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15 results for “MetFrag”
Zebrafish Pathway Metabolite MetFrag Local CSV
<p>This is a local CSV file of Zebrafish metabolites for MetFrag (https://msbi.ipb-halle.de/MetFrag/) extracted from PubChem, based partially on previous data extracted from Wikipathways, KEGG and literature (DOI: <a href="https://doi.org/10.1371/journal.pone.0213661">10.1371/journal.pone.0213661</a>), combined in previous versions of this record (DOI: <a href="https://doi.org/10.5281/zenodo.3541624">10.5281/zenodo.3541624</a>).</p> <p>This file was created as documented on the <a href="https://gitlab.com/uniluxembourg/lcsb/eci/pubchem-docs/-/tree/main/taxonomy/Danio_rerio">ECI GitLab</a>. </p> <p>This file is designed for identification using 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> </p>
PubChem OECD PFAS Larger PFAS Parts file for MetFrag
<p>This is a <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a> database file constructed from the "Molecule contains PFAS parts larger than CF<sub>2</sub>/CF<sub>3</sub>" subnode of the OECD PFAS Definition node in the <a href="https://pubchem.ncbi.nlm.nih.gov/classification/#hid=120"> PFAS and Fluorinated Organic Compounds in PubChem Tree</a> on the Classification Browser in PubChem.</p> <p>This file was constructed by downloading the node contents, selecting the columns of interest, changing the headers to MetFrag-compatible headers. Entries containing Xe, Pr, Po, Ru and W were removed; charges were also removed from formulas to avoid issues with MetFragCL.</p> <p>The construction of the tree is documented <a href="https://gitlab.com/uniluxembourg/lcsb/eci/pubchem-docs/-/raw/main/pfas-tree/PFAS_Tree.pdf?inline=false">here</a>.</p> <p>Note: PubChem authors have been removed from this version to comply with a presidential decree. This version was prepared exclusively by the remaining author. </p>
OntoChem PFAS CORE and Patent Files for MetFrag
<p>These are MetFraggable versions of the PFAS lists produced by OntoChem by performing literature mining of the CORE database (27K entries) and Google Patent collections (1.7M entries). The MetFrag versions have undergone filtering to remove entries that prevent MetFrag running (i.e. multiple-entry formulas and certain elements). Each file contains a tag whether the PFAS fits three definitions, A, B and C. The CORE database also contains the number of references in which the PFAS entry was found. Each file is available as CSV or in compressed form.</p> <ul> <li>PFAS Definition A: Each compound that contains a CF<sub>2</sub> group</li> <li>PFAS Definition B: Each compound that contains a (AH)(AH)(F)C-C(AH)F<sub>2</sub> group, where AH groups could be hydrogen or any other atom and the bond between both aliphatic carbon atoms is a single bond</li> <li>PFAS Definition C: Each compound that contains a (R<sup>1</sup>)(R<sup>2</sup>)(F)C-C(R<sup>3</sup>)F<sub>2</sub> group is considered a PFAS, where the R groups are any atom except hydrogen and the bond between both aliphatic carbon atoms is a single bond</li> </ul> <p><strong><em>Please note these files are very large (especially patents) and should not be uploaded to MetFragWeb directly - they will be available from the dropdown menu. These are provided for command line users, and any other workflows interested in these files! </em></strong>The patent file is 1.7 million entries and can cause some delay in the command line, compared with smaller database files.</p> <p>Full details are available in this preprint by Barnabas et al (2022) DOI: <a href="https://doi.org/10.26434/chemrxiv-2022-nmnnd-v2">10.26434/chemrxiv-2022-nmnnd-v2</a></p> <p>Update 20/04/2022: uploaded files with updated CID mappings post-PubChem deposition.</p>
MetFrag Local CSV: CompTox (7 March 2019 release) MetaData File
<p>These are the CSV files that can be used as a local database in MetFrag (https://msbi.ipb-halle.de/MetFrag/), for those who wish to integrate this into the command line version.</p> <p>Note that this file is TOO LARGE to be uploaded via the web interface, updated versions of these files are integrated in the web interface.</p> <p>This upload includes the SelectMetaData version of the CompTox MetFrag file from the 7 March 2019 release (DOI:<a href="https://doi.org/10.23645/epacomptox.7525199.v2">10.23645/epacomptox.7525199.v2</a>).</p>
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>
MetFrag Local CSV: CompTox (7 March 2019 release) Smoking MetaData File
<p>This is the CSV file that can be used as a local database in MetFrag (https://msbi.ipb-halle.de/MetFrag/), for those who wish to integrate this into the command line version.</p> <p>Note that this file is TOO LARGE to be uploaded via the web interface, this is already integrated in the web interface.</p> <p>This file is based off the "SelectMetaData" CompTox MetFrag file from the 7 March 2019 release, available from:</p> <p><a>ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/MetFrag_metadata_files</a></p> <p>The Smoking MetaData file contains the following fields, in addition to the regular (basic) CompTox data fields:</p> <p>- PubMedNeuro: the <a href="https://comptox.epa.gov/dashboard/chemical_lists/LITMINEDNEURO">LITMINEDNEURO</a> list with total PubMed reference counts in the column</p> <p>- <a href="https://comptox.epa.gov/dashboard/chemical_lists/CIGARETTES">CIGARETTES</a>, <a href="https://comptox.epa.gov/dashboard/chemical_lists/INDOORCT16">INDOORCT16</a>, <a href="https://comptox.epa.gov/dashboard/chemical_lists/SRM2585DUST">SRM2585DUST</a>, <a href="https://comptox.epa.gov/dashboard/chemical_lists/SLTCHEMDB">SLTCHEMDB</a>, <a href="https://comptox.epa.gov/dashboard/chemical_lists/THSMOKE">THSMOKE</a> as suspect lists.</p> <p>First release (July 2019, not archived) contained a smaller subset of the SRM2585DUST list.</p>
