Zebrafish Pathway Metabolite MetFrag Local CSV (Beta)
收藏资源简介：
This is a local CSV file of Zebrafish metabolites extracted from wikipathways and KEGG for MetFrag (https://msbi.ipb-halle.de/MetFrag/) and literature (currently DOI: 10.1371/journal.pone.0213661). All metabolites associated with wikipathways entries were extracted by Egon Willighagen using the following query: http://sparql.wikipathways.org/sparql?default-graph-uri=&query=PREFIX+gpml%3A++++%3Chttp%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml%23%3E%0D%0APREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0D%0APREFIX+dc%3A++++++%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0D%0APREFIX+rdf%3A+++++%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E+%0D%0A%0D%0Aselect+distinct+%3Fmetabolite+%28str%28%3FtitleLit%29+as+%3Ftitle%29+where+%7B%0D%0A++%3Fmetabolite+a+wp%3AMetabolite+%3B%0D%0A++++dcterms%3AisPartOf+%3Fpw+.%0D%0A++%3Fpw+dc%3Atitle+%3FtitleLit+%3B%0D%0A++++wp%3AorganismName+%22Danio+rerio%22%5E%5Exsd%3Astring+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on Open pathway data from the KEGG Zebrafish pathway (https://www.genome.jp/kegg-bin/show_pathway?dre01100) was extracted by Marek Ostaszewski. The resulting identifiers were mapped to chemical structures using the Chemical Translation Service (https://cts.fiehnlab.ucdavis.edu/batch), the CompTox Chemistry Dashboard batch search (https://comptox.epa.gov/dashboard/dsstoxdb/batch_search) and individual resources (KEGG, ChEBI, HMDB) where applicable. Conversions between structural formats were performed using Open Babel (http://openbabel.org/wiki/Main_Page). 13 Nov update: DOI: 10.1371/journal.pone.0213661 was added and mapped up using PubChem services (https://pubchem.ncbi.nlm.nih.gov/); PubChem CIDs and two additional columns "annothits" and "annothitcnt" from the PubChem download files were added. This file is a <strong>BETA </strong>version to start a collection of Zebrafish metabolites 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. TODO: to add PubChem "Zebrafish" query: https://pubchem.ncbi.nlm.nih.gov/#query=zebrafish&tab=pathway&selected_id_type=cid
