README.rdoc in bio-1.5.2 vs README.rdoc in bio-1.6.0.pre.20181210

@@ -28,11 +28,11 @@
 Ruby's String class and with regular expressions.  Daily tools like
 Blast, Fasta, Hmmer and many other software packages for biological
 analysis can be executed within the BioRuby script, and the results
 can be fully parsed to extract the portion you need.  BioRuby supports
 major biological database formats and provides many ways for accessing
-them through flatfile indexing, SQL, web services etc.  Various web
+them through flatfile indexing, web services etc.  Various web
 services can be easily utilized by BioRuby.
 
 
 == FOR MORE INFORMATION
 
@@ -138,29 +138,12 @@
 
 * {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
   (which took over {bdb}[https://github.com/ruby-bdb/bdb])
   (No RubyGems available)
   * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required.
-  
-Accessing BioSQL database created by other Open Bio* libraries:
 
-* {gem install activerecord}[http://rubygems.org/gems/activerecord]
-  and at least one driver (or adapter):
-  * {gem install mysql}[http://rubygems.org/gems/mysql] or
-    {gem install mysql2}[http://rubygems.org/gems/mysql2]
-  * {gem install pg}[http://rubygems.org/gems/pg]
-  * {gem install sqlite-ruby}[http://rubygems.org/gems/sqlite-ruby] or
-    {gem install sqlite3}[http://rubygems.org/gems/sqlite3]
-  * {gem install activerecord-oracle_enhanced-adapter}[http://rubygems.org/gems/activerecord-oracle_enhanced-adapter]
 
-For parsing PhyloXML format files:
-
-* {gem install libxml-ruby}[http://rubygems.org/gems/libxml-ruby]
-  * {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/] and C compiler will be
-    required.
-
-
 == INSTALL
 
 === INSTALL by using RubyGems (recommended)
 
 If you are using RubyGems, just type
@@ -284,9 +267,19 @@
 
 Many plugins (called Biogem) are now available. See http://biogems.info/
 for list of plugins and related software utilizing BioRuby.
 
 * http://biogems.info/
+
+Plugins (Biogems) listed below had been included in BioRuby in former days,
+and were split to separate packages to reduce complexity and external
+dependencies.
+
+* {bioruby-phyloxml}[http://rubygems.org/gems/bioruby-phyloxml]
+  * NOTE: Please uninstall bio-phyloxml, that have been created as a
+    preliminary trial of splitting a module in 2012 and have not been
+    maintained after that.
+* {bio-biosql}[http://rubygems.org/gems/bio-biosql]
 
 To develop your own plugin, see "Plugins" pages of BioRuby Wiki.
 
 * http://bioruby.open-bio.org/wiki/Plugins