Is there any annotation package for MSEA?
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knishida ▴ 20
@knishida-8230
Last seen 4.2 years ago
United States

I am considering submitting https://github.com/afukushima/MSEApdata as an annotation package of bioconductor.

It seems that there is no data package (metabolite set for each function) for metabolite set enrichment analysis (MSEA) yet in bioconductor.

Could you give me some advice on data packaging for MSEA?

My data is basically same with gmt format for GSEA. 

https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

https://github.com/afukushima/MSEApdata/blob/master/data-raw/R-ATH_format_HMDB.gmt

The difference is that gene is replaced by metabolite.

metabolite data • 1.1k views
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shepherl 3.8k
@lshep
Last seen 13 hours ago
United States

By quick glance I do not see any of this data currently in Bioconductor and would be a good addition. We are encourage new data submission to utilize the Bioconductor Hubs. I'm not sure if your data would be a better fit for ExperimentHub or AnnotationHub. The following is taken from our Package Submission Page

Annotation packages are database-like packages that provide information linking identifiers (e.g., Entrez gene names or Affymetrix probe ids) to other information (e.g., chromosomal location, Gene Ontology category). It is also encouraged to utilize AnnotationHub for storage and access to large raw data files and their conversion to standard R formats. Instructions for adding data to AnnotationHub and designing a annotaiton package to use AnnotationHub can be found here: Creating AnnotationHub Packages.

Experiment data packages provide data sets that are used, often by software packages, to illustrate particular analyses. These packages contain curated data from an experiment, teaching course or publication and in most cases contain a single data set. It is also encouraged to utilize ExperimentHub for storage and access to larger data files. ExperimentHub is also particularly useful for hosting collections of related data sets. Instructions for adding data to ExperimentHub and designing an experiment data package to use ExperimentHub can be found here: Creating ExperimentHub Packages.

The idea behind the Hubs is to keep a package lightweight and not include the data directly. Not much would change from the currently constructed package repository except the data would be moved to a server and out of the package directly, the needed inst/extdata/metadata.csv file would need to be created, and the packages updated to download the data from the hubs.

You might consider looking at GSEABase::GeneSet() GSEABase::GeneSetCollection() for commone structures used for GSEA data.

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