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Some Historical Context

In the context of GN code, a "dataset" specifically refers to a grouping of traits. It's easy to confuse that with individual GN traits (which can best be defined as a single set of sample data). So Time Series (TS) data would consist of multiple GN traits, one trait for each time point.

A phenotype is an observed 'feature' such as body weight. In genetics, traits are characteristics about humans and other living organisms that can be described or measured. Sex is a trait. In GN we mixed them up.

When we do an experiment we take measurements across a range of individuals at a time point. Each time point is a vector of data. When repeated with the same individual/strain we can take the mean (meaningfully). That is another vector.

As alluded to earlier, 'datasets' are combinations of measurements referring to one (or more?) experiments. [Suggestion] Link dataset to measurements/phenotypes in an experiment at a certain time point. Thus we have a matrix of data (columns are measurements and means). For probesets and RNA-seq we treat them the same as simple vectors of measurements.

When we have time series we get a 3rd dimension which can be represented in metadata. No need to account for that at the storage level. We'll need to handle it in the UI and with any computations.

We invented the term “attribute” for trait OR metadata type that is even broader. For example an attribute can include an indicator for inclusion of a case in a study. An attribute can be alphanumeric and can be used as a co-factor. Does get messy.


Extracting TS Data from a provided data set

Suppose you have the following CSV file (snippet):

  mouse_ID                   BW       day         strain        sex    inf_dose animal.no.
  241   CC001_m_1       100     perc_d00        CC001   m       10 FFU  1
  242   CC001_m_1       98.56   perc_d03        CC001   m       10 FFU  1
  243   CC001_m_1       NA      perc_d13        CC001   m       10 FFU  1
  244   CC001_m_1       NA      perc_d12        CC001   m       10 FFU  1
  245   CC001_m_1       NA      perc_d10        CC001   m       10 FFU  1
  246   CC001_m_1       100.92  perc_d04        CC001   m       10 FFU  1
  247   CC001_m_1       98.08   perc_d01        CC001   m       10 FFU  1
  248   CC001_m_1       76.21   perc_d08        CC001   m       10 FFU  1
  249   CC001_m_1       93.22   perc_d05        CC001   m       10 FFU  1
  250   CC001_m_1       90.42   perc_d06        CC001   m       10 FFU  1
[...]

Each day (d1, d2, d3) represents a different data set. From the above, a "dataset" is grouped by "day".

In the above, Strain is CC001. It is male and animal no 1. For mapping, only the strain name and group will matter. Combine sex and days and infection status to a data set for mapping. A target file is provided that describes all of this.


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