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diff --git a/topics/data-uploads/datasets.gmi b/topics/data-uploads/datasets.gmi new file mode 100644 index 0000000..af5ad02 --- /dev/null +++ b/topics/data-uploads/datasets.gmi @@ -0,0 +1,38 @@ +# 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. |