ORACLE9i INSTALLATION AND GUS ARCHITECTURE DOCUMENT
AT Center for Tropical and Emerging Global Diseases
Chetna Warade
chetna@uga.edu
waradec@yahoo.com
To install Genomics Unified Schema following the are the softwares/packages required:
First lets take a step by look at the installation process.
CHAPTER 1
ORACLE 9i
Important Note: Some browsers will uncompress the files but leave the
extension the same (gz) when downloading. If the above steps do not work
for you, try skipping step 1 and go directly to step 2 without changing
the filename. Eg. "cpio -idmv <Linux9i_Disk1.cpio.gz"
c. Create a user id in the oracle website. This user id is very useful for
debugging purposes. With this user id one can use the online documentation.
2) Installation of following modules from Oracle9i Enterprise Edition:
Oracle9i Database
- Data Warehouse
Oracle9i Client
- Administrator
- Runtime
Oracle9i Management and Integration
- Oracle Management Server
- Oracle Internet Directory (failed installation)
3) Preinstallation steps:
Setup Tasks to Perform as root User
S11kernelpara -> /etc/init.d/kernelpara.sh In /etc/rc.d/rc3.d create symbolic link
S11kernelpara -> /etc/init.d/kernelpara.sh
Login Name: oracle Primary GID: 510 (dba) Secondary GID: 511 (oinstall) Home directory: /home/oracle
Setup Tasks to Perform as oracle User
DISPLAY The name, server number and screen number where
of the system where Oracle Universal Installer
display its GUI
PATH Shell's search path for executables
4) Installation
Oracle Universal Installer
If this is the first time any Oracle9i product has been installed on the current system, the File Locations window appears. Specify the base directory where you want to install the Oracle software. i.e /home/oracle/OraHome1
The File Locations window appears. Do not change the text in the Source field. The Source field specifies the location of the installation files.
You must install Oracle9i products into a new Oracle home directory. You
cannot install Oracle9i products into a directory that contains older
versions of the software.
After selecting Oracle9i database from the Available Products window, the
Installation Types window appears.
- Select Enterprise, Standard, then click Next.
Oracle9i Enterprise Edition Installation
1. Select the appropriate database and click Next.
If you select... Then Oracle Universal Installer...
General Purpose Installs a preconfigured database
optimized for general purpose usage.
Transaction Processing Installs a preconfigured database optimized
for transaction processing.
Data Warehouse Installs a preconfigured database optimized
for data warehousing and OLAP.
Customized Allows you to create a customized database.
This option takes longer than the
pre-configured options.
Software Only Installs software only and does not run any
configuration tools.
NOTE - I selected Data Warehouse option. GUS is a Dataware House
- Click Next.
- The Database Identification window appears.
- Enter the Global Database Name and System Identifier (SID) in the
appropriate fields: i.e GUS (TGUS)
- Click Next. The Database File Location window appears.
- In the Directory for Database Files field, enter the directory location
of the database file, i.e /db_storage.
- Click Next. The Database Character Set window appears
Choose the database character set that you want to use from the
available options i.e default
- Click Next. The Summary window appears.
- Review the information to ensure that you have enough disk space and
click Install.
The Install window appears and displays a progress meter. The Installer
goes through the install and relinking phases, so the meter adjusts for
each phase completion.
NOTE - It takes a while for completion.
- Run the root.sh script when prompted.
The Installer creates the root.sh script in the Oracle home directory and prompts you to run the script when it finishes installing Oracle products. Log in as the root user and run the script. The root.sh script sets the
necessary file permissions for Oracle products and performs other
root-related configuration activities. To run the root.sh script use the following commands:
# cd $ORACLE_HOME
# ./root.sh
When the root.sh script runs successfully, return to the Oracle Universal Installer, and click OK in the Alert window.
Click Exit to exit the Oracle Universal Installer, or click Next Install
to install additional products. Selecting Next Install returns you to the Oracle Universal Installer File Locations window.
