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README.md

MetaboliteIDConverter

Version:0.4.0

Short description

Open source software to enrich metabolomic data sets with well known databases identifiers such as InChIKey or ChEBI identifiers

Description

This module allows to convert Metabolite Identifiers to and from database identifiers. This open source software uses the Chemical Translation Service (CTS)[1] to convert metabolite identifiers, any of the following database can be used as input database:

  • InChIKey
  • KEGG ID
  • ChEBI
  • Chemical Name

The output file will contain the following metabolite identifiers :

  • InChiKey
  • InChI
  • ChEBI
  • KEGG ID
  • PubChem CID
  • HMDB ID
  • ChemSpider
  • CAS

Functionality

  • Post-processing

Tool Authors

Container Contributors

Git Repository

Installation

For local installation of the container:

docker pull docker-registry.phenomenal-h2020.eu/phnmnl/metaboliteidconverter

Usage Instructions

For direct usage of the docker image:

docker run docker-registry.phenomenal-h2020.eu/phnmnl/metaboliteidconverter -inDB  <inputDB> -inFile <inputfile> -outFile <file_out> 

The <inputDB> parameter can be one of the following: InChIKey, KEGG, ChEBI, Chemical Name If your tsv file has columns headers on the first line, add the parameter -headers. This will allow the software to find the column where the identifiers to convert from are.

Future Developments

  • Enable users to choose the desired output databases from the list of databases available in the CTS WebService
  • Link the metabolites to our Metabolic Network database (available on www.metexplore.fr). And in particular the Human Global Metabolism Reconstruction, Recon2 [2].

Publications

  • Wohlgemuth G, Haldiya PK, Willighagen E, Kind T, Fiehn O. The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports. Bioinformatics. 2010;26(20):2647-2648. doi:10.1093/bioinformatics/btq476.
  • Thiele I, Swainston N, Fleming RMT, et al. A community-driven global reconstruction of human metabolism. Nature biotechnology. 2013;31(5):10.1038/nbt.2488. doi:10.1038/nbt.2488.