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58 results for “mapping database”
Oil and Gas Infrastructure Mapping (OGIM) database
<p>The Oil and Gas Infrastructure Mapping (OGIM) database is a global, spatially explicit, and granular dataset of oil and gas infrastructure. It is developed by Environmental Defense Fund (EDF) (<a href="https://www.edf.org/">www.edf.org</a>) and MethaneSAT, LLC (<a href="https://www.methanesat.org/">www.methanesat.org</a>), a wholly owned subsidiary of EDF. The OGIM database helps fill a crucial geospatial data need, by supporting the quantification and source characterization of oil and gas methane emissions. The database is developed via acquisition, analysis, curation, integration, and quality-assurance (performed at EDF) of publicly available geospatial data sources. These oil and gas facility datasets are reported by governments, industry, academics, and other non-government entities.</p> <p>OGIM is a collection of data tables within a GeoPackage. Each data table within the GeoPackage includes locations and facility attributes of oil and gas infrastructure types that are important sources of methane emissions, including: oil and gas production wells, offshore production platforms, natural gas compressor stations, oil and natural gas processing facilities, liquefied natural gas facilities, crude oil refineries, and pipelines. OGIM v2.7 includes approximately 6.7 million features, including 4.5 million point locations of oil and gas wells and over 1.2 million kilometers of oil and gas pipelines.</p> <p>Please see the PDF document in the “Files” section of this page for more information about this version, including attribute column definitions, key changes since the previous version, and more. Full details on database development and related analytics can be found in the following Earth System Science Data (ESSD) journal paper. Please cite this paper when using any version of the database:</p> <p><span>Omara, M., Gautam, R., O'Brien, M., Himmelberger, A., Franco, A., Meisenhelder, K., Hauser, G., Lyon, D., Chulakadabba, A., Miller, C., Franklin, J., Wofsy, S., and Hamburg, S.: Developing a spatially explicit global oil and gas infrastructure database for characterizing methane emission sources at high resolution, Earth Syst. Sci. Data Discuss., </span><a href="https://doi.org/10.5194/essd-15-3761-2023"><span>https://doi.org/10.5194/essd-15-3761-2023</span></a><span>, 2023.</span></p> <p>Important note: While the results section of this manuscript is specific to v1 of the OGIM, the methods described therein are the same methods used to develop and update v2.7. Additionally, while we describe our data sources in detail in the manuscript above, and include maps of all acquired datasets, this open-access version of the OGIM database does not include the locations of about 300 natural gas compressor stations in Russia. Future updates may include these locations when appropriate permissions to make them publicly accessible are obtained. </p> <p>OGIM v2.7 is based on public-domain datasets reported in February 2025 or prior. Each record in OGIM indicates a date (SRC_DATE) when the original source of the record was published or last updated. Some records may contain out-of-date information, for example, if a facility’s status has changed since we last visited a data source. We anticipate updating the OGIM database on a regular cadence and are continually including new public domain datasets as they become available.</p> <p>---</p> <p>Point of Contact at Environmental Defense Fund and MethaneSAT, LLC: Madeleine O’Brien (maobrien@methanesat.org) and Mark Omara (momara@edf.org).</p>
LIPID MAPS® Structure Database (LMSD) formatted for MetFrag
<p>This repository contains the LIPID MAPS® Structure Database (<a href="https://www.lipidmaps.org/databases/lmsd/overview">LMSD</a>) formatted for use in <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a> (and other workflows).</p> <p><em>LIPID MAPS® Lipidomics Gateway is a free, comprehensive website for researchers interested in lipid biology. Use <a href="https://www.lipidmaps.org"> https://www.lipidmaps.org</a> to stay abreast of developments each month from across the field, and explore the rich information collections, tools and resources from the LIPID Metabolites And Pathways Strategy (LIPID MAPS®) Consortium. </em><br> </p> <p>The workflow used to create this file (by B. Talavera Andújar) can be found here: <a href="https://gitlab.lcsb.uni.lu/eci/simple-utilities/sdf2csv">https://gitlab.lcsb.uni.lu/eci/simple-utilities/sdf2csv</a></p> <p><strong>Reference:</strong> LMSD: LIPID MAPS® structure database, Sud M., Fahy E., Cotter D., Brown A., Dennis E., Glass C., Murphy R., Raetz C., Russell D., and Subramaniam S., Nucleic Acids Research, 2006, DOI: <a href="https://doi.org/10.1093/nar/gkl838"> 10.1093/nar/gkl838 </a></p>
DigiMedFor Forest Management Map Database
<p>Geodatabase of Forest Management Map created in DigiMedFor project.</p>
SeMRA Gene Mappings Database
<p>Analyze the landscape of gene nomenclature resources, species-agnostic. See instructions for reproduction and usage in the attached README.md.</p>
SeMRA Protein Complex Mappings Database
<p>Analyze the landscape of protein complex nomenclature resources, species-agnostic. See instructions for reproduction and usage in the attached README.md.</p>
SeMRA Anatomy Mappings Database
<p>Supports the analysis of the landscape of anatomy nomenclature resources. See instructions for reproduction and usage in the attached README.md.</p>
SeMRA Cell and Cell Line Mappings Database
<p>Originally a reproduction of the EFO/Cellosaurus/DepMap/CCLE scenario posed in the Biomappings paper, this configuration imports several different cell and cell line resources and identifies mappings between them. See instructions for reproduction and usage in the attached README.md.</p>
SeMRA Disease Mappings Database
<p>Supports the analysis of the landscape of disease nomenclature resources. See instructions for reproduction and usage in the attached README.md.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Fungi 49)
<p>Ensembl Fungi 49 derived ID mapping database for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Public database of geological-paleontological mapping in the surroundings of Vălioara
<p>The database contains the coordinates of the geological-paleontological mapping sites and measurements in the area of V<span>ă</span>lioara (Romania) from 2019 onwards. The Excel format file data tables contain in separate worksheets the localities, the measurements and the explanation of the mapping units. The coordinates are given in UTM34 coordinate system and also with latitude-longitude data (WGS84 datum).</p>
Database for GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.
