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svn path=/bioperl-db/trunk/; revision=473
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commit 373aadd08873ad6431b6b7458c14d19e25228ed9 1 parent c36a078
bosborne authored

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  1. +34 25 README
59 README
... ... @@ -1,19 +1,18 @@
1 1 # $Id$
2 2
3   -
4 3 This package contains 2 logical projects under the common hood of
5 4 interfaces and adaptors for relational databases for serializing and
6 5 de-serializing bioperl objects.
7 6
8 7 ===================================================================
9   -Information about Bio::DB::BioSQL interface, a sequence database.
  8 +Information about BioSQL and bioperl-db
10 9 ===================================================================
11 10
12 11 This project was started by Ewan Birney with major work by Elia Stupka
13   -with continued support by the bioperl community. It's purpose is a
14   -standalone sequence database with little external dependancies and
15   -tight integration with bioperl. Support for more databases and
16   -bindings in java and python by Biojava and Biopython projects is
  12 +with continued support by the bioperl community. It's purpose is to
  13 +create a standalone sequence database with little external dependancies and
  14 +tight integration with Bioperl. Support for more databases and
  15 +bindings in Java and python by Biojava and Biopython projects is
17 16 welcomed, and a working prototype was one of the accomplishments of
18 17 the February 2002 hackathon in South Africa. All questions and
19 18 comments should be directed to the bioperl list
@@ -23,14 +22,25 @@ http://www.open-bio.org.
23 22
24 23 I. Related scripts located in the scripts directory:
25 24
26   -load_seqdatabase.pl - an example and a very flexible script to load seqs
27   - into the database
28   -bioentry2flat.pl - dump sequence data into rich sequence
29   - format flatfile representation
30   -caching_corba_server.pl - setup a corba sequence caching server
31   -test_bioenv.pl - test the bioenv of a running server
32   -bioenv_server.pl - setup a CORBA sequence server
33   -
  25 +biosql/load_seqdatabase.pl - a very flexible script to load
  26 + sequences into the database
  27 +biosql/bioentry2flat.pl - dump sequence data into rich sequence
  28 + format flatfile from the database
  29 +biosql/load_ontology.pl - load GO or SOFA ontology data into
  30 + the database
  31 +biosql/merge-unique-ann.pl - script used by load_seqdatabase.pl,
  32 + it merges features and annotations
  33 +biosql/update-on-new-date.pl - script used by load_seqdatabase.pl,
  34 + it will update based on date
  35 +biosql/update-on-new-version.pl - script used by load_seqdatabase.pl,
  36 + it will update based on version
  37 +corba/caching_corba_server.pl - setup a corba sequence caching server
  38 +corba/test_bioenv.pl - test the bioenv of a running server
  39 +corba/bioenv_server.pl - setup a CORBA sequence server
  40 +
  41 +There is also a script called scripts/load_taxonomy.pl in the BioSQL
  42 +package itself that loads taxonomic data from NCBI, you may find it
  43 +useful.
34 44
35 45 II. Some background information and how it all works:
36 46
@@ -41,7 +51,7 @@ following things are unsupported or do not work yet:
41 51
42 52 - sub-seqfeatures
43 53 - round-tripping fuzzy locations (they will be stored according
44   - to their Bio::Location::CoordinatePolicyI interpretation)
  54 + to their Bio::Location::CoordinatePolicyI interpretation)
45 55 - Bio::Annotation::DBLink::optional_id
46 56
47 57 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
70 80 object implements. E.g., a persistent sequence object will implement
71 81 Bio::DB::PersistentObjectI and Bio::PrimarySeqI (or Bio::SeqI).
72 82
73   -4) A persistence adaptor will implement
74   -Bio::DB::PersistenceAdaptorI. Apart from actually implementing all the
75   -persistence methods for persistent objects, a persistence adaptor
76   -allows you to locate objects in the database by key and by query. You
77   -can find_by_primary_key(), find_by_unique_key(),
78   -find_by_association(), and find_by_query(). The latter allows you to
79   -formulate object queries as Bio::DB::Query::BioQuery objects and
80   -retrieve the matching objects.
  83 +4) A persistence adaptor will implement Bio::DB::PersistenceAdaptorI.
  84 +Apart from actually implementing all the persistence methods for
  85 +persistent objects, a persistence adaptor allows you to locate
  86 +objects in the database by key and by query. You can
  87 +find_by_primary_key(), find_by_unique_key(), find_by_association(),
  88 +and find_by_query(). The latter allows you to formulate object queries
  89 +as Bio::DB::Query::BioQuery objects and retrieve the matching objects.
81 90
82 91 5) The guiding principle for the redesign of the adaptors was to
83 92 separate business logic from schema logic. While business logic is
@@ -132,8 +141,8 @@ integrate different map locations with sequence data.
132 141 Scripts for loading private genetic and marker maps are also to be
133 142 provided.
134 143
135   -Related scripts located in the scripts directory:
136   -
  144 +The following scripts have been removed from the bioperl-db package
  145 +(please contact Jason Stajich for more information):
137 146
138 147 download_marker_data.pl - automate downloading of marker information
139 148 for local testing and faster installation

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