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231 results for “Natural Products”
Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching
<div>In order to obtain a high-quality LC-MS/MS reference database for spectral library matching, we selected 22 high-quality GNPS tandem mass spectrometry databases generated under the positive ion mode. Further preprocessing similar to Huber et al involving mass-to-charge (m/z) and intensity filtering yields the database found in the file LCMS_GNPS_reference_library.csv which contains 14,705 electrospray ionization (ESI) mass spectra, each of which corresponds to a unique compound. The NIST WebBook database was used to construct GC-MS database contained in the file GCMS_NIST_WebBook.csv. This database contains 23,721 electron ionization (EI) mass spectra, each of which corresponds to a unique non-hyphenated Chemical Abstract Service (CAS) Registry Number.</div> <div> </div> <div>Both LC-MS/MS and GC-MS databases are organized into three columns: one for the identifier, one for the m/z values, and one for the intensity values. For example, if spectrum A has 20 ion fragments, then there will be 20 rows corresponding to spectrum A in the corresponding database with the identifier A repeated 20 times with the corresponding m/z and intensity values.</div>
Data for: Techno-economic and environmental assessment of converting mixed prairie to renewable natural gas with co-product hydroxycinnamic acid, Iowa, USA, 2022-2023.
This dataset compiles model outputs, parameter sets, and documentation supporting a techno‑economic analysis (TEA) and life‑cycle assessment (LCA) of co‑digesting beef cattle manure with pretreated mixed prairie biomass to produce renewable natural gas (RNG), with hydroxycinnamic acids (HCA) and digestate‑derived biochar co‑products. It accompanies the study by Katherine Wild, Elmin Rahic, Lisa A Schulte Moore, and Mark Mba Wright "Techno-economic and environmental assessment of converting mixed prairie to renewable natural gas with co-product hydroxycinnamic acid," in Biofuels, Bioproducts, & Biorefining, 2024 (https://doi.org/10.1002/bbb.2710). The integrated simulation and assessment framework quantifies process performance, economics, and greenhouse‑gas intensity across five scenarios representing combinations of alkaline‑ethanol pretreatment for HCA extraction, liquid recirculation fractions, and biochar addition. This data collection includes: stream‑level mass flow/composition tables for each scenario; RNG, biochar, and HCA annual production summaries; literature‑based methane/biogas yield benchmarks; equipment‑level capital costs; TEA assumptions; emission‑factor inventories and displacement credits; and full sensitivity/uncertainty matrices for MFSP and GWP.
Natural Products Atlas (NPAtlas) MetFrag Local CSV
<p>This is a local CSV file of the Natural Products Atlas (NPAtlas, <a href="https://www.npatlas.org/joomla/">https://www.npatlas.org/joomla/</a>) for MetFrag (<a href="https://msbi.ipb-halle.de/MetFrag/">https://msbi.ipb-halle.de/MetFrag/</a>).</p> <p>Data was extracted to CSV from the TSV download from the NPAtlas <a href="https://www.npatlas.org/download">website</a>, with column headers for compulsory fields adjusted to fit the MetFrag format. Several entries with charged formulas (one +3, 7 +2, 125 +, 6 negative) had the charges removed from the formula to produce results consistent with other MetFrag files (where neutral formula is required; no adjustment for +/-H was performed so these remained consistent with the mass entries with minimum manipulation). Several overflowing lines were removed (due to new metadata) and NPA023832 was removed as "Ho" is not recognised by MetFrag. </p> <p>This file is for users wanting to integrate the latest NPAtlas into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one.</p> <p>Please credit the data source in any use of this file as the licence is CC-BY - details at <a href="https://www.npatlas.org/">https://www.npatlas.org/</a></p>
S59 | NPINESCT | Natural Product Insecticides
<p>This is the collection associated with list S59 NPINSECT on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>A list of 83 naturally occurring insecticides curated and provided by Reza Aalizadeh (University of Athens).</p> <p>Update 19 Nov 2019: modified CAS numbers for methyl salicylate, replaced "Benzaldehyde" with IUPAC name and changed Evonine to "Euonymine" based on feedback via Twitter.</p> <p> </p>
COCONUT: the COlleCtion of Open NatUral producTs.