5. Post Installation
Configuration Tasks to Perform as the root User
-Automating Database Startup and Shutdown The dbstart and dbshut scripts are located in the $ORACLE_HOME/bin directory
Perform the following tasks to set up the dbstart and dbshut scripts so that they are called at system startup. This process must be completed for every new database that you want to configure for automated startup and shutdown.
ORACLE_SID:ORACLE_HOME:{Y|N}
In the preceding command, Y or N specifies whether you want the dbstart
and dbshut scripts to start up and shut down the database. For each
database that you want to start up, find the ORACLE_SID entry identified by the sid in the first field. Change the last field for each to Y.
2. In the /etc/rc.d/init.d directory, create a dbora script.
3. Create symbolic links to the dbora script in the appropriate run-level
script directories, as follows:
/etc/rc.d/rc0.d/K10dbora
/etc/rc.d/rc3.d/S30dbora
/etc/rc.d/rc4.d/S30dbora
/etc/rc.d/rc5.d/S30dbora
Configuration Tasks to Perform as the oracle User
umask 0022
EPC_DISABLED=F
export EPC_DISABLED
ORACLE_BASE=/db_storage/Oracle
export ORACLE_BASE
ORACLE_HOME=/home/oracle/OraHome1
export ORACLE_HOME
CLASSPATH=$ORACLE_HOME/JRE/lib:$ORACLE_HOME/product/jlib
export CLASSPATH
LD_LIBRARY_PATH=$ORACLE_HOME/lib
export LD_LIBRARY_PATH
ORACLE_SID=GUS
export ORACLE_SID
TNS_ADMIN=$ORACLE_HOME/network/admin
export TNS_ADMIN
DISPLAY=mango.ctegd.uga.edu:0.0
export DISPLAY
HOME=/home/oracle
export HOME
PATH=:$ORACLE_HOME/bin:/usr/local/netscape:/usr/local/Acrobat5/bin/:$PATH:$HOME/bin
export PATH
unset USERNAME
Post-Installation for Installed Oracle Products
Basic configuration of Oracle Net Services is done by Oracle Net Configuration Assistant when it is started by Oracle Universal Installer during installation.
Verify and complete your initial configuration with the following steps:
listener_name 1521/tcp #Oracle Net listener
i.e LISTENER 1521/tcp
In the preceding command, 1521 is the default port number. If you chose a different port when you configured the Oracle Net listener, specify that
port in the /etc/services file.
2. Check the status of the listener following the installation by using the following command:
$ lsnrctl status listener_name
i.e $ /home/oracle/OraHome1/bin/lsnrctl status LISTENER
The listener_name field is required if the listener has a name other than the default listener.
If the listener is not running, start it by using the following command:
$ lsnrctl start listener_name
i.e $ /home/oracle/OraHome1/bin/lsnrctl start LISTENER
3. Install and configure Oracle client software on a remote system, if
necessary, then start SQL*Plus to test the connection to the server.
$ sqlplus username/password@net_service_name
i.e sqlplus scott/tiger@gus
If you can successfully connect to the server with SQL*Plus, you have
established network connectivity over TCP/IP.
5. Using Oracle Net Configuration Assistant After installation is complete, a more detailed configuration can be accomplished using the Oracle Net Configuration Assistant by using the following command in the $ORACLE_HOME/bin directory:
$ netca
Oracle Net Configuration Assistant configures the Oracle client/server network environment. It modifies the configuration files located in the default $ORACLE_HOME/network/admin directory. Review the Oracle Net Configuration Assistant procedure for your product installation choice.
Oracle9i Database Enterprise Edition and Standard Edition Installation
For Enterprise and Standard installations, the Oracle Net Configuration Assistant performs the following task:
Configures the Oracle Net server environment by configuring the following files:
listener.ora: Oracle Net Services configures a listener with the name and protocol address you select. Oracle Net Services also configures a protocol address and static service information for external procedures.
sqlnet.ora: Oracle Net Services configures the server's network domain as the default domain, which is the same as the network domain of your system. The domain is automatically appended to any unqualified net service name given in the connect string. The sqlnet.ora file also configures the naming methods the server uses to resolve a name to connect descriptor.
tnsnames.ora: Oracle Net Services creates a net service name entry to use for external procedure connections.
