Docs: genotyping

2 files changed, 50 insertions, 11 deletions

diff --git a/doc/Architecture.org b/doc/Architecture.org
index ed19889c..9a561568 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -1,19 +1,19 @@
-* GeneNetwork Architecture
-
 #+TITLE: Installing GeneNetwork services
 
 * Table of Contents                                                     :TOC:
- - [[#genenetwork-architecture][GeneNetwork Architecture]]
-   - [[#introduction][Introduction]]
-   - [[#webserver][Webserver]]
-   - [[#gnserver-rest][GnServer (REST)]]
+ - [[#introduction][Introduction]]
+ - [[#webserver][Webserver]]
+ - [[#gnserver-rest][GnServer (REST)]]
+ - [[#database-][Database ]]
+   - [[#phenotypes][Phenotypes]]
+   - [[#genotypes][Genotypes]]
 
-** Introduction
+* Introduction
 
 This document describes the architecture of GN2. Because GN2 is
 evolving, only a high-level overview is given here.
 
-** Webserver
+* Webserver
 
 The main [[https://github.com/genenetwork/genenetwork2][GN2 webserver]] is built on [[http://flask.pocoo.org/][Python flask]] and this GN2 source
 code can be found on [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask][github]] in the wqflask directory. The routing
@@ -44,7 +44,7 @@ Consortium M430v2 (Jun06) PDNN to find all records with MEAN between
 15 and 16 and with LRS between 23 and 46.'. Then the results are added
 to a table which is displayed using a JS [[https://datatables.net/][DataTable container]].
 
-** GnServer (REST)
+* GnServer (REST)
 
 The [[https://github.com/genenetwork/gn_server][GnServer REST API]] is built on high performance [[http://elixir-lang.org/][Elixir]] with [[https://github.com/falood/maru][Maru]].
 Mainly the GnServer serves JSON requests, for example to fetch data
@@ -52,4 +52,44 @@ from the database. To get the menu data in YAML you can do something like
 
 : curl localhost:8880/int/menu/main.json|ruby extra/json2yaml.rb
 
-(json2yaml.rb is in the gn_server repo).
+(json2yaml.rb is in the gn_server repo). For the current API definition
+see [[https://github.com/genenetwork/gn_server/doc/API.md][GnServer REST API]] documentation.
+
+* Database 
+
+** Phenotypes
+
+Phenotypes are stored in the SQL database.  For what happens at the
+database level see [[database.org]]. A test database can be downloaded -
+see the installation [[./README.org][instructions]].
+
+** Genotypes
+
+Genotypes are stored in genotype files. These are part of the GNU Guix
+distribution, see the installation [[./README.org][instructions]]. Genotype files are
+currently in GN1 format, and will be aligned with the R/qtl2 format. Now it is
+for BXD.geno:
+
+#+begin_src js
+@name:BXD
+@type:riset
+@mat:B
+@pat:D
+@het:H
+@unk:U
+Chr Locus cM  Mb  BXD1  BXD2  BXD5  BXD6  BXD8  BXD9  BXD11 BXD12 BXD13 BXD14 BX
+D15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a  BXD24 BXD25 BXD27 BXD28 BX
+D29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD4
+2 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59
+BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BX
+D73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD8
+7 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100
+  BXD101  BXD102  BXD103
+1 rs6269442 0.0 3.482275  B B D D D B B D B B D D B D D D D B B B D B D D B B B
+B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B
+D D D D D H B D D B D B B D D B D D B B B B B B B D
+1 rs6365999 0.0 4.811062  B B D D D B B D B B D D B D D D D B B B D B D D B B B
+B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B
+D D D D D H B D D B D B B D D B D D B B B B B B U D
+etc
+#+end_src
diff --git a/doc/database.org b/doc/database.org
index df34e7ed..2c7dc887 100644
--- a/doc/database.org
+++ b/doc/database.org
@@ -506,7 +506,6 @@ select count(*) from ProbeSet limit 5;
 +------+--------+----------+----------+--------+----------------------------------------------+------+-----------+----------+--------+-----------+------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+--------------+-------------+--------+----------+-------------------------+-----------------------+----------------------+-------------------------+-----------------------+------------------+----------------------+------+----------+---------------+--------------+------+---------+----------+---------+----------+--------------------------+---------------------+---------+-----------+-----------------------------+---------------------------+--------------+-------------+-----------+-------------+------------+---------+------------+----------+-----------+------------+------------+---------------+---------+-----------+---------+------------------+-------------+------+--------+-------------+----------------+-----------------+
 2 rows in set (0.00 sec)
 
-
 ** ProbeSetXRef (phenotypes/dataset_name.json)
 
 For every probe set (read dataset measuring point):