Plotting The Paradigm Shift Of Research Focus From Genomics To Metagenomics

Question

[Monzoor]

Is there a nice plot or graphic that essentially captures the paradigm shift of life-sciences R&D focus from genomics to metagenomics?

I remember a few years ago, people used to show a plot of growing amounts of genomic data in public databases. Is there a similar plot/graphic to capture the proliferation of metagenomics in a short duration and also shows some extrapolation

[Gaffa]

Well, are you sure there has actually been such a paradigm shift? I'm not so sure. Metagenomics has grown dramatically, sure, but so has every sequencing-based field.

[Michael]

There have been too many paradigm shifts already, this term is simply overused and I wouldn't use it. Remember genome sequencing, microarrays, systems biology, next-generation sequencing, 3rd generation seq.,..., all great technologies for sure, and progressive, all called paradigm shifts.

[Michael]

Further, the mere amount of growing data volume is not an argument in itself.

Answer 1

[User 59]

When all else fails use Google trends

No, I don't think it's representative really, and I don't think there is a shift from genomics to metagenomics. Metagenomics is just an application of genomics after all...

[User 59]

I think the rise of personal genomics is the counter-argument to that. More than ever are we focused on the individual. Whilst I agree we are more into studying 'systems' than ever before, I think genomics in particular is getting more focused. I may be biased, I deal with NGS data quite a bit in the research context of the University I am at, and whilst I'm sure this differs from place to place, the sequencing of individuals - for diagnostics or discovery, is in the ascendancy.

[Monzoor]

I partially agree. But is is not true that We have sort of shifted focus from studying isolated individual organisms to studying them with respect to a community. Of course the culturability aspect is also now not an issue with the advent of metagenomics

Answer 2

[Neilfws]

You can retrieve data about genome/metagenome projects from several sources. A couple of suggestions:

Start with the NCBI Genomes resource. It has links to projects by organism, grouped into Eukaryota, Prokaryota, Viruses and Metagenomes. The Entrez Genome Projects database can also be searched programmatically using EUtils. It should be possible to retrieve projects by type with dates, that you can use for plotting.

GOLD (Genomes Online Database) has a statistics page. It includes a chart of genome projects over time by category (eukaryote, bacteria, archaea, metagenome), up to September 2009 and some other relevant charts. Again, you could probably extract data from this resource to make your own plots.