mouse-over definitions of terms

[gregcaporaso]

Add mouseover definitions for technical terms:

• [x] OTU
• [x] beta diversity
• [x] alpha diversity
• [x] ordination

@gregcaporaso will add definitions here, and @jrrideout will add the mouseover functionality.

[gregcaporaso]

Operational Taxonomic Units or OTUs: An OTU is a functional definition of a taxonomic group, often based on percent identity of the 16S ribosomal RNA (rRNA) gene. In this study, we began with a reference collection of 16S rRNA sequences (derived from the Greengenes database), and each of those sequences was used to define an Opertational Taxonomic Unit. We then compared all of the sequence reads that we obtained in this study (from your microbial communities and everyone else's) to those reference OTUs, and if a sequence read matched one of those sequences at at least 97% identity, the read was considered an observation of that reference OTU. This process is one strategy for OTU picking, or assigning sequence reads to OTUs.

[gregcaporaso]

Alpha diversity: Alpha diversity refers to within sample diversity, and can be a measure of the number of different types of organisms that are present in a sample (i.e., the richness of the sample), the shape of the distribution of counts of different organisms in a sample (i.e., the evenness of the sample), or some other property of a single sample. This is in contrast to beta diversity, which is a measure of between-sample diversity.

[gregcaporaso]

Beta diversity: Beta diversity measures between sample diversity tells us the similarity or dissimilarity of a pair of samples. This information is most useful when you're comparing more than two samples, which is almost always, as beta diversity can then tell you about the relative similarity or dissimilarity between all pairs of your samples. For example, if you have human gut microbial communities from three individuals (say, individuals A, B, and C), and compute beta diversity for each pair of those three samples, you results may tell you that individual A is more similar to individual B than either is to individual C. Ecologists use many different metrics to measure beta diversity. The metric we use here is called UniFrac (see Lozupone and Knight, 2005 for a discussion of UniFrac).

[gregcaporaso]

Ordination: Ecologists often use ordination techniques to visually summarize the relative similarity of collections of samples (i.e., the beta diversity values between all of their pairs of samples). In the Student Microbiome Project, for example, we compared over 3700 samples. This resulted in over 6,841,300 pairwise distances between samples, so visualization is essential to exploring that data. An ordination technique can be used to arrange this large number of distances in a few dimensions, which are often viewed in two or three dimensional scatter plots. In an ordination plot, the distances between the points represent their relative similarity, such that points (i.e., samples) that are closer to one another in the scatter plot are more similar to each other than points that are farther apart. Two of the most commonly used ordination techniques in microbial ecology are Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS).