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-rw-r--r--doc/README.org2
-rw-r--r--doc/database.org42
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'.