LCSB Environmental Cheminformatics Group

There is a newer version of the record available.

Published November 14, 2019 | Version v2
Dataset Open

Zebrafish Pathway Metabolite MetFrag Local CSV (Beta)

Creators

  • 1. LCSB, Uni Luxembourg
  • 2. Maastricht University

Description

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 BETA 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

Notes

Beta version - (semi-)automated extraction and mapping only, no experimental verification

Files

Zebrafish_13Nov2019_Beta.csv

Files (135.2 kB)

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md5:eb71a03ab1e7d354e9c8023729c9461c
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Additional details

Related works

Is derived from
https://www.genome.jp/kegg-bin/show_pathway?dre01100 (URL)
http://sparql.wikipathways.org (URL)
Journal article: 10.1371/journal.pone.0213661 (DOI)
Is supplement to
https://msbi.ipb-halle.de/MetFrag/ (URL)