Metanetxmapper¶
- metanetxMapper(metInfo, varargin)[source]¶
This function maps metabolite IDs to each other using Beta MetaNetX database
- USAGE
[metData] = metanetxMapper (metInfo, varargin)
- INPUTS
name – string name of the metabolite (Common names, VMH names, CHEBI ids,
swiss lipids id, HMDB ids, and lipidmaps are supported)
- OPTIONAL INPUT
outputStyle – same as the input, choose an output option between
‘name’, ‘vmh’, and ‘chebi’ for more accurate respond
- OUTPUT
metData – A structure variable including fields of metabolite Identifiers: -metName: Common Name -metMetaNetXID: MetaNetX ID -metVMHID: VMH Symbol -metCheBIID: ChEBI ID -metHMDBID: HMDB ID -metKEGGID: KEGG ID -metBiGGID: BIGG ID -metSwissLipidsID: Swiss Lipids ID(only for lipids) -metInChIString: InChI String -metInChIkey: InChI key -metSmiles: SMILES ID
Example
- >> metData = metanetxMapper(‘SLM:000390086’)
metData =
struct with fields:
metName: “O-3-methylbutanoyl-(R)-carnitine” metMetaNetXID: “MNXM1101229” metVMHID: “ivcrn” metCheBIID: “70819” metHMDBID: “HMDB0000688” metKEGGID: “C20826” metBiGGID: “ivcrn” metSwissLipidsID: “SLM:000390086” metInChIString: “InChI=1S/C12H23NO4/c1-9(2)6-12(16)17-10(7-11(14)15)8-13(3,4)5/h9-10H,6-8H2,1-5H3/t10-/m1/s1” metInChIkey: “IGQBPDJNUXPEMT-SNVBAGLBSA-N” metSmiles: “[CH3:1][CH:9]([CH3:2])[CH2:6][C:12](=[O:16])[O:17][C@H:10]([CH2:7][C:11](=[O:14])[O-:15])[CH2:8][N+:13]([CH3:3])([CH3:4])[CH3:5]”
- >> metData = metanetxMapper(‘glu_L’, ‘VMH’)
metData =
struct with fields:
metName: “L-glutamate” metMetaNetXID: “MNXM741173” metVMHID: “glu_L” metCheBIID: “16015” metHMDBID: “HMDB0000148” metKEGGID: “C00025” metBiGGID: “glu__L” metSwissLipidsID: “” metInChIString: “InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1” metInChIkey: “WHUUTDBJXJRKMK-VKHMYHEASA-M” metSmiles: “[CH2:1]([CH2:2][C:4](=[O:7])[OH:8])[C@@H:3]([C:5](=[O:9])[OH:10])[NH2:6]”
Note
In the case of more than one matches for the metabolite, this functions returns the first match This function adds “+” sign at the begining of the metabolites name to find the exact match in MetaNetX website