6. Using Database Configuration Assistant Start Database Configuration Assistant by using the dbca command located in the $ORACLE_HOME/bin directory:
$ dbca
Database Configuration Assistant enables you to copy an Oracle9i preconfigured database, or create a fully customized database to match your selected environment and database configuration. It starts automatically after Oracle9i software has been installed during Oracle9i installation.
When installing Oracle9i software using any database configuration option other than the Custom and Software Only, the Oracle Universal Installer prompts for a global database name and System Identifier (SID). After Oracle9i installation is completed, the Database Configuration Assistant uses this information to create the database. In addition, the Database Configuration Assistant automatically configures the static service information for the Oracle9i database in the listener.ora file.
In our case we need Data Warehouse option: If you select this, the Database Configuration Assistant creates a database that is fully enabled for data warehousing applications. The OLAP option, consisting of support for analytic workspaces and the OLAP catalog metadata repository (CWMLite), is included in the database.
7. Using Oracle Enterprise Manager Configuration Assistant Oracle Enterprise Manager Configuration Assistant is used to configure the local Oracle Management Server. You can configure the local Oracle Management Server by creating, upgrading or deleting an Oracle Enterprise Manager repository.
Start OEM by
$ oemapp console
8. Installation logs are generated in the directory /home/oracle/oraInventory/logs
Logs can be viewed to preview what options were selected during installation.
9. Whenever a new database is created system file called as initYourDataBaseName.ora is created in the directory $ORACLE_HOME/dbs.
Alternative:
CREATING A SERVER PARAMETER FILE
The server parameter file must initially be created from a traditional text initialization parameter file. It must be created prior to its use in the STARTUP command. The CREATE SPFILE statement is used to create a server parameter file. You must have the SYSDBA or the SYSOPER system privilege to execute this statement.
The following example creates a server parameter file from initialization parameter file /u01/oracle/dbs/init.ora. In this example no SPFILE name is specified, so the file is created in a platform-specific default location and is named spfile$ORACLE_SID.ora.
CREATE SPFILE FROM PFILE='/u01/oracle/dbs/init.ora';
Another example, below, illustrates creating a server parameter file and supplying a name.
CREATE SPFILE='/u01/oracle/dbs/test_spfile.ora' FROM PFILE='/u01/oracle/dbs/test_init.ora';
The server parameter file is always created on the machine running the database server. If a server parameter file of the same name already exists on the server, it is overwritten with the new information.
Oracle recommends that you allow the database server to default the name and location of the server parameter file. This will ease administration of your database. For example, the STARTUP command assumes this default location to read the parameter file.
When the server parameter file is created from the initialization parameter file, comments specified on the same lines as a parameter setting in the initialization parameter file are maintained in the server parameter file. All other comments are ignored.
The CREATE SPFILE statement can be executed before or after instance startup. However, if the instance has been started using a server parameter file, an error is raised if you attempt to recreate the same server parameter file that is currently being used by the instance.
Note:
When you use the Database Configuration Assistant (DBCA) to create a database, it can automatically create a server parameter file for you.
10. Starting up the database using the oracle user login. Login as oracle user.
$sqlplus "/ as sysdba" Because this is considered as the most secure
oracle login no password is asked.
SQL> startup
STARTUP USAGE
Starts an Oracle instance with several options, including mounting, and opening a database.
STARTUP options | migrate_options
where options has the following syntax:
[FORCE] [RESTRICT] [PFILE=filename] [QUIET] [ MOUNT [dbname] |
[ OPEN [open_options] [dbname] ] |
NOMOUNT ]
where open_options has the following syntax:
READ {ONLY | WRITE [RECOVER]} | RECOVER
and where migrate_options has the following syntax:
[PFILE=filename] MIGRATE [QUIET]
BUGS
Whenever oracle user logs in, should set the ORACLE_SID env variable
$ ORACLE_SID=GUS
$ export ORACLE_SID
$ sqlplus /nolog
CHAPTER 2
GUS 3.0 SCHEMA INSTALLATION
GUS 3.0 source code/binaries (doesn't matter as PERL is used) are available at http://cvsweb.sanger.ac.uk/ under project name GUS. Follow the cvs instructions on the web site.
