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LipidLynxX

A data transfer hub to support integration of large scale lipidomics datasets

Description

LipidLynxX was developed to provide efficient and accurate data transfer between analytical lipidomics datasets and data integration tools. It consists of three main modules supporting the conversion of diverse lipid annotations deriving from experimental lipidomics to unified identifier of user choice (Converter), cross-matching and equalizing lipid identifications obtained at different levels of structural confirmation (Equalizer), and mapping of annotated lipids to identifiers in a collection of databases and knowledge bases such as LIPID MAPS, SwissLipids, KEGG, Rhea, UniprotKB etc. that can be connected to ontology, pathway and network analysis workflows (Linker). LipidLynxX has built-in support to read and generate abbreviation of lipids while keeping the information e.g. modifications types and positions to perform hierarchical comparison. Based on this, LipidLynxX can reduce the over reporting of lipid identifiers and obtain associated identifiers from multiple databases. LipidLynxX provides a high-thoughput solution to format large-scale lipidomics identifiers and assist data integration workflows.

Technical Information

License:
GPL
GUI:
Yes
CLI:
Yes
Desktop client:
No
Input formats:
REST service,
Excel,
CSV,
Text
Output formats:
Excel,
CSV,
HTML
Platforms:
MacOS,
Linux,
Windows
Programming languages:
JavaScript,
Python

Tasks

7.1) Lipid annotations and ID converters
Supported lipid classes:
5 out of 8 LIPID MAPS classes
Normenclature:
LIPID MAPS classification, Nomenclature, and Shorthand notation (PMID: 33037133)
Supported levels of structural annotations:
Structure defined levels,
Molecular species,
Species
Input annotations or ids:
Common name,
Shorthand notation (according to PMID: 33037133),
MZmine2,
MS-DIAL,
MetFrag,
LPPtiger,
LIQUID,
Lipostar,
LipidSearch,
LipidPro,
LipidMatch,
LipidHunter,
LipidFrag,
LipiDex,
LipidCreator,
LipidBlast,
LDA 2,
Greazy,
ALEX123 lipid calculator,
SwissLipids,
RefMet,
LipidHome,
LIPID MAPS COMP_DB,
LIPID MAPS LMSD,
HMDB
Output annotations or ids:
LipidLynxX,
BioPAN,
Shorthand notation (according to PMID: 33037133)
Link to the external databases:
Uniprot KB,
Rhea,
KEGG,
PubChem,
ChEBI,
LION/Web,
HMDB,
SwissLipids,
LIPID MAPS LMSD
Other features:
Linker: cross link lipid identifiers to the identifiers from a collection of databases and knowledge bases used by ontology, pathway and network analysis tools.,
Equalizer: cross-match and equalize lipid identifications obtained from various sources at different levels of structural confirmation.