from KEGG KOGs (KEGG Orthologous Groups) </div> <div>against eukaryotic profiles constituting each EPOC</div> <div> </div> <div>Query: query name equal to tree_name from EPOC_data</div> <div>Target: target name equal to kogid in KEGG_category_mapping and KEGG_metadata</div> <div>Prob: data from HHblits, see https://github.com/soedinglab/hh-suite/wiki</div> <div>E-value : as above</div> <div>P-value : as above</div> <div>Score: as above</div> <div>SS: as above</div> <div>Cols: as above</div> <div>Identities: as above</div> <div>Similarity: as above</div> <div>Sum_probs: as above</div> <div>Query-HMM-start: as above</div> <div>Query-HMM-end: as above</div> <div>Template-HMM-start: as above</div> <div>Template-HMM-end: as above</div> <div>Template_columns: as above</div> <div>Template_Neff : as above</div> <div>Pairwise_cov: calculated pairwise coverage from Query and Target start and end</div> <div>Description: category_name from KEGG_category_mapping</div> <div> </div> <div># KEGG_category_mapping.tsv</div> <div>Mapping of relevant KOG identifiers to their higher order categories as </div> <div>"Maps" "Modules" or "Reactions" as per KEGG see https://www.kegg.jp/kegg/pathway.html</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>category_id: KEGG map, module, or reaction number</div> <div>category_name: cleartext name for KOG identifier</div> <div> </div> <div># KEGG_metadata.tsv</div> <div>File mapping KOGs to BRITE classification and to additional databases of chemical properties.</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>name: cleartext name for KOG identifier</div> <div>brite_A: list of BRITE-A sets including KOG</div> <div>brite_B: list of BRITE-A sets including KOG</div> <div>brite_C: list of BRITE-A sets including KOG</div> <div>EC: list of Enzyme commission numbers associated with KOG, see https://enzyme.expasy.org/</div> <div>TC: list of transporter classification numbers associated with KOG, see https://www.tcdb.org/</div> <div>RN: list of KEGG reaction numbers associated with KOG</div> <div>CA: list of CAZY numbers associated with KOG, see http://www.cazy.org/</div> <div>GO: list of GO terms associated with KOG, see https://geneontology.org/</div> </div> <div> </div> </div>
STAR4BBS D1.3 Report impact and contribution SCS and Labels_Appendix II dataset
<p>This dataset contains the full coding sheet for the systematic mapping that formed STAR4BBS deliverable D1.3 (Appendix II). The systematic mapping exercise reviewed literature on the impact of and contribution to GHG emissions reductions of existing sustainability systems and certification schemes (SCS) and B2B labels used within the bioeconomy. A coding sheet in the context of a systematic map is a structured tool used to extract and record specific data from studies being reviewed, ensuring consistency and accuracy in data collection. It forms the basis of the analysis and is included for transparency.</p>
MCR LTER: Coral Reef: Asynchrony in coral community structure contributes to reef‑scale community stability, data for Srednick et al., Nature 2023
These data were generated in support of the manuscript: Srednick G, Davis K, and Edmunds P, Nature To evaluate whether spatial insurance effects are important on coral reefs, we explored variation over 2006–2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. The daily range in seawater temperature among habitats suggests it could be a factor contributing to the variation in coral community structure. Wave-forced seawater flow facilitated larval exchange among connected habitats, differing in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
Differential contributions of ventral striatum subregions in the motivational and hedonic components of the affective response to reward
Open the record for dataset details and reuse information.
Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection [Primary data]
<p>Primary data underlying journal article titled "<strong>Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection</strong>"</p>
A Lagrangian study of the contribution of the Canary coastal upwelling to the nitrogen budget of the open North Atlantic
<p>The attached datasets constitute the particle trajectory data produced in the experiment for Hailegeorgis et al..</p> <p>The "traj_upwell_1d_70m_1d-variables.nc" contains variables that describe different aspects of each upwelled particle (mostly regarding a particle's release or its initial or final conditions).</p> <p>The rest of the files with the format "traj_upwell_1d_70m_XXX-traj.nc" describe an attribute XXX (location or nutrient concentration) along the trajectory of upwelled particles tracked as part of the experiment.</p> <p>With ARIANE, particles are released and tracked in a ROMS simulation of the Canary coastal upwelling region. Out of the ~10M particles, the trajectories of the ~353K (~3.6%) that upwell are included. The variable "index_in_full_exp" in file "traj_upwell_1d_70m_1d-variables.nc" shows the index of each of these upwelling particles in the larger pool of released particles. For each upwelled particle, out of the 720-day trajectories starting from its release into the coast, the values from its upwelling step to its exit from the experiment are included, with the values outside this range being filled with a generic value (1.e20). An upwelled particle exits the experiment when it leaves the regional ROMS simulation altogether or when it leaves the coast and returns to the coast to re-upwell (more details in the paper).</p> <p>Be mindful of the different values of time. In "traj_upwell_1d_70m_1d-variables.nc", the variable "release_time" tells each particle's release time, in days since onset of the ROMS simulation, while variable "coast_exit_time" tells each particle's day of exiting coast, in days since its release. In each particle's trajectory (in traj_lon, traj_lat, etc), the first and last steps with valid values are the same as the days of its upwelling and its exit, respectively, since its release.</p> <p>The files contain the name and description of each variable. Along with the details in the publication, the descriptions here should be enough to fully interpret the information and replicate our analysis.</p>
Diffraction images used to solve the structures published in the article "Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase"
<p>Raw diffraction images used for generating the structures published in the article "Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase" (available <a href="https://doi.org/10.1021/jacs.6b10075">here</a>). Full single-crystal datasets are published. The software used for the processing of each dataset is listed in their respective PDB entries.</p> <p> </p> <p>If you find this useful, please contact me at <a href="mailto:lukasz.sobala@hirszfeld.pl">lukasz.sobala@hirszfeld.pl</a>, I am just interested in how these data are used!</p>
Data of Survey on National Contributions to EOSC 2022
<p>This is the data set of the annual survey on National Contributions to EOSC 2022 for the EOSC Steering Board</p><p>The annual survey on National Contributions to EOSC was developed by the EOSC Future project and EOSC Steering Board to monitor policies, practices, and impacts related to EOSC and Open Science at national and institutional levels in Europe</p><p>The annual survey for 2022 was published in the EOSC Observatory on 19 January 2023 and ran until 09 June 2023 whereby 32 member states and associated countries in Europe responded to the survey</p><p>The data of the annual survey for 2022 is now available and exploitable in the online dashboard of the EOSC Observatory developed by Technopolis Group and OpenAIRE: [<a href="https://eoscobservatory.eosc-portal.eu">https://eoscobservatory.eosc-portal.eu</a>]</p><p>Disclaimer: The annual survey on National Contributions to EOSC is in an initial stage of implementation and will be improved in future iterations whereby the data should for now be taken as a best-effort attempt by participating countries</p>
Dataset for "Fertilizer value of dairy processing waste materials and contributions of soil microorganisms towards phosphorus uptake in grasses."
<p>This file includes the dataset used for the analysis of the fertilizer value from dairy processing waste materials and the contribution of soil microorganisms towards P uptake. More information in the linked future publication</p>
Data of Survey on National Contributions to EOSC and Open Science 2023
<p>This is the data set of the annual survey on National Contributions to EOSC and Open Science 2023 for the EOSC Steering Board</p> <p>The annual survey on National Contributions to EOSC and Open Science was developed by the EOSC Future project and EOSC Steering Board to monitor policies, practices, and impacts related to EOSC and Open Science at national and institutional levels in Europe</p> <p>The annual survey for 2023 was published in the EOSC Open Science Observatory on 17 January 2024 and ran until 01 July 2024 whereby 32 European member states, associated countries, and other countries responded to the survey</p> <p>The data of the annual survey for 2023 is available and exploitable in the online dashboard of the EOSC Open Science Observatory developed by Technopolis Group and OpenAIRE in the EOSC Future project and continued in the EOSC Track project: [<a href="https://eoscobservatory.eosc-portal.eu">https://eoscobservatory.eosc-portal.eu</a>]</p> <p>Disclaimer 1: The annual survey on National Contributions to EOSC and Open Science is in an initial stage of implementation and will be improved in future iterations whereby the data should for now be taken as a best-effort attempt by participating countries</p> <p>Disclaimer 2: V1 of the data set included an error in the data set and has thus been restricted and replaced by an updated V2 of the data set</p>
Reconstruction of Mediterranean sea-level changes and contributions for 1960-2018
