obo-envo

[Obo-envo] Toilet metagenome

[Chris M. <cjm...@lb...>]

interesting article in PLOS ONE: Microbial Biogeography of Public Restroom Surfaces
	http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028132

Jonathan Eisen's blog has a nice summary, with potential ENVO terms highlighted in yellow:
	http://phylogenomics.blogspot.com/2011/11/journal-club-today-on-bacteria-in.html

The authors find correlations in community composition between bathroom locations and human body sites. There was no correlation between the bathroom locations and external environments like soil, but this isn't ruled out.

More broadly and of relevance to us, the SourceTracker analysis has similarities to standard GO enrichment analysis. SourceTracker takes an input metadata file that associates each sample with a source vs sink tag and an environment type - this is just a free text field like "gut". There's no hierarchy and distinctions that may be useful for certain analyses are collapsed (e.g. mouth+tongue to "osal"). It's up to the person doing the analysis to collect this metadata. 

What if there were a shared repository for these metadata files, together with use of ENVO rather than free text? I think this would be of enormous benefit to people doing metagenomic analyses. It could also help discover unexpected links. And it would be great for us if every metagenomic analysis paper had a figure with ENVO terms in it. What would it take to get there?

Re: [Obo-envo] Toilet metagenome

[Hilmar L. <hl...@ne...>]

Do you know Ontogrator (https://github.com/Ontogrator and http://ontogrator.org)? It won the iEvoBio Challenge in 2011. Not sure this is what you were looking for, though.

-hilmar

Sent with a tap.

On Dec 3, 2011, at 3:09 PM, Chris Mungall <cjm...@lb...> wrote:

> interesting article in PLOS ONE: Microbial Biogeography of Public Restroom Surfaces
>    http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028132
> 
> Jonathan Eisen's blog has a nice summary, with potential ENVO terms highlighted in yellow:
>    http://phylogenomics.blogspot.com/2011/11/journal-club-today-on-bacteria-in.html
> 
> The authors find correlations in community composition between bathroom locations and human body sites. There was no correlation between the bathroom locations and external environments like soil, but this isn't ruled out.
> 
> More broadly and of relevance to us, the SourceTracker analysis has similarities to standard GO enrichment analysis. SourceTracker takes an input metadata file that associates each sample with a source vs sink tag and an environment type - this is just a free text field like "gut". There's no hierarchy and distinctions that may be useful for certain analyses are collapsed (e.g. mouth+tongue to "osal"). It's up to the person doing the analysis to collect this metadata. 
> 
> What if there were a shared repository for these metadata files, together with use of ENVO rather than free text? I think this would be of enormous benefit to people doing metagenomic analyses. It could also help discover unexpected links. And it would be great for us if every metagenomic analysis paper had a figure with ENVO terms in it. What would it take to get there?
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