<p>GWAS SVatalog is a novel visualization tool and database for structural variants (SV) found in a predominantly European population of 101 individuals with Cystic Fibrosis (CF). Aside from the CF-causing variants on chromosome 7 and the LD block in which they lie, the remainder of the genome is comparable to a the 1000 Genomes healthy European population. This data is a collection of SV calls and their linkage disequilibrium (LD) statistics with GWAS-significant SNPs reported in the GWAS Catalog.</p> <p> </p> <p>The goal of this project is to provide a resource to aid fine mapping of GWAS loci using SVs. GWAS loci are generally identified by SNPs which account for an incomplete proportion of genetic variation and phenotypic heritability. Their relevance to the phenotype might be limited, tagging other polymorphisms, such as SVs, that could be the cause of the association signal. To leverage this data to its full potential, visit the <a href="https://svatalog.research.sickkids.ca/" target="_blank" rel="noopener">GWAS SVatalog</a> web tool. Here, interactive visualizations can illustrate SVs identified in high LD with GWAS-significant SNPs, suggesting putative causal variation that could guide additional functional investigation.</p> <p> </p> <p>For more information on how to use GWAS SVatalog, visit the<a href="https://gwas-svatalog-docs.readthedocs.io/en/latest/index.html" target="_blank" rel="noopener noreferrer"> documentation</a>.</p> <p> </p> <p>This project was accomplished in collaboration with the <a href="https://lab.research.sickkids.ca/strug/" target="_blank" rel="noopener">Strug Lab</a> at <a href="https://www.sickkids.ca/en/" target="_blank" rel="noopener">The Hospital for Sick Children (SickKids)</a>, <a href="https://www.tcag.ca/" target="_blank" rel="noopener">The Center for Applied Genomics (TCAG)</a>, and <a href="https://www.utoronto.ca/" target="_blank" rel="noopener">University of Toronto</a>.</p>
SeMRA Raw Semantic Mappings Database
<p>An automatically assembled dataset of raw semantic mappings produced by <code>python -m semra.database</code>. This incorporates mappings from the following places:</p> <ol> <li>Ontologies indexed in the Bioregistry (primary)</li> <li>Databases integrated in PyOBO (primary)</li> <li>Biomappings (secondary)</li> <li>Wikidata (primary/secondary)</li> <li>Custom resources integrated in SeMRA (primary)</li> </ol> <p>This is a database of raw mapping without further processing. For processed mapping datasets, we suggest smaller domain-specific processing rules (see <a href="https://github.com/biopragmatics/semra/tree/main/notebooks/landscape">https://github.com/biopragmatics/semra/tree/main/notebooks/landscape</a> for examples). It can be accessed directly via:</p> <ul> <li><code>mappings.sssom.tsv.gz</code> - loadable through any tools supporting SSSOM</li> <li><code>mappings.jsonl.gz</code> - loadable through SeMRA using <a href="https://semra.readthedocs.io/en/latest/api/semra.io.from_jsonl.html" target="_blank" rel="noopener"><code>semra.from_jsonl</code></a></li> </ul> <h2>How to Run the Web App</h2> <ol> <li>Download all artifacts from this Record</li> <li>Make sure that you have Docker running locally</li> <li>Run <code>sh run_on_docker.sh</code> from the command line</li> <li>Navigate to http://localhost:8773 to see the SeMRA dashboard or to http://localhost:7474 for direct access to the Neo4j graph database</li> </ol> <h2>Licensing</h2> <p>Mappings are licensed according to their primary resources. These are explicitly annotated in the SSSOM file on each row (when available) and on the mapping set level in the Neo4j graph database artifacts.</p>
Geographic range maps for Mammal Diversity Database v1.3 taxonomy
<p>Update of mammal maps based on the taxonomy of the Mammal diversity database. These maps are different from the original, have been downscaled and are distributed under the R package mdd (github.com/alrobles/mdd).</p>
GRASS GIS database for CASAS-PBDM (www.casasglobal.org) geospatial mapping and analysis
<p>GRASS GIS database for geospatial mapping and analysis of physiologically based demographic modeling (PBDM) implemented by the Center for the Analysis of Sustainable Agricultural Systems (CASAS, <a href="https://www.casasglobal.org/" target="_blank" rel="noopener">www.casasglobal.org</a>).</p> <p>The <code>casas_gis_grass8data.zip</code> archive includes data updated for use with GRASS GIS version 8.</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 103)
<p>Ensembl 103 derived ID mapping database for use with BridgeDb.</p> <p><br> This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 104)
<p>Ensembl 104 derived ID mapping database for use with BridgeDb.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl 105)
<p>Ensembl 105 derived ID mapping databases for use with BridgeDb.</p> <p>The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Metazoa 49)
<p>Ensembl Metazoa 49 derived ID mapping databases for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).<br> </p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 49)
<p>Ensembl Plants 49 derived ID mapping database for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Derby database for mapping secondary to primary HMDB identifiers
<p>The data (hmdb_metabolites, released on 17/11/2021) used to create this ID mapping database was downloaded from HMDB (<em>Human Metabolome Database, </em>website URL: https://hmdb.ca/). </p> <p>This database was used for the <a href="https://github.com/tabbassidaloii/BridgeDbDemoBioSB2022">BridgeDb demo at BioSB 2022</a> conference.</p> <p>The scripts used to create this database based on HGNC: https://github.com/tabbassidaloii/create-bridgedb-secondary2primary</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</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.