<p><strong>Data supporting the paper:</strong></p> <p><strong>Calafat, F. M., Frederikse, T., and Horsburgh, K. (2022). The Sources of Sea-Level Changes in the Mediterranean Sea since 1960, Journal of Geophysical Research Oceans, under review.</strong></p> <p>Please cite the paper above when using this data set.</p> <p>This new version of the data set has been published to support the paper above and includes more data than the previous version as well as several improvements and refinements. Version 2.3 has been created to include regional estimates of rates due to the inverse barometer effect.</p> <p><em>Data description:</em></p> <ul> <li><strong>Bayesian_estimates_Mediterranean_sea_level.nc:</strong> this file contains gridded estimates of relative sea-level changes and their instantaneous rates for 1960-2018 in the Mediterranean Sea, separated into the individual contributions of: <ol> <li>Sterodynamic changes (i.e., ocean dynamics and thermal expansion).</li> <li>Contemporary GRD (i.e., changes in Earth gravity, Earth rotation, and solid-earth deformation due to land-mass changes).</li> <li>GIA (i.e., glacial isostatic adjustment).</li> <li>Short-term variability (interannual to decadal). </li> <li>Inverse barometer effect.</li> </ol> </li> <li><strong>data_input.mat:</strong> this file contains all of the data needed to run the Bayesian hierarchical model. This includes the observational data from tide gauges and satellite altimetry as well as the ensemble-mean and ensemble covariance matrices for the sea-level fingerprints associated with contemporary GRD effects and GIA.</li> </ul> <p>The Bayesian estimates have been obtained using a spatiotemporal Bayesian hierarchical model (see paper). This work has been carried out within the framework of the EuroSea project funded by European Union’s Horizon 2020 research and innovation programme under grant agreement No 862626.</p>
Local explanation SHAP approach applied to MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions
<p>The repository contains materials for analysing the results of the Local explanation named SHAP-CTREE (Redelmeier et al., 2020) approach applied to the MIROC5,RCP8.5-forced multi-model ensemble study of GrIS future sea-level contributions from Goelzer et al. (2020).</p> <p>The available files are:<br> - run_SupplMat.R: the main R script to perform the diagnostics and the different analyses (levels 1 - 3)<br> - utilsPLOT.R: functions for plotting<br> - Diagnostics.zip: the zip file with the png figures, named 'GrIS_CaseXXX_yYYY.png', that depict the diagnostic for case XXX for prediction time YYY<br> - SupplementaryMaterials.zip<br> - RData files for each prediction time YYY "Shapley_yYYY" with:<br> S: matrix N=55 cases x d+1: SHAP values for the d inputs (+ average sea level value at time YYY)<br> YHAT: ML-based predictions of the sea level for the 55 cases<br> YTRUE: true values for the 55 cases<br> mae: mean absolute error<br> - RData file containing the design of experiments "DOE_GrIS_MIROC5-RCP85.RData"<br> doe: matrix with values of the d=9 inputs</p> <p>These constitute the supplementary materials of Rohmer et al. (2022, The Cryosphere). All technical details are provided in this reference.</p>
Contribution of allelic imbalance to colorectal cancer
<p><strong>Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge, and unbiased CRISPR-Cas9 knockout and activation screens identified altogether 79 genes within AI peaks regulating cell growth. Genetic and functional data implicates loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.</strong></p>
Database of indicators to evaluate the contribution of urban nature-based solutions to climate change adaptation, biodiversity conservation, and social justice
<p>Supplementary data used within the publication: Goodwin, S., Olazabal, M., Castro, A. J., & Pascual, U. (2024). Measuring the contribution of nature-based solutions beyond climate adaptation in cities. <em>Global Environmental Change</em>, <em>89</em>, 102939. <a href="https://doi.org/10.1016/j.gloenvcha.2024.102939">https://doi.org/10.1016/j.gloenvcha.2024.102939</a>. Please also cite this paper when citing this database.</p> <div> <div>Within this database, you can find a list of indicators used to evaluate the contribution of a collection of 74 nature-based solutions (NbS) to climate change adaptation and related biodiversity and social justice challenges in cities. This list of indicators may be useful to those working in cities to provide inspiration for similar indicators they may wish to use to evaluate NbS in their city. This collection of NbS was drawn from previous work published in <em>Nature Sustainability</em> <a href="https://rdcu.be/c4tjk">here</a>.</div> <div> </div> </div> <p><em>The project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434). The fellowship code is “LCF/BQ/DI20/11780006”. Marta Olazabal’s research is funded by the European Union (ERC, IMAGINE adaptation, 101039429). This research is further supported by María de Maeztu Excellence Unit 2023-2027 (ref. CEX2021-001201-M), funded by the Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (AEI) (Spain) (MCIN/AEI/10.13039/501100011033/); and by the Basque Government through the BERC 2022-2025 program. </em></p> <p><em>Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.</em></p>
Data of Survey on National Contributions to EOSC 2021
<p>This is the data set from the EOSC Steering Board pilot survey on National Contributions to EOSC 2021</p> <p>The annual survey on National Contributions to EOSC monitors policies, practices, and impacts related to EOSC and Open Science at national and institutional levels in Europe</p> <p>The pilot survey for 2021 was published and the data was collected and is now available in the online dashboard of the EOSC Observatory: [<a href="https://eoscobservatory.eosc-portal.eu">https://eoscobservatory.eosc-portal.eu</a>]</p> <p>This data set has removed confidential information on financial estimations in questions 4-14 and also descriptions of use cases in question 19 which will be presented in an EOSC Catalogue of Best Practices</p>
Contribution of CO2 and CH4 emissions at ice-melt to annual emissions from 450 and 270 lakes, respectively, 1986 to 2014
The ice-covered period on lakes in the northern hemisphere can be extensive, lasting up to 7 months of the year. During this time, C cycling in lakes is altered affecting CO2 and CH4 dynamics below ice. Lake ice impedes atmospheric exchange, trapping CO2 and CH4 in the lake over winter. As lake ice-melts, CO2 and CH4 that has accumulated over winter is emitted from the into the atmosphere. To investigate the importance of CO2 and CH4 emissions during the ice-melt period, we conducted a literature search for studies that had CO2 and CH4 emission estimates for both the ice-melt and open water period. From these literature values, we could calculate the percent contribution of the ice-melt period to annual CO2 and CH4 emissions. We obtained data for 271 (n= 258) and 447 (n= 689) individual lakes, for CH4 and CO2, respectively.