WormJam Metabolites Local CSV for MetFrag
<p>This is a local CSV file of WormJam (https://www.tandfonline.com/doi/full/10.1080/21624054.2017.1373939) for MetFrag (https://msbi.ipb-halle.de/MetFrag/).</p> <p>The text file provided by Michael (also part of this dataset) was modified into CSV by adding identifiers and adjusting headers for MetFrag import. </p> <p>This CSV file is for users wanting to integrate WormJam 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>Update 10 Sept 2019: curated truncated InChIKey, InChI entries, added missing SMILES, added DTXSIDs by InChIKey match.</p>
YMDB2.0 MetFrag Local CSV
<p>This is a local CSV file of YMDB 2.0 (http://www.ymdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/).</p> <p>Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. One entry with no SMILES was filled in using the InChI in OpenBabel; entries with no monoisotopic mass or formula were filled in using functions in RChemMass (https://github.com/schymane/RChemMass/), finally one generic formula (row 746) was replaced with the formula from the InChI. </p> <p>This file is for users wanting to integrate the latest YMDB 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>
MetFrag Local CSV: CompTox (7 March 2019 release) Wastewater MetaData File
<p>This is the CSV file that can be used as a local database in MetFrag (<a href="https://msbi.ipb-halle.de/MetFrag/">https://msbi.ipb-halle.de/MetFrag/</a>), for those who wish to integrate this into the command line version.</p> <p>Note that this file is TOO LARGE to be uploaded via the web interface, this is already integrated in the web interface.</p> <p>This file is based off the "SelectMetaData" CompTox MetFrag file from the 7 March 2019 release, available from:</p> <p>ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/MetFrag_metadata_files</p> <p>The Wastewater MetaData file contains the following fields, in addition to the regular (basic) CompTox data fields:</p> <p>Suspect Lists (1=presence, 0=absence):</p> <p>- ITNANTIBIOTIC, STOFFIDENT, REACH2017, ZINC15PHARMA and PFASMASTER</p> <p>Suspect Lists with scores from KEMI (see details on <a href="https://www.norman-network.com/nds/SLE/">NORMAN-SLE</a> and hyperlinks below):</p> <p>- <a href="https://zenodo.org/record/2628787">KEMIMARKET_EXPO</a>, <a href="https://zenodo.org/record/2628787">KEMIMARKET_HAZ</a>, <a href="https://zenodo.org/record/2653567">KEMIWW_WDUIndex</a>, <a href="https://zenodo.org/record/2653567">KEMIWW_StpSE</a>, <a href="https://zenodo.org/record/2653567">KEMIWW_SEHitsOverDL</a></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>
Exposome Boot Camp Lab 4: MetFrag in Practice
<p>This is the full set of materials used for the MetFrag in Practice Lab at the Exposome Boot Camp</p> <p>https://www.mailman.columbia.edu/research/precision-prevention/exposome-boot-camp-measuring-exposures-omic-scale</p> <p>Overview: see PDF. Examples: see word document. Additional files are required for specific examples for upload to MetFrag. Remaining information is in the word document, in hyperlinks, online at MetFrag and MassBank or in screenshots in the PDF.</p>
HMDB4.0 MetFrag Local CSV
<p>This is a local CSV file of HMDB4.0 (http://www.hmdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/).</p> <p>Data was extracted from the XML, metals and entries with no monoisotopic mass were removed, one naming error for http://www.hmdb.ca/metabolites/HMDB0037436 was fixed and the XML fields adjusted to headers for MetFrag import. </p> <p>This file is for users wanting to integrate the latest HMDB 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>The two versions are identical, the two names fit various formatting conventions used behind the scenes in MetFragWeb.</p>
Blood Exposome Database: MetFrag Local CSV
<p>This is a local CSV file of the Blood Exposome Database (<a href="http://bloodexposome.org/">http://bloodexposome.org/</a>) for MetFrag (<a href="https://msbi.ipb-halle.de/MetFrag/">https://msbi.ipb-halle.de/MetFrag/</a>).</p> <p>Data was trimmed to necessary columns from parent-mapped TSV provided by Dinesh Barupal. Approx. 15 entries containing elements not processed by MetFrag were removed. Entries with singly charged formulas had the charge 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 - see xlsx file for traceback). Subsequent versions could be adjusted for different behaviour if desired. </p> <p>This file is for users wanting to integrate the latest Blood Exposome Database 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: <a href="http://bloodexposome.org/">http://bloodexposome.org/</a></p>
[MetFrag] MoNA Export LC-MS-MS Spectra for MetFrag
<p>This is an updated version of the LC-MS/MS MoNA library for use in <a href="https://ipb-halle.github.io/MetFrag/">MetFrag</a>. </p> <p>Once you download this file, you can use it in <a href="https://github.com/ipb-halle/MetFragRelaunched/releases/latest">MetFrag Command Line</a> with the following command: </p> <pre><code>OfflineSpectralDatabaseFile = ~/MoNA-export-LC-MS-MS_Spectra-20241014-0.005.mb</code></pre> <p>Thanks to Bego for thoroughly testing this file and to Christoph for his tips throughout the years!</p>
ECMDB2.0 MetFrag Local CSV
<p>This is a local CSV file of ECMDB 2.0 (<a href="http://ecmdb.ca/">http://ecmdb.ca/</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 SDF, with column headers for compulsory fields adjusted to fit the MetFrag format.</p> <p>This file is for users wanting to integrate the latest ECMDB 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>The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about <em>Escherichia coli</em> (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases.</p>
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OpenNeuro
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