Response to call merenlab#3 -- adding a definition for 'Virome', or r…

…ather two definitions because of course it is used in two different ways ...

vocabulary/index.md

@@ -142,6 +142,17 @@ Works for us. :)
 
 The entire RNA content of a given environment. Unlike metagenomes, metatranscriptomes can shed light on the activity of environmental populations. But they bring unique challenges, such as the short half-life of RNA molecules, and secondary-structure driven varaition in their coverages.
 
+
+{:data-tags="virome"}
+### Virome
+
+A metagenome derived from the viral fraction of a sample. OR, the assemblage of viruses in a specific sample of environment. Yes, the same word ended up designating two different concepts, sorry... Unfortunately, at this point there are no great alternative to either use of "virome", so both are regularly encountered in the literature and the specific meaning typically has to be deduced from context (fortunately, this is often relatively straightforward). 
+
+In the first case, "Virome" is used as shorthand for "Viral metagenome". Pragmatically, a virome is a metagenome generated from a sample that has been specifically processed to be (i) enriched in viral particles and/or (ii) depleted in cellular (micro)organisms, through a combination of filtering, precipitation, and other (almost) magic tricks. These datasets are sometimes designated as "metavirome", but this terminology is also not satisfying because it does not follow the use of "meta" as a prefix to "extend that term to all the things within a given sample" (see Metagenome above). Here instead, the notion of "extend to all the things" is already built into "virome", and the meta prefix is redundant while not providing the extra information required. 
+
+In the second use, "Virome" is essentially the counterpart of "Microbiome", and is built the same way: while the microbi-ome would designate the community of microorganisms found in a single habitat, the vir-ome would designate the community of viruses found in this habitat. This makes a lot of sense, and is typically the definition provided by encyclopedia (see e.g. https://en.wikipedia.org/wiki/Virome). The only (major) flaw of course is that this term was already used to designate "viral metagenomes".. Sadly, the fact that (viral) metagenomics is often the methods of choice to explore "viromes" only adds to the confusion.
+
+
 {:data-tags="metagenomics"}
 ### Metagenomics