There are two domains in GUS 3.0 a project domain and a central
place for gus installation. The GUS build system (ANT based) allows
users to install latest copies of the source at one central location
(also accessible for all users on the system). More information is
available http://www.gusdb.org/documentation/install-setup.html
SCHEMA INSTALLATION:
In order to install the GUS 3.0 schema in the database create a new database in Oracle using instructions for Oracle 9i in chapter 1 or use an existing Oracle database. Use the oracle user account "sys" for creating the GUS 3.0 schema and users. Run the script create-db.sh after modifying the sys password (depending on what passwd you have selected for your database) in it. The script create-db.sh creates five schemas/users Core,SRes, DoTS, TESS and RAD3 with passwords password1, password2, password3, password4 and password5 respectively for simplicity. It is recommended that the database administrator should change the passwords for security reasons.
CHAPTER 3
JAVA 2 PLATFORMS
Following are the Java Platforms required for GUS user/www interface development.
JAVA 2 STANDARD EDITION - J2SDK 1.4.1_01
Download Java 2 SDK, Standard Edition 1.4.1_01
-----------------------------------------------------------------
Go to web page http://java.sun.com/j2se/1.4.1/download.html
Click on the "Download" link in the row that contains Linux self-
extracting file and column SDK.
Read the license agreement and if you agree with it Click on Accept.
Click on the link "Download j2sdk-1_4_1_01-linux-i586.bin"
Save this file to your disk.
Refer to the link for installation help at (if required)
http://java.sun.com/j2se/1.4.1/install-linux.html
1) Check the download file size.
2) Copy j2sdk-1_4_1_01-linux-i586.bin to the /usr/local directory
to provide java environment system-wide.
3) Run j2sdk-1_4_1_01-linux-i586.bin
Unbundling the software automatically creates a directory called
j2sdk1.4.1_01. Note that if you choose to install the Java 2 SDK into
system-wide location such as /usr/local, you must first become root to
gain the necessary permissions. If you do not have root access, simply
install the Java 2 SDK into your home directory, or a subdirectory that you have permission to write to.
JAVA 2 ENTERPRISE EDITION - J2SDKEE 1.3.1
Download Java 2 SDK, Enterprise Edition 1.3.1
-----------------------------------------------------------------
Go to web page http://java.sun.com/j2ee/download.html
Under the section "1.3.1 FCS Release January 31, 2002" click the
link "Software & Documentation" or http://java.sun.com/j2ee/sdk_1.3/
Scroll down the web page and select a platform (Linux) and click
continue.
Read the license agreement and if you agree with it Click on Accept.
Select a mode of tranfer either HTTP or FTP.
Save this file to your disk.
Refer to the link for installation help at (if required)
http://java.sun.com/j2ee/sdk_1.3/install.html#linux_soft
1) Check the download file size.
2) cd /usr/local
Unpacking the bundle automatically creates a subdirectory in this
directory called j2sdkee1.3.1.
3) The download bundle for the software is in the
j2sdkee-1_3_1-linux.tar.gz file. To uncompress and unpack the download
bundle and run this command:
tar xvzf j2sdkee-1_3_1-linux.tar.gz
The j2sdkee1.3.1 directory is created and the software is installed
into it.
4) Set the environment variables.
Before running the J2EE SDK, you must set these environment variables
in your .profile or .bash_profile file of your login:
J2EE_HOME - the directory where you've installed this release.
JAVA_HOME - the directory where the Java 2 SDK Standard Edition is
installed.
PATH - include the bin directory beneath the directory where you've installed this release.
If you need help setting these variables, paste the link
http://java.sun.com/j2ee/sdk_1.3/install.html#env-var.
You need to logout and login again for these changes to take effect.