<p>COCONUT is a COlleCtion of Open NatUral producTs.</p> <p> </p> <p>The database is now available at <a href="https://coconut.naturalproducts.net/">coconut.naturalproducts.net</a>, where the latest updates will appear before being available here.</p> <p>To assemble COCONUT, data from 55 open access collections and databases of natural products was retrieved and curated.</p> <p>This archive contains two files:</p> <ul> <li>The MongoDB dump, the most complete version of the dataset, with extensive molecular annotations</li> <li>The COCONUT4MetFrag file, used for <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a>. The last version of COCONUT4MetFrag is in the file "COCONUT4MetFrag_april.csv"</li> <li>The COCONUT.sdf file containing all unique NP molecules with selected metadata</li> </ul> <p>To restore the dataset in MongoDB:</p> <pre><code class="language-bash">unzip COCONUT_2021_03.zip cd COCONUT_2021_03/COCONUT_2021_03/ mongorestore --db=COCONUT --noIndexRestore . </code></pre> <p>It is generally useful to avoid restoring indexes, as they can interfere with the local installation. Here are the commands to rebuild indexes:</p> <pre><code class="language-json">mongo use COCONUT db.sourceNaturalProduct.createIndex( {source:1}) db.sourceNaturalProduct.createIndex( {simpleInchi:"hashed"}) db.sourceNaturalProduct.createIndex( {simpleInchiKey:1}) db.sourceNaturalProduct.createIndex( {originalInchiKey:1}) db.sourceNaturalProduct.createIndex( {originalSmiles:"hashed"}) db.sourceNaturalProduct.createIndex( {absoluteSmiles:"hashed"}) db.sourceNaturalProduct.createIndex( {idInSource:1}) db.uniqueNaturalProduct.createIndex( {inchi:"hashed"}) db.uniqueNaturalProduct.createIndex( {inchikey:1}) db.uniqueNaturalProduct.createIndex( {clean_smiles: "hashed"}) db.uniqueNaturalProduct.createIndex( {molecular_formula:1}) db.uniqueNaturalProduct.createIndex( {name:1}) db.uniqueNaturalProduct.createIndex( {coconut_id:1}) db.uniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"}) db.uniqueNaturalProduct.createIndex( {fragments:"hashed"}) db.fragment.createIndex({signature:1}) db.fragment.createIndex({signature:1, withsugar:-1}) db.sourceNaturalProduct.createIndex( {source:1}) db.sourceNaturalProduct.createIndex( {simpleInchi:"hashed"}) db.sourceNaturalProduct.createIndex( {simpleInchiKey:1}) db.sourceNaturalProduct.createIndex( {originalInchiKey:1}) db.sourceNaturalProduct.createIndex( {originalSmiles:"hashed"}) db.sourceNaturalProduct.createIndex( {absoluteSmiles:"hashed"}) db.sourceNaturalProduct.createIndex( {idInSource:1}) db.uniqueNaturalProduct.createIndex( {inchi:"hashed"}) db.uniqueNaturalProduct.createIndex( {inchikey:1}) db.uniqueNaturalProduct.createIndex( {clean_smiles: "hashed"}) db.uniqueNaturalProduct.createIndex( {molecular_formula:1}) db.uniqueNaturalProduct.createIndex( {name:1}) db.uniqueNaturalProduct.createIndex( {coconut_id:1}) db.uniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"}) db.uniqueNaturalProduct.createIndex( {fragments:"hashed"}) db.fragment.createIndex({signature:1}) db.fragment.createIndex({signature:1, withsugar:-1}) </code></pre> <p><br> <strong>This version of COCONUT is beta and will be curated further, but can already be used as it is.</strong></p>
Natural Products of ChemBioSys
<p>Documented collection of natural product structures that have been discovered, described or mentioned in a review by members of the CRC ChemBioSys (chembiosys.de)</p>
Predicted 13C NMR Chemical Shifts of Natural Products
<p>The Natural Product structures are those from the <a href="https://zenodo.org/record/5336220">COCONUTv5 database</a> .</p> <p>Predictions were obtained by means of the "Check Chemical Shifts" method from <a href="https://www.acdlabs.com/">ACD/Labs</a> C+H NMR Predictors and DB software, version 2020.1.0.</p> <p>The acd_coconut.zip archive contains a single file, acd_coconut.sdf, a collection of 2D structures from COCONUT supplemented by <sup>13</sup>C NMR chemical shifts values from ACD/Labs CNMR Predictor in verification mode.</p> <p>The file mol1.sdf describes the first compound in acd_coconut.sdf and indicates how chemical shift values are encoded.</p> <p>SDF tags related to NMR:</p> <ul> <li><CNMR_SHIFTS> for ACD/Labs DB software</li> <li><Predicted 13C shifts>, <Quaternaries>, <Tertiaries>, <Secondaries>, <Primaries> for <a href="https://sourceforge.net/projects/mixonat/">MixONat</a></li> <li><NMREDATA_ASSIGNMENT>, <NMREDATA_ORIGIN> in the style of <a href="https://nmredata.org/">NMReDATA</a></li> </ul> <p>The calculation workflow is based on tools developped <a href="https://github.com/nuzillard/KnapsackSearch/">here</a>.</p> <p>No attempt was made to change unlikely tautomers (like aliphatic iminols standing for aliphatic amides). Unlikely structures are likely associated to unlikely predicted chemical shift value sets.</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 2
<p>1996-1999, entomofauna inventory in cities and countrysides on 20 different habitats in The Netherlands using pitfalls and sweeping nets Jagers op Akkerhuis G, Dimmers W (2016). Alterra (NL) - Comparison entomofauna in cities en countrysides. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/guxqfv">https://doi.org/10.15468/guxqfv</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 3
