Klaus' recently shared with us some mouse data. Here's a snip of how that looks like:
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
I've been working on adding the above to the GN2 database. The current challenge I have is that this data is Time Series---for the same strain, we have values indexed by time. Also, we tag data by "animal.no." and "sex". So for a male version of "CC001" with animal number 1, we have "CC001_m_1". This is a problem---storing TS data---that Rob/Suheeta have highlighted in the past. How do we go about doing this? Currently, in GN2 we store averages of the aforementioned data. This doesn't work out well for us: we don't have, AFAIU, a concept for "animal.no." I would suggest we use lmdb to store this data, and work out a way to integrate it with the rest of GN2 - so that we display this info on the main page.
Here's how to extract the data from the provided data-set:
Just extract the data for d1, d2, d3 separately and use each day as a separate data set.
> unique(dat2$day)  d0 d1 d2 d3 Levels: d0 d1 d2 d3 > table(dat2$day) d0 d1 d2 d3 44 44 44 44 dat10 <- subset(dat2,dat2$day=="d1") dat10 > dat10 mouse_ID BW day 45 BXD 50_3 94.85000 d1 46 BXD 64_1 96.36000 d1 47 BXD 29_1 96.85000 d1 48 BXD 40_3 97.69000 d1 49 BXD 49_2 97.06000 d1 50 BXD 6_5 89.03000 d1 [...]
Some comments from Zach:
I think that Klaus is referring to what we store in GN as phenotype traits. So you'd have a separate trait page for each time series "step".' He's probably referring to these traits: Day 1 - https://genenetwork.org/show_trait?trait_id=13005&dataset=BXDPublish Day 2 - https://genenetwork.org/show_trait?trait_id=13006&dataset=BXDPublish And continues from there - you can see them with the following search (with a few other random traits mixed in; I first just searched for "Schughart" in the global search) - https://genenetwork.org/gsearch?type=phenotype&terms=H1N1 You're correct about there not being a (good) way to deal with something like animal number currently. The way we deal with something like that is to create a new group, with the "strain list" being a list of individuals.
Current script that enters data into gn2:
The last 2 tasks will/should probably be broken down into smaller issues.