The LipidLynxX project is aimed to provide a unified identifier for major lipids, especially oxidized lipids in the epilipidome.
Thanks to LIPID MAPS, you can now use LipidLynxX on LIPID MAPS® Lipidomics Gateway
http://lipidmaps.org/lipidlynxx/
D:\LipidLynxX
LipidLynxX.exe
to run!LipidLynxX Converter
LipidLynxX Equalizer
LipidLynxX Linker
The current LipidLynxX source code was tested using our collection of lipid abbreviations for major lipid classes from following databases and programs:
Databases (5):
HMDB
, LIPID MAPS LMSD & COMP_DB
, LipidHome
, RefMet
, SwissLipids
Programs (17):
ALEX123 lipid calculator
, Greazy
, LDA 2
, LipidBlast
, LipidCreator
, LipiDex
, LipidFrag
, LipidHunter
,
LipidMatch
, LipidPro
, LipidSearch
, Lipostar
, LIQUID
, LPPtiger
, MetFrag
, MS-DIAL
, MZmine2
Shorthand Notations
Common abbreviations (customizable):
defined alias
.
detailed settings can be found in lynx/configurations/defined_alias.json
If your database / program is not included in the list above, you can test if any of the configuration files located in lynx/configurations/rules/input
would fit to your database / program.
If conversion is not possible, please contact us so that we can help you to generate suitable configuration file.
A robust and accurate converter can only be achieved by community-wide collaborations, thus any issue reports from general users and developers are welcome and will improve LipidLynxX project.
Thus, if you meet any issues during using LipidLynxX, please report your issue here
An easy to use .exe version for Windows platform users is available for test purpose only.
LipidLynxX.exe
and double clickSince the code is still changing rapidly, the definitions of API and documentations in the source code may not be updated accordingly. We kindly ask if you have any plans to use LipidLynxX API contact us first, or follow this repository to get timely notifications when new changes are introduced.
New features of LipidLynxX is generally developed using repository https://github.com/ZhixuNi/LipidLynxX.
python LipidLynxX.py
to start GUI.python cli_lynx.py
to start GUI.lynx\config.ini
for more settings of ports and max clients/workersLipidLynxX/doc/sample_data/input
LipidLynxX/doc/sample_data/output
Please find our user guide in folder doc
.
mybinder.org
This demo is always updated automatically to the latest source code on the master branch. To preview the latest changes on the converter without dealing with source code.
And wait a bit ☕ Binder and Jupyter Notebook will prepare LipidLynxX demo for you.
You can paste a list of lipid abbreviations, select export style, and download the output table as .csv
or .xlsx
.
If you observed some IDs not converted in the Windows .exe version, try this demo to see if it got fixed.
You can run the notebook named converter_notebook.ipynb
in this repository as well.
GUI
API
Terminal Tools
python cli_lynx.py
Use as Python module
LipidLynxX levels
Lipid level:
B: Bulk
M: Molecular species
S: sn Specific
Modification levels:
0 : no modification
1 : mass shift
2 : element shift
3 : number and type of modification
4 : modification position information
5 : additional information (e.g. R-/S-)
Double bond levels:
.0 : no information of double bond position (.0 should always be skipped, e.g. B0.0 -> B0)
.1 : double bond position information given
.2 : cis- / trans- information of all C=C bond
LipidLynxX level matrix
Mod | DB | Bulk | Molecular species | sn Specific | |||||
---|---|---|---|---|---|---|---|---|---|
0 | B | M | S | ||||||
.1 | M0.1 | S0.1 | |||||||
.2 | M0.2 | S0.2 | |||||||
1. | B1 | M1 | S1 | ||||||
.1 | M1.1 | S1.1 | |||||||
.2 | M1.2 | S1.2 | |||||||
2. | B2 | M2 | S2 | ||||||
.1 | M2.1 | S2.1 | |||||||
.2 | M2.2 | S2.2 | |||||||
3. | B3 | M3 | S3 | ||||||
.1 | M3.1 | S3.1 | |||||||
.2 | M3.2 | S3.2 | |||||||
4. | M4 | S4 | |||||||
.1 | M4.1 | S4.1 | |||||||
.2 | M4.2 | S4.2 | |||||||
5. | M5 | S5 | |||||||
.1 | M5.1 | S5.1 | |||||||
.2 | M5.2 | S5.2 |
Currently supported modification controlled vocabularies
Some examples of LipidLynx abbreviations:
Fatty acids
FA18:0
O-16:0
P-18:0
20:4<2OH,oxo>
20:4{5Z,9E,11Z,14Z}<OH{8S}>
20:4{5Z,9E,12E,15E}<2OH{8S,11R},oxo{14}>
Phospholipids
PC(O-16:0/18:1)
PE(P-16:0_18:1)
PC(16:0/20:4<2OH,oxo>)
PE(16:0/20:4{5,9,12,15}<2OH{8,11},oxo{14}>)
LipidLynxX is configured to use travis-ci and GitHub Actions with py.test
to test
cross-platform compatibility on Linux, macOS and Windows.
Current status of the master branch
You can also use py.test to test LipidLynxX in your python environment, all test files can be found in ./test
folder.
In case you experienced any problems with running LipidLynxX, please report an issue in the issue tracker or contact us.
LipidLynxX is using GPL V3 License
Please cite our publication in an appropriate form.
LipidLynxX preprint on bioRxiv.org
Zhixu Ni, Maria Fedorova. "LipidLynxX: a data transfer hub to support integration of large scale lipidomics datasets"
LipidLynxX is powered by open-source projects, main dependencies are:
FastAPI
, starlette
, Typer
, and uvicorn
jsonschema
, pandas
, and regex
LipidLynxX is based on the previous project epiLION
We acknowledge all projects that supports the development of LipidLynxX:
BMBF - Federal Ministry of Education and Research Germany:
e:Med Systems Medicine Network:
SysMedOS Project :