JAVA WEB SERVICES DEVELOPER PACK - JWSDP 1_0_01
Download Java Web Services Developer Pack 1.0_01
-----------------------------------------------------------------
Go to web page http://java.sun.com/webservices/downloads/webservicespack.html
Scroll down the web page and select platform as UNIX because there is no specific differences in Linux/UNIX version of JWSDP and click continue.
Read the license agreement and if you agree with it Click on Accept.
Select a mode of tranfer either HTTP or FTP.
Save this file to your disk.
Refer to the link for installation help at (if required)
http://java.sun.com/webservices/downloads/install-unix.html
1) Check the download file size
If you saved the self-installing executable to disk without running it from the download page at the Java Software website, check to see that you have the complete file:
example: jwsdp-1_0_01-unix.sh 31,732,238 bytes
2) Run the Java WSDP installer
$ /bin/sh jwsdp-1_0_01-unix.sh
Installed Directory Tree
Verify that the Java WSDP has the directory structure shown below.
* jwsdp-1_0_01
* LICENSE
* bin
* common
* conf
* config
* docs
* images
* lib
* logs
* samples
* server
* services
* shared
* temp
* tools
* unist
* webapps
* work
* xsl
3) Update the PATH variable
You can run the Java WSDP without setting the PATH variable, or you can optionally set it as a convenience.
4) Set the PATH variable if you want to be able to conveniently run the Java WSDP executables (startup.sh, shutdown.sh, ant, etc.) from any
directory without having to type the full path of the command. If you don't set the PATH variable, you need to specifythe full path to the executable every time you run it, such as:
$ /home/myuser/jwsdp-1_0_01/bin/startup.sh
It's useful to set the PATH permanently so it will persist after
rebooting. To set the PATH permanently, add the full path of the bin directory in the Java WSDP installation directory to the beginning of your PATH variable. Typically this full path looks something like
/home/myuser/jwsdp-1_0_01/bin.
Download Ant build tool version 1.5.1 for building (compilation) and installation of source code and binaries on the machine from http://ant.apache.org/bindownload.cgi.
Note: GUS 3.0 is tested with Ant 1.5.1 version and is used as the build tool at CBIL and CTEGD.
SETTING ENVIRONMENT/LOGIN FOR GUS 3.0
A sample .bash_profile file for using Oracle9i, GUS schema, Java and Perl in entirety is:
# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
# User specific environment and startup programs
export ORACLE_HOME=/home/oracle/OraHome1
export J2EE_HOME=/usr/local/j2sdkee1.3.1
export JAVA_HOME=/usr/local/j2sdk1.4.1_01
export JWSDP_HOME=/usr/local/jwsdp-1_0_01
export TOMCAT_PATH=:/usr/local/jwsdp-1_0_01/common/lib/servlet.jar:/usr/local/jwsdp-1_0_01/docs/tutorial/examples/cb/jaxrpc/build/client:/usr/local/jwsdp-1_0_01/docs/tutorial/examples/cb/jaxrpc/build/server:/usr/local/jwsdp-1_0_01/docs/tutorial/examples/cb/jaxrpc/build/service-class:/usr/local/jwsdp-1_0_01/docs/tutorial/examples/cb/jaxrpc/build/registry
export CLASSPATH=$JAVA_HOME/lib/tools.jar:$JAVA_HOME/jre/lib/rt.jar:$TOMCAT_PATH
export PATH=:/usr/local/netscape:/usr/local/Acrobat5/bin/:$JAVA_HOME/bin:$JWSDP_HOME/bin:$ORACLE_HOME/bin:$PATH:$HOME/bin
export GUS_HOME=/home/gusdev/gus.2.0.1/source-code/gusdev-src-sep-10-2002
export LD_LIBRARY_PATH=/home/oracle/OraHome1/lib
export PERL5LIB=$GUS_HOME/perl/lib:$GUS_HOME/lib
export CATALINA_HOME=/usr/local/jwsdp-1_0_01
export GUS_CFG=$GUS_HOME
export DBI_DSN="dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS"
export ORACLE_SID=GUS
NOTE
1) Setting up the env variable CLASSPATH is very important otherwise it
may cause problems in using java compilers and java tools like run-time
linker/debugger.
