ZhixuNi / epiLION

epiLipidome Identifier and Optimized Nomenclature

epiLipidome Identifier and Optimized Nomenclature

The epiLION project is aimed to provide a unified identifier for major lipids, especially oxidized lipids in the epilipidome.

• Main Features

  • Optimized for manual interpretation and computer processing
  • Unified modification controlled vocabularies
  • Unified position specific annotations
  • Special optimization for prostane containing lipids
  • Suitable for head group modified phospholipids
  • Hierarchical abbreviation system
  • Capable to parse fuzzy site unspecific annotations

• epiLION abbreviation converter

  • Convert different abbreviations to uniformed epiLION abbreviations

• epiLION structure and MS property generator

  • Abbreviation to SMILES/ MOL / SDF conversion using python

• Currently supported modifications

  • DB: C=C bond
  • OH: hydroxy
  • Hp: hydroperoxy
  • NH2: amino
  • Me: methyl
  • Ke: keto/oxo
  • Ep: epoxy
  • SH: thio
  • My: methylene
  • Br: bromo
  • Cl: chloro
  • F: fluoro
  • CN: cyano

• Example of epiLION abbreviations

  • Fatty acids

    • FA18:0
    • O-16:0
    • P-18:0
    • 20:4[4DB,2OH,1Ke]
    • 20:4[4DB{5Z,9E,11Z,14Z},1OH{8S}]
    • 20:4[4DB{5Z,9E,12E,15E},2OH{8S,11R},1Ke{14}]

  • Phospholipids

    • PC(O-16:0/18:1)
    • PC(P-16:0_18:1)
    • PC(16:0/20:4[4DB,2OH,1Ke])
    • PC(16:0/20:4[4DB{5,9,12,15},2OH{8,11},1Ke{14}])

Instructions

How to install epiLION from source code

• Download the source code as zip file for your system

  • Download epiLION source Code as .zip. Please notice the date and version of LipidHunter source code.

  • Professional users can use git to clone the whole repository, please make sure that you switched to the correct branch.

  • Only the released version is recommended for real data processing. Other development branches may lead to unknown issues and miss interpretation of the data.

• Rename the downloaded file to epiLION.zip

• Unzip epiLION.zip file to any folder.

• Install epiLION source code

  • epiLION is developed under python 3.6+.

  • The best way is to use virtual environment such as conda

  • Main dependencies are:

    • Data processing: pandas

    • SDF generation: rdkit

  • Test source code installation

    • epiLION is configured to use travis-ci with py.test to test on Windows, Linux, and macOS.

    • Current status of the master branch

    • you can also use py.test to test epiLION in your python environment

      • unit test for epiLION converter is provided in Test/test_convLION.py

      • unit test for epiLION generator is provided in Test/test_epiLION.py

• Run epiLION converter

  • Run python convLION.py -i Test/TestInput/test_crosscheck.xlsx -o Test/TestOutput/test_crosscheck_output.xlsx

  • convLION read list of different abbreviations in the test_crosscheck.xlsx and generate the converted epiLION abbreviations in the output file.

  • convLION can read an write both .xlsx and .csv file.

  • sample input

    

  • sample output

    

• Run epiLION generator

  • Run python epiLION.py -i Test/TestInput/test_names.txt -o Test/TestOutput/test_sdf.sdf

  • epiLION read list of epiLION abbreviations in the test_names.txt and generate the structure in a combined sdf file.

• SDF output

  • The sdf file is generated by using rdkit https://www.rdkit.org

  • The sdf output can be used by:

    • Progenesis SDF studio, free for academic use: http://www.nonlinear.com/progenesis/sdf-studio/

    • ChemAxon Instant Jchem, academic license available: https://chemaxon.com/products/instant-jchem

• Errors/bugs

  In case you experienced any problems with running LipidHunter

  please report an issue in the issue tracker or contact us.

License

• LipidHunter is Dual-licensed

  • For academic and non-commercial use: GPLv2 License:

    • The GNU General Public License version 2

  • For commercial use: please contact the develop team by email.

• Please cite our publication in an appropriate form.

  • Ni, Zhixu, Laura Goracci, Gabriele Cruciani, and Maria Fedorova. "Computational solutions in redox lipidomics–Current strategies and future perspectives." Free Radical Biology and Medicine (2019). - DOI: 10.1016/j.freeradbiomed.2019.04.027

Report issues

• Report any issues here: https://github.com/SysMedOs/epiLION/issues

Fundings

We acknowledge all projects that supports the development of LipidHunter:

• BMBF - Federal Ministry of Education and Research Germany:

  https://www.bmbf.de/en/

• e:Med Systems Medicine Network:

  http://www.sys-med.de/en/

• SysMedOS Project :

  https://home.uni-leipzig.de/fedorova/sysmedos/