Inference based decisions in a hidden state foraging task: differential contributions of prefrontal cortical areas
<p>Tabular dataset of behavioral data in the hidden state foraging task. The data is stored as a unique table, with one row per "attempt", i.e. a poke for mice and a tap for humans.</p> <p>The table includes four distinct experiments, encoded in the Experiment column. Experiment "Learning" refers to Fig. 2, experiment "VaryingParameters" refers to Fig. 2h and Fig.3. Experiment "LearningAndVaryingParameters" refers to Fig. 4. Experiment "OptogeneticInactivation" refers to Fig. 5.</p> <p>The column "TestingSession" defines whether those sessions were used for the analysis. It is used to exclude adaptation sessions to a new protocol for rodents in the "VaryingParameters" and "OptogeneticInactivation" experiments.</p> <p>In the human case, after an incorrect transition the subject receives an error cue and does not tap. This is considered a "trial" (and also a "streak") but not an attempt. This causes the StreakNumber and PokeNumber columns to increase by 2 after an error cue.</p>
Estimate of the atmospherically-forced contribution to sea surface height variability based on altimetric observations
<p>This repository contains the estimate of the atmospherically-forced contribution to sea level variability described in <a href="http://doi.org/10.1016/j.pocean.2020.102314">Close et al, 2020</a>, and derived from the Ssalto/Duacs altimeter products produced and distributed by the Copernicus Marine and Environment Monitoring Service (CMEMS) (<a href="http://www.marine.copernicus.eu">http://www.marine.copernicus.eu</a>).</p> <p>The files contain successive 5-day averages of sea level anomaly, with the same global coverage and 0.25° grid as the Ssalto/Duacs altimeter products. The estimate is created using a spatial bandpass filter, with cutoff scales of ~1.5° and 10.5°. Zeros in the mask file indicate regions in which it has not been possible to evaluate the quality of the estimate.</p> <p>The cutoff scales applied to the altimetry data were determined through analysis of output from the OceaniC Chaos – ImPacts, strUcture, predicTability (Penduff et al, 2014) experiment, comprising a 50-member ensemble of ocean-sea ice model hindcasts with 0.25° horizontal resolution (<a href="http://doi.org/10.5194/gmd-10-1091-2017">Bessières et al., 2017</a>). The spatiotemporal coherence between the model-based estimates of the atmospherically-forced (ensemble mean) and total simulated sea surface height signals was analysed, and found to exhibit distinct partitioning between the atmospherically-forced and intrinsic contributions in a spatial (but not temporal) sense, thus suggesting that meaningful estimation of the two components can be achieved based on simple spatial filtering. Verification of the method using the model data indicates good accuracy, with a global mean correlation of 0.9 between the estimate based on spatial filtering and the ensemble mean sea surface height. Full details of the methodology and verification may be found in <a href="http://doi.org/10.1016/j.pocean.2020.102314">Close et al, 2020</a>.</p> <p>----</p> <p><strong>References</strong>:</p> <p>Bessières, L., Leroux, S., Brankart, J.-M., Molines, J.-M., Moine, M.-P., Bouttier, P.-A., Penduff, T., Terray, L., Barnier, B., and Sérazin, G., 2017. Development of a probabilistic ocean modelling system based on NEMO 3.5: application at eddying resolution, Geosci. Model Dev., 10, 1091–1106, <a href="https://doi.org/10.5194/gmd-10-1091-2017">doi: 10.5194/gmd-10-1091-2017</a>.</p> <p>Close, S., Penduff, T., Speich, S. and Molines J.-M., 2020. A means of estimating the intrinsic and atmospherically-forced contributions to sea surface height variability applied to altimetric observations. Progr. Oceanogr. <a href="https://doi.org/10.1016/j.pocean.2020.102314">doi: 10.1016/j.pocean.2020.102314</a></p> <p>Penduff, T., Barnier, B. , Terray, L., Bessières, L., Sérazin, G., Grégorio, S., Brankart, J., Moine, M., Molines, J., Brasseur, P., 2014. Ensembles of eddying ocean simulations for climate, CLIVAR Exchanges, Special Issue on High Resolution Ocean Climate Modelling, 19.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.