Data folder containing Datasets and Reference mappings (SpacePath input)

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The 'data/' folder: structure and usage The data folder centralizes all the data that is given as input to SpacePath. It contains two data types: 1. Datasets: Each one of the collected MALDI-MSI datasets (e.g. 'Gut-mouse'), with a unique tissue name: └── data/ ├── Gut-mouse/ ├── Gut-mouse.h5ad --> MSI intensities and metadata (AnnData) ├── Gut-mouse-HMDB.csv --> Annotations, original ├── Gut-mouse-LipidMaps.csv --> Annotations, original └── ... --> new data files are added here by SpacePath The tissues names are specified within the public and novel ("private") .csv files provided here. 2. Reference mappings: This second and last type of data is represented by a unique subfolder:metabolites-mappings/. SpacePath uses it as reference to perform the mappings of the compound identifiers found within the Datasets. └── data/ ├── Gut-mouse/ --> an example Dataset └── metabolites-mappings/ --> reference mappings, required by SpacePath This metabolites-mappings/ subfolder contains ready-to-use files to map compound identifiers in three different modalities: from no-KEGG identifiers (HMDB, LipidMaps) to KEGG identifiers: `CoreMetabolome-to-KEGG_05-07-24.tsv`, `LipidMaps-to-KEGG_10-18-24.tsv`, `HMDB-to-KEGG_05-07-24.tsv` mapping no-KEGG and KEGG identifiers to Wikipathways: `WIKIPATHWAYS_human_multi_id_redundant.mmt` mapping KEGG identifiers to KEGG pathways: `KEGG_hsa_pathways_compounds_R110.gmt` Download and unzip 'data.zip' from this Zenodo record. The final size of the unzipped 'data/' folder is 8.6 GB. Usage Place the unzipped `data/` inside your working directory, at the same level as your SpacePath local clone. The working directory can be your `$HOME` or the location your preference in your system. Also, if not yet done, create a `figures/` folder, where the output will be stored: cd $HOME; mkdir figures the final expected structure is: $HOME ├── data <-- all the downloaded data│ ├── ... ├── SpacePath <-- local clone│ ├── .... └── figures <-- your created empty folder └── ... <-- all output will be saved here Please visit the Wiki page of https://github.com/cbib/SpacePath for running the pipeline on this provided data. Supplementary information: the spots pre-processing was performed on all the datasets using SpacePath auxiliary scripts, so specific datasets resulted associated to .json files of discarded spots.

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