Index of /full/2003-04-01

Icon  Name                               Last modified      Size  Description
[DIR] Parent Directory - [   ] DATESTAMP 18-Apr-2003 18:00 11 [TXT] README 18-Apr-2003 18:00 5.3K [   ] go_200304-assocdb-data.gz 03-Apr-2003 13:12 86M [   ] go_200304-assocdb-summary.txt.gz 03-Apr-2003 13:26 833 [   ] go_200304-assocdb-tables.tar.gz 03-Apr-2003 13:02 82M [   ] go_200304-assocdb.xml.gz 08-Apr-2003 13:12 4.2M [   ] go_200304-schema-mysql.sql.gz 01-Apr-2003 12:36 4.6K [   ] go_200304-seqdb-tables.tar.gz 08-Apr-2003 09:18 142M [   ] go_200304-seqdblite-data.gz 08-Apr-2003 11:32 76M [   ] go_200304-seqdblite-summary.txt.gz 08-Apr-2003 11:35 737 [   ] go_200304-seqdblite-tables.tar.gz 08-Apr-2003 11:51 74M [   ] go_200304-seqdblite.fasta.gz 08-Apr-2003 12:38 13M [   ] go_200304-termdb-data.gz 01-Apr-2003 12:52 2.4M [   ] go_200304-termdb-summary.txt.gz 01-Apr-2003 12:30 315 [   ] go_200304-termdb-tables.tar.gz 01-Apr-2003 12:52 2.2M [   ] go_200304-termdb.xml.gz 01-Apr-2003 12:48 710K [   ] go_200304-utilities-src.tar.gz 01-Apr-2003 12:13 3.6M
GO DATABASE DOWNLOADS
=====================

releases are now named

  go_<200304>-<DATASET><TYPE>

200304 is the release date (the release export usually follows some
time after the monthly release, due to time taken to build)

the DATASET is one of:
    -------

* termdb - a database containing just the information on the
GO terms and relationships. These are the table that are populated:

term                        GO controlled vocab terms
term2term                   relationships between GO terms
term_definition             definitions of terms
dbxref                      external database identifier entities
term_dbxref                 links from terms to other databases
term_synonym                synonyms for terms
graph_path                  transitive closure (all paths) in graph

* assocdb - a database containing both the GO vocabulary and
associations between GO terms and gene products. This database
subsumes termdb. These are the extra tables that are populated:

gene_product                 gene or protein or entity annotated
association                  link between gene product and GO term
evidence                     evidence type and reference for an assoc
gene_product_count           recursive product counts per GO term

*seqdb - a database containing GO terms, gene products and the
sequences associated with these gene products. This db subsumes the
two above. It populates these additional tables:

seq                          biological sequence
gene_product_seq             link between a product and a sequence
seq_dbxref                   external database links for a sequence

NOTE: there are other unpopulated tables - we may or may not decide to
populate these at some point in the future.

*seqdblite - this is the same as seqdb, except all IEA associations
have been removed. The IEA associations provide relatively little
value compared to the curated associations, and they slow querying
down immensely. This is the distribution that AmiGO runs off of. We
are working on optimisations to allow AmiGO to run off of the full
seqdb release.

the TYPE is either
    ----

.xml - RDF XML export of the database. this comes as one single
file. Note there is no RDF XML export of seqdb, as we do not include
sequences in the xml yet. We do not include IEA evidence associations
in the xml. We may decide to split this xml file into multiple files
at a later date.

.tables - this is a directory containing the MySQL dump, see below

.sql - SQL CREATE TABLE and INSERT statements for building a local
instance of the database. equivalent to the .tables TYPE (but slower
to load)

.fasta - Fasta format sequence files. These are generated from a
combination of the source gene association data and SwissProt sequence
files. There will usually be far fewer sequences than gene products,
as the sequence information is often not provided by the data source
provider. Also, we only include sequences for which a non-IEA
association could be made. The header line includes the GO annotations
for the gene product corresponding to that sequence.


SCHEMA DOCUMENTATION
********************

In this distribution, uncomporess the file:

go_200304-schema-mysql.sql.gz

Which contains the (MySQL ported) schema used in this release 

You can also look at the HTML marked up version of the schema, or
schema diagrams here:

Go to http://www.godatabase.org/dev/database

To guarantee that your schema, code and database release are in sync
you should use the files from the same release.

**********************************
MYSQL USERS

The database export was prepared from a mysql db - you should have no
problem importing it:

tar -zxvf go-200304-TYPE-tables.gz
cd <releasedir>
echo "create database mygo" | mysql
cat *.sql | mysql mygo
mysqlimport mygo *.txt

**********************************
OTHER DBMS USERS

Your database is not supported; but we do have some tips below:

also: the perl api code is mostly DBMS neutral, it should in theory
work on non mysql setups

**********************************
POSTGRES USERS:

TIP: for converting mysql dumps to postgres, try my2pg

http://www.ziet.zhitomir.ua/~fonin/code/

Thanks to Joe Morris of Affymetrix for the tip

************************************
ORACLE USERS:

see the directory sql/oracle/ in the go_200304-utilities_src software
distribution

************************************
PROGRAMMERS:

you can access the data using the perl API - see
http://www.godatabase.org/dev

OR look at the perl API release for the data release:

tar -zxvf go_200304-utilities_src.tar.gz
cd go_200304-utilities_src
cd perl-api
perldoc GO/AppHandle.pm

sometimes the perl API must be in sync with the database, eg if the
schema changes in a way to break old code

*************************************
AMIGO:

you can build a local AmiGO installation using the source code and
data included in this distribution. You can load your own data into it
using either the scripts in go-dev/apps/db-loading, or the configure
script and makefile in go-dev/sql


volunteers to write documentation on making this process simple much
appreciated - if you want to contribute,

email: Chris Mungall <cjm@fruitfly.org>
or:    go-database@fruitfly.org

note - you will have a better chance of response emailing the mail
list. even then, don't be miffed if you don't get a response for a
while, other projects often divert me from GO related stuff.