<p>1996-1999, entomofauna inventory in cities and countrysides on 20 different habitats in The Netherlands using pitfalls and sweeping nets Jagers op Akkerhuis G, Dimmers W (2016). Alterra (NL) - Comparison entomofauna in cities en countrysides. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/guxqfv">https://doi.org/10.15468/guxqfv</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment
<p>1996 till 2000, entomofauna inventory on clay digged off riversides and on reference site in The Netherlands using pyramidtraps Faber J, Dimmers W (2016). Alterra (NL) - Entomofauna inventory in riverside grasslands. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/hlhr1r">https://doi.org/10.15468/hlhr1r</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 7
<p>Spring 2010 and Summer 2011, microarthropod fauna inventory for foodweb analysis in five European countries using soil cores and tullgren extraction</p> <p>Bloem J, Dimmers W (2016). Alterra (NL) - Microarthropods inventory in European countries. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/zkqto2">https://doi.org/10.15468/zkqto2</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 5
<p>2001 till 2002 and 2004, inventory of entomofauna in forestwalls banks, diches, road verges in The Netherlands using pitfalls and sweeping net</p> <p>Jagers op Akkerhuis G, Dimmers W (2016). Alterra (NL) - Comparison of entomofauna in four different habitats. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/mkoqqh">https://doi.org/10.15468/mkoqqh</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 6
<p>2007, 2011 and 2012, microarthropod fauna inventory in a nature restauration experiment (re-introduction) on a calcareous grassland and three reverence sites in the province of Limburg using pF-cores</p> <p>Smits N, Dimmers W (2016). Alterra (NL) - Microarthropods inventory in calcareous grasslands. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/28jocn">https://doi.org/10.15468/28jocn</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 4
<p>1993 till 2001, entomofauna inventory in cattle grazed versus non-grazed dune grassland using pitfalls</p> <p>van Wingerden W, Dimmers W (2016). Alterra (NL) - Entomofauna inventory in cattle grazed dune grassland. Version 2.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/zp5oif">https://doi.org/10.15468/zp5oif</a> accessed via GBIF.org</p>
Agriculture - General: Animal Production and Health, Natural Resources and Environment 8
<p>2000-2003, microarthropod fauna inventory of arable land and grassland on sandy soil using pF-cores. Points of interest are biodiversity, nutrients and disease suppression</p> <p>Faber J, Dimmers W (2016). Alterra (NL) - Microarthropods inventory in grassland and arable land. Version 1.1. Alterra, Wageningen UR. Occurrence dataset <a href="https://doi.org/10.15468/fwvi7m">https://doi.org/10.15468/fwvi7m</a> accessed via GBIF.org</p>
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
The LOTUS Initiative for Open Natural Products Research: waste to recycle
<p>Dataset not uploaded to Wikidata. </p> <p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p> <p>Shared for further curation.</p>
The LOTUS Initiative for Open Natural Products Research: metadata
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
<p>De novo assembly of ancient metagenomes to reconstruct biosynthetic machinery and access Pleistocene bacterial metabolites. This Zenodo archive belongs to the following publication (DOI: <a href="https://doi.org/10.1126/science.adf5300" target="_blank" rel="noopener">10.1126/science.adf5300</a>):</p> <p>Klapper, M., Hübner, A., Ibrahim A. et al. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. <em>Science</em> <strong>380</strong>, 619–624 (2023).</p> <p>This Zenodo archive contains the GitHub repository <a href="https://github.com/paleobiotechnology/EMN001_Paleofuran" target="_blank" rel="noopener">Paleobiotechnology/EMN001_Paleofuran</a> with all code and and data used for the publication mentioned above, as well as additional figures, huge NMR and GCMS data, which are not stored in the GitHub repository but have been deposited in this long-term Zenodo archive (see directory tree below).</p> <p>All datasets and scripts required for the project analysis can be found in this directory: <br>├── GCMS.tar.gz<br>├── github.tar.gz<br>├── licenses.tar.gz<br>├── MS_figures.tar.gz<br>└── NMR.tar.gz</p>
Copernicus High Resolution Vegetation Phenology and Productivity for Doñana Natural Space
<p>GeoTIFF rasters with the following phenometrics obtained from Sentinel 2 Data:.</p> <p> </p> <p>* Start of the season Day of the Year (SOSD)</p> <p>* Maximun of the Season Day of the Year (MAXD)</p> <p>* End of the Season Day of the Year (EOSD)</p> <p>* Start of the season Value (SOSV)</p> <p>* Maximun of the Season Value (MAXV)</p> <p>* End of the Season Value (EOSV)</p> <p> </p> <p>These rasters have been downloaded, mosaicked and croped with Doñana Natural Space DEIMS.ID through Pyvpp python package. </p>
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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)
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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.