DRAFT: Add notebook which integrates metag, metap, metab data

[bmeluch]

This PR will add a new notebook to the repo that connects metag, metap, and metab data from the same samples together. It relies heavily on the KEGG orthology annotations provided by the NMDC workflows for each of these data types.

Links

nbviewer https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/91-create-notebook-integrating-metag-metap-metab-data-r/omics_types_integration/R/integration_notebook.ipynb

colab https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/91-create-notebook-integrating-metag-metap-metab-data-r/omics_types_integration/R/integration_notebook.ipynb

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[bmeluch]

@samobermiller I got the first part of the notebook rendered - does it look ok in reviewNB? and does it make sense so far? thank you :)

[samobermiller]

I'd suggest rewriting the title to something more action based. Maybe 'How can we relate different types of omics data in the NMDC database?'

see my later note about looking at crossover in kegg ids before using the kegg api, if you decide to follow that idea maybe add to the beginning of your note 'NOTE: After finding overlap in KO identifications across omics types, this notebook uses the KEGGREST R package to interface with the KEGG API and determine the biological relevance of these identifications. Use of............' My thinking is this will underline that there is a use for your notebook even if you dont use the licensed packages

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[samobermiller]

'(upset plot)'? typo?

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[samobermiller]

Since the KEGG api and package are restricted, would it make sense to add something beforehand looking at the crossover in kegg ids identified between the metagenomic and metaproteomic data? i know it won't show biological relevance until you use the licensed api to pull info, but it could show the use of your notebook even without the licensed api? 'here is what you can do to see overlap in multi-omic identifications and if you'd like more information on their biological relevance, you can follow the below tutorial using the kegg api but it will require a licence blah blah blah'

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[samobermiller]

maybe add clarifying sentence along the lines of:

'In this case, we want to look at the processed data results for our three omics types of interest. Specifically, we want the files containing KEGG Orthology and Enzyme Commission annotations. Note that these annotations are available in separate files for the metagenomics data (in 'Annotation Enzyme Commission' and 'Annotation KEGG Orthology') and in combined files for the metabolomic ('GC-Metabolomics Results') and proteomic ('Protein Report') data.

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[samobermiller]

I'm confused by 'we can look up the corresponding annotations in other KEGG databases'...what are 'other KEGG databases'?

Are you saying there is more than place to search for corresponding annotations using the KEGG ids found in this data? Based on the rest of the notebook I think what you're saying is that you're gonna look up annotation information for the KEGG ids in a sample's metabolomic, proteomic and genomic data, then compare overlap of the annotation information between the three omics types?

this confusion is probably due to my own lack of background knowledge, but i think it could use some clarification

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[samobermiller]

what's a circos plot and what are sector/arc?

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[samobermiller]

I would add a bit more context on how to interpret the chord diagram and maybe an example observation. also could you clarify what you mean by 'connections'? is it the overlap in annotations? to me it looks like the figure is showing nearly all protein annotations and about half the metabolomic annotations are also seen in the gene annotations. does overlap of all three arcs mean anything like it does in a venn diagram?

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[samobermiller]

great explanation

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[samobermiller]

SO COOL! Are the biosamples being grouped or clustered by anything?

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[samobermiller]

is this figure the same as the one above but with color and human readable names? if so, i would maybe combine the code and just keep this figure

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[samobermiller]

This would be cool, but if you're feeling short on time I think you are already generating some cool figures and we could keep this as a stretch goal for the symposium

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