2) Refer http://www.gusdb.org/documentation/install-setup.html for setting environment variables for GUS 3.0
JAVA SERVLET INTERFACE INSTALLATION INSTRUCTIONS: GENERAL
-Download the external Java libraries mentioned in the prerequisites. -Edit $GUS_HOME/www/install/installServletNew.pl; the section labeled "EDIT THIS SECTION AS NEEDED" contains a number of variables that must be set to tell the script where to find and place a number of files.
-Set the ORACLE_HOME and LD_LIBRARY_PATH environment variables as described in the
prerequisites; both in the environment of the user that will run Tomcat and also
in the Apache httpd.conf file (with 'SetEnv' directives)
-cd into the $GUS_HOME/www/install directory and run installServletNew.pl
-Edit the installed web.xml file as neeeded
-Start the servlet engine
-Check the following logs for any errors:
/var/log/httpd/error_log (i.e., httpd error log)
$CATALINA_HOME/logs/*
servlet log file (location depends on what is specified in web.xml)
JAVA SERVLET INTERFACE INSTALLATION INSTRUCTIONS: GUS 3.0
In addition to following the steps the section JAVA SERVLET INTERFACE INSTALLATION INSTRUCTIONS: GENERAL you need to download tag libraries (binary) from http://www.apache.org/dist/jakarta/taglibs/standard/binaries/ for GUS 3.0
CHAPTER 4
LEARNING GUS 3.0
GUS 3.0 source code/binaries (doesn't matter as PERL is used) are
available at http://cvsweb.sanger.ac.uk/ under project name GUS. Follow
the cvs instructions on the web site.
PERL MODULES:
Following are the PERL modules needed for GUS 3.0 and are available at http://cpan.org:
Note: The latest GD 2.07 is available but requires libgd 2.0.12 or higher located in /usr/lib directory (default linux installation - may vary depending on system configuration)
Background:
Suppose in a bioinformatics laboratory there are different projects
undertaken and there are several groups working on projects. A
GUS/database user belongs to a group (e.g. to the bioinformatics lab)
and can work on several projects at the same time. Accordingly then
information goes to table Core.ProjectInfo, Core.GroupInfo and
Core.UserInfo (read further for more information).
Creating GUS 3.0 users:
There are two types of users in GUS system: an Oracle/database user and
the GUS 3.0 user. The Oracle/DB user account allows user to login into
Oracle database using command line utility like SQLPlus and perform
various database related operations. A GUS user account is created
using both Oracle user account and the machine/system/operating system
user account. This two level user account helps maintain tight security
and controlled information flow within the organization and GUS as well
(GUS/database could be synonyms in this case).
Following are steps required for GUS Administrator/DBA to start GUS 3.0 from scratch (could also create am .sql script): INSERT INTO CORE.AlgorithmParamKeyType VALUES(0,'string',SYSDATE,1,1,1,1,1,1,1,1,1,1); INSERT INTO CORE.AlgorithmParamKeyType VALUES(1,'float',SYSDATE,1,1,1,1,1,1,1,1,1,1); INSERT INTO CORE.AlgorithmParamKeyType VALUES(2,'int',SYSDATE,1,1,1,1,1,1,1,1,1,1); INSERT INTO CORE.AlgorithmParamKeyType VALUES(3,'ref',SYSDATE,1,1,1,1,1,1,1,1,1,1); INSERT INTO CORE.AlgorithmParamKeyType VALUES(4,'boolean',SYSDATE,1,1,1,1,1,1,1,1,1,1); INSERT INTO CORE.AlgorithmParamKeyType VALUES(5,'date',SYSDATE,1,1,1,1,1,1,1,1,1,1);
NOTE: It is imperative that the DBA will set the read/write permission according to the security and row_user_id, row_group_id and row_project_id depending on custom data.
Following are steps required for GUS Administrator/DBA to create GUS 3.0 users:
Help can be viewed by e.g.
ga GUS::Common::Plugin::LoadTaxon --help
Debugging can be done using --debug, --verbose or --veryVerbose options and not using --commit option. By default --commit is set as off.
NOