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-rw-r--r--doc/database.org165
-rw-r--r--doc/database.svg882
2 files changed, 1044 insertions, 3 deletions
diff --git a/doc/database.org b/doc/database.org
index e06ac1ff..2221c4fb 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,
@@ -678,7 +681,21 @@ No longer used
** Species & Strain (should be sample)
-Menu
+select * from Species;
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+| Id | SpeciesId | SpeciesName | Name | MenuName | FullName | TaxonomyId | OrderId |
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+| 1 | 1 | Mouse | mouse | Mouse | Mus musculus | 10090 | 30 |
+| 2 | 2 | Rat | rat | Rat | Rattus norvegicus | 10116 | 40 |
+| 3 | 3 | Arabidopsis thaliana | arabidopsis | Arabidopsis thaliana | Arabidopsis thaliana | 3702 | 60 |
+| 4 | 4 | Human | human | Human | Homo sapiens | 9606 | 10 |
+| 5 | 5 | Barley | barley | Barley | Hordeum vulgare | 4513 | 70 |
+| 6 | 6 | Drosophila | drosophila | Drosophila | Drosophila melanogaster | 7227 | 50 |
+| 7 | 7 | Macaque monkey | macaque monkey | Macaque monkey | Macaca mulatta | 9544 | 20 |
+| 8 | 8 | Soybean | soybean | Soybean | Soybean | 3847 | 80 |
+| 9 | 9 | Tomato | tomato | Tomato | Tomato | 4081 | 90 |
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+
** InbredSet
@@ -708,3 +725,145 @@ 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'.
+
+select * from ProbeSetXRef limit 5;
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old | LRS_old | pValue_old | mean | se | Locus | LRS | pValue | additive | h2 |
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+| 1 | 1 | 1 | 10.095.400 | 13.3971627898894 | 0.163 | 5.48794285714286 | 0.08525787814808819 | rs13480619 | 12.590069931048001 | 0.269 | -0.28515625 | NULL |
+| 1 | 2 | 2 | D15Mit189 | 10.042057464356201 | 0.431 | 9.90165714285714 | 0.0374686634976217 | CEL-17_50896182 | 10.5970737900941 | 0.304 | -0.11678333333333299 | NULL |
+| 1 | 3 | 3 | D5Mit139 | 5.43678531742749 | 0.993 | 7.83948571428571 | 0.0457583416912569 | rs13478499 | 6.0970532702754 | 0.988 | 0.112957489878542 | NULL |
+| 1 | 4 | 4 | D1Mit511 | 9.87815279480766 | 0.483 | 8.315628571428569 | 0.0470396593931327 | rs6154379 | 11.774867551173099 | 0.286 | -0.157113725490196 | NULL |
+| 1 | 5 | 5 | D16H21S16 | 10.191723834264499 | 0.528 | 9.19345714285714 | 0.0354801718293322 | rs4199265 | 10.923263374016202 | 0.468 | 0.11476470588235299 | NULL |
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+
+i.e., for Strain Id 1 (DataId) 1, the locus '10.095.400' has a
+phenotype value of 5.742.
+
+GeneNetwork1 already has a limited REST interface, if you do
+
+: curl "http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=1443823_s_at&db=HC_M2_0606_P"
+
+we get
+
+: ProbeSetID B6D2F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD15 BXD16 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24 BXD27 BXD28 BXD29 BXD31 BXD32 BXD33 BXD34 BXD38 BXD39 BXD40 BXD42 BXD67 BXD68 BXD43 BXD44 BXD45 BXD48 BXD50 BXD51 BXD55 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD69 BXD70 BXD73 BXD74 BXD75 BXD76 BXD77 BXD79 BXD73a BXD83 BXD84 BXD85 BXD86 BXD87 BXD89 BXD90 BXD65b BXD93 BXD94 A/J AKR/J C3H/HeJ C57BL/6ByJ CXB1 CXB2 CXB3 CXB4 CXB5 CXB6 CXB7 CXB8 CXB9 CXB10 CXB11 CXB12 CXB13 BXD48a 129S1/SvImJ BALB/cJ BALB/cByJ LG/J NOD/ShiLtJ PWD/PhJ BXD65a BXD98 BXD99 CAST/EiJ KK/HlJ WSB/EiJ NZO/HlLtJ PWK/PhJ D2B6F1
+: 1443823_s_at 15.251 15.626 14.716 15.198 14.918 15.057 15.232 14.968 14.87 15.084 15.192 14.924 15.343 15.226 15.364 15.36 14.792 14.908 15.344 14.948 15.08 15.021 15.176 15.14 14.796 15.443 14.636 14.921 15.22 15.62 14.816 15.39 15.428 14.982 15.05 15.13 14.722 14.636 15.242 15.527 14.825 14.416 15.125 15.362 15.226 15.176 15.328 14.895 15.141 15.634 14.922 14.764 15.122 15.448 15.398 15.089 14.765 15.234 15.302 14.774 14.979 15.212 15.29 15.012 15.041 15.448 14.34 14.338 14.809 15.046 14.816 15.232 14.933 15.255 15.21 14.766 14.8 15.506 15.749 15.274 15.599 15.673 14.651 14.692 14.552 14.563 14.164 14.546 15.044 14.695 15.162 14.772 14.645 15.493 14.75 14.786 15.003 15.148 15.221
+
+getTraitData is defined in the file [[https://github.com/genenetwork/genenetwork/blob/master/web/webqtl/textUI/cmdClass.py#L134][web/webqtl/textUI/cmdClass.py]].
+probe is None, so the code at line 199 is run
+
+query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s,
+%sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and
+%sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and
+%sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix,
+prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix,
+prefix, dbId, prefix, prefix, prefix)
+
+where prefix is ProbeSet (one presumes). So, let's see if we can do this by hand
+
+SELECT Strain.Name, ProbeSetData.value from ProbeSetData, Strain, ProbeSet,
+ProbeSetXRef WHERE ProbeSet.Name = '1443823_s_at' and ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+ProbeSetXRef.ProbeSetFreezeId = $dbid and ProbeSetXRef.DataId = ProbeSetData.Id and
+ProbeSetData.StrainId = Strain.Id ORDER BY Strain.Id
+
+The $dbid is listed in the ProbeSetFreeze table,
+
+SELECT ProbeFreezeId,Name FROM ProbeSetFreeze WHERE Name='HC_M2_0606_P' limit 5;
+
++---------------+--------------+
+| ProbeFreezeId | Name |
++---------------+--------------+
+| 30 | HC_M2_0606_P |
++---------------+--------------+
+
+select id,name from ProbeSet WHERE Name = '1443823_s_at' limit 5;
++--------+--------------+
+| id | name |
++--------+--------------+
+| 106556 | 1443823_s_at |
++--------+--------------+
+
+So
+
+query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s,
+%sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and
+%sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and
+%sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix,
+prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix,
+prefix, dbId, prefix, prefix, prefix)
+
+CORRECT NAME:
+
+SELECT Strain.Name, ProbeSetData.value from ProbeSetData, Strain,
+ProbeSet, ProbeSetXRef WHERE ProbeSet.Name = 'at_probe' and
+ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+ProbeSetXRef.ProbeSetFreezeId = dbid and ProbeSetXRef.DataId =
+ProbeSetData.Id and ProbeSetData.StrainId = Strain.Id order by
+Strain.Id
+
+
+select * from ProbeSetXRef WHERE probesetfreezeid=30 limit 5;
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old | LRS_old | pValue_old | mean | se | Locus | LRS | pValue | additive | h2 |
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+| 30 | 1 | 445962 | 01.059.350 | 7.1753152078069595 | 0.961 | 30.0646 | 1.79763935596594 | rs13475891 | 7.1753152078069204 | 0.973 | 4.71778125 | NULL |
+| 30 | 2 | 445963 | D4Mit156 | 7.58944292943285 | 0.724 | 232.38328571428602 | 9.00278909374791 | CEL-4_118751423 | 7.57513435426218 | 0.793 | 25.2660951417004 | NULL |
+| 30 | 3 | 445964 | D1Mit134 | 9.766065497826819 | 0.737 | 47.206 | 1.58413526287766 | mCV23431007 | 9.76606549782677 | 0.797 | -4.82405952380952 | NULL |
+| 30 | 4 | 445965 | D1Mit155 | 18.0045829157241 | 0.033 | 132.29248571428602 | 4.37799472291842 | rs3689947 | 17.9365068406286 | 0.049 | -16.945619047619 | NULL |
+| 30 | 5 | 445966 | D5Mit197 | 9.51068902627823 | 0.476 | 271.309971428571 | 7.4294268316065395 | rs6239372 | 10.4214974316601 | 0.41 | -25.6148045454546 | NULL |
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+
+So, apparently ProbeSetFreezeID points to the database identifier in
+ProbeSetFreeze which has the name of the 'DB'. OK, that kinda makes
+sense now. Meanwhile Probeset.name points to the phenotype name.
+
+ProbeSetXRef binds these tables together. Finally there is the data in
+
+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 |
++----+----------+-------+
+5 rows in set (0.00 sec)
+
+linked by ProbeSetXRef.dataid.
diff --git a/doc/database.svg b/doc/database.svg
new file mode 100644
index 00000000..9ddc2f47
--- /dev/null
+++ b/doc/database.svg
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