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Updated

svn path=/bioperl-db/trunk/; revision=473
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commit 373aadd08873ad6431b6b7458c14d19e25228ed9 1 parent c36a078
bosborne authored
Showing with 34 additions and 25 deletions.
  1. +34 −25 README
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59 README
@@ -1,19 +1,18 @@
# $Id$
-
This package contains 2 logical projects under the common hood of
interfaces and adaptors for relational databases for serializing and
de-serializing bioperl objects.
===================================================================
-Information about Bio::DB::BioSQL interface, a sequence database.
+Information about BioSQL and bioperl-db
===================================================================
This project was started by Ewan Birney with major work by Elia Stupka
-with continued support by the bioperl community. It's purpose is a
-standalone sequence database with little external dependancies and
-tight integration with bioperl. Support for more databases and
-bindings in java and python by Biojava and Biopython projects is
+with continued support by the bioperl community. It's purpose is to
+create a standalone sequence database with little external dependancies and
+tight integration with Bioperl. Support for more databases and
+bindings in Java and python by Biojava and Biopython projects is
welcomed, and a working prototype was one of the accomplishments of
the February 2002 hackathon in South Africa. All questions and
comments should be directed to the bioperl list
@@ -23,14 +22,25 @@ http://www.open-bio.org.
I. Related scripts located in the scripts directory:
-load_seqdatabase.pl - an example and a very flexible script to load seqs
- into the database
-bioentry2flat.pl - dump sequence data into rich sequence
- format flatfile representation
-caching_corba_server.pl - setup a corba sequence caching server
-test_bioenv.pl - test the bioenv of a running server
-bioenv_server.pl - setup a CORBA sequence server
-
+biosql/load_seqdatabase.pl - a very flexible script to load
+ sequences into the database
+biosql/bioentry2flat.pl - dump sequence data into rich sequence
+ format flatfile from the database
+biosql/load_ontology.pl - load GO or SOFA ontology data into
+ the database
+biosql/merge-unique-ann.pl - script used by load_seqdatabase.pl,
+ it merges features and annotations
+biosql/update-on-new-date.pl - script used by load_seqdatabase.pl,
+ it will update based on date
+biosql/update-on-new-version.pl - script used by load_seqdatabase.pl,
+ it will update based on version
+corba/caching_corba_server.pl - setup a corba sequence caching server
+corba/test_bioenv.pl - test the bioenv of a running server
+corba/bioenv_server.pl - setup a CORBA sequence server
+
+There is also a script called scripts/load_taxonomy.pl in the BioSQL
+package itself that loads taxonomic data from NCBI, you may find it
+useful.
II. Some background information and how it all works:
@@ -41,7 +51,7 @@ following things are unsupported or do not work yet:
- sub-seqfeatures
- round-tripping fuzzy locations (they will be stored according
- to their Bio::Location::CoordinatePolicyI interpretation)
+ to their Bio::Location::CoordinatePolicyI interpretation)
- Bio::Annotation::DBLink::optional_id
To understand the layout of the API and how you can interact with the
@@ -70,14 +80,13 @@ implement all interfaces and all methods that the non-persistent base
object implements. E.g., a persistent sequence object will implement
Bio::DB::PersistentObjectI and Bio::PrimarySeqI (or Bio::SeqI).
-4) A persistence adaptor will implement
-Bio::DB::PersistenceAdaptorI. Apart from actually implementing all the
-persistence methods for persistent objects, a persistence adaptor
-allows you to locate objects in the database by key and by query. You
-can find_by_primary_key(), find_by_unique_key(),
-find_by_association(), and find_by_query(). The latter allows you to
-formulate object queries as Bio::DB::Query::BioQuery objects and
-retrieve the matching objects.
+4) A persistence adaptor will implement Bio::DB::PersistenceAdaptorI.
+Apart from actually implementing all the persistence methods for
+persistent objects, a persistence adaptor allows you to locate
+objects in the database by key and by query. You can
+find_by_primary_key(), find_by_unique_key(), find_by_association(),
+and find_by_query(). The latter allows you to formulate object queries
+as Bio::DB::Query::BioQuery objects and retrieve the matching objects.
5) The guiding principle for the redesign of the adaptors was to
separate business logic from schema logic. While business logic is
@@ -132,8 +141,8 @@ integrate different map locations with sequence data.
Scripts for loading private genetic and marker maps are also to be
provided.
-Related scripts located in the scripts directory:
-
+The following scripts have been removed from the bioperl-db package
+(please contact Jason Stajich for more information):
download_marker_data.pl - automate downloading of marker information
for local testing and faster installation
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