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| -rw-r--r-- | doc/README.org | 2 | ||||
| -rw-r--r-- | doc/database.org | 42 |
2 files changed, 41 insertions, 3 deletions
diff --git a/doc/README.org b/doc/README.org index 345341e1..278dd31c 100644 --- a/doc/README.org +++ b/doc/README.org @@ -548,7 +548,7 @@ configuration. At some point you may want to fix the source code. Assuming you have Guix and Genenetwork2 installed (as described above) clone the GN2 -repository from https://github.com/genenetwork/genenetwork2_diet +repository from https://github.com/genenetwork/genenetwork2. Copy-paste the paths into your terminal (mainly so PYTHON_PATH and R_LIBS_SITE are set) from the information given by guix: diff --git a/doc/database.org b/doc/database.org index e06ac1ff..cf3781a8 100644 --- a/doc/database.org +++ b/doc/database.org @@ -1,7 +1,11 @@ - github Document reduction issue +* The small test database (2GB) -* GeneNetwork Database +The default install comes with a smaller database which includes a +number of the BSD's and the Human liver dataset (GSE9588). + +* GeneNetwork database ** Estimated table sizes @@ -487,7 +491,6 @@ select count(*) from ProbeSet limit 5; - ** ProbeSetData Probedata - main molecular data. Probesets, metabolome, @@ -708,3 +711,38 @@ User selection - retained ** Vlookup +* Fetching Data + +** Fetch phenotypes + +To get at phenotype data ProbeSetData is the main table (almost all +important molecular assay data is in this table including probe set +data, RNA-seq data, proteomic data, and metabolomic data. 2.5 billion +rows March 2016) + +select count(*) from ProbeSetData limit 5; ++---------------+ +| count(*) | ++---------------+ +| 2,510,566,472 | ++---------------+ + +select * from ProbeSetData limit 5; ++----+----------+-------+ +| Id | StrainId | value | ++----+----------+-------+ +| 1 | 1 | 5.742 | +| 1 | 2 | 5.006 | +| 1 | 3 | 6.079 | +| 1 | 4 | 6.414 | +| 1 | 5 | 4.885 | ++----+----------+-------+ + +This table is used in + +: wqflask/base/do_search.py +: wqflask/base/data_set.py +: wqflask/utility/AJAX_table.py +: wqflask/wqflask/correlation/show_corr_results.py + +In there we find 'ProbeSetData.Id = ProbeSetXRef.dataId'. |