MetabolomicsWorkbenchAPI.jl
The Metabolomics Workbench operates as an international repository for metabolomics data and metadata while delivering analysis tools and access to metabolite standards, protocols, and more. The Metabolomics Workbench was developed by the Metabolomics Common Fund's National Metabolomics Data Repository(NMDR) to support the development of next-generation technologies, increase the inventory and availability of high-quality reference standards, and facilitate data sharing and collaboration.
MetabolomicsWorkbenchAPI.jl is a Julia package to work with Metabolomics Workbench REST service. The official MW REST API documentation can be downloaded here. Several request examples of REST urls are presented in the Metabolomics WorkBench REST service web page that includes an interactive "REST url" creator. The current MetabolomicsWorkbenchAPI.jl version provides only access to the database but not to the analysis functions.
Check connection
To check if the website is responding properly:
julia> check_mw()
MetabolomicsWorkbench.org is alive.
200
Get Metabolites Properties
To get properties for a list of metabolites names.
julia> vNames = ["LPC(16:0p)", "PC(18:0p/18:1(9Z))", "CE(18:0)", "PC(O-32:1)", "TG(O-52:2)"];
julia> fetch_properties(vNames)
5×6 DataFrame
Row │ exactmass formula main_class refmet_name sub_class super_class
│ String? String? String String String String
─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 479.3376 C24H50NO6P Glycerophosphocholines LPC P-16:0 O-LPC Glycerophospholipids
2 │ missing missing Glycerophosphocholines PC P-18:0/18:1(9Z)* PC Glycerophospholipids
3 │ 652.6158 C45H80O2 Sterol esters CE 18:0 Chol. esters Sterol Lipids
4 │ 717.5672 C40H80NO7P Glycerophosphocholines PC O-32:1 O-PC Glycerophospholipids
5 │ missing missing Triradylglycerols TG O-52:2* O-TAG Glycerolipids
Get metabolites Data
To get metabolites data for a study.
julia> df = fetch_data("ST001710");
julia> df[1:5,1:3]
5×3 DataFrame
Row │ Metabolite 1022385746 1022385747
│ String String String
─────┼─────────────────────────────────────────────
1 │ CE(16:0) + CE(18:1) 0.1062 -1.9080
2 │ CE(18:0) 0.2580 0.2774
3 │ CE(18:2) 1.0654 0.1419
4 │ CE(20:4) 0.7983 -0.3442
5 │ Cer(d18:1/23:0) 1.2658 0.9246
Get metabolites
To get the list of metabolites for a study.
julia> df = fetch_metabolites("ST000001");
julia> select(df, Not(["inchi_key", "other_id_type"]))[1:5,:]
5×7 DataFrame
Row │ Metabolite moverz_quant ri ri_type pubchem_id kegg_id other_id
│ String String String String String String String
─────┼───────────────────────────────────────────────────────────────────────────────────────
1 │ 1,2,4-benzenetriol 239 522741 Fiehn 10787 C02814 205673
2 │ 1-monostearin 399 959625 Fiehn 107036 D01947 202835
3 │ 2-hydroxyvaleric acid 131 310750 Fiehn 98009 218773
4 │ 3-phosphoglycerate 299 611619 Fiehn 724 C00597 217821
5 │ 5-hydroxynorvaline NIST 142 494838 Fiehn 95562 200384
Get Samples variables
To get samples and experimental variables for a study.
julia> df = fetch_samples("ST000001");
julia> first(df, 3)
3×3 DataFrame
Row │ Sample ID Arabidopsis Genotype Plant Wounding Treatment
│ String String String
─────┼─────────────────────────────────────────────────────────────
1 │ LabF_115873 Wassilewskija (Ws) Control - Non-Wounded
2 │ LabF_115878 Wassilewskija (Ws) Control - Non-Wounded
3 │ LabF_115883 Wassilewskija (Ws) Control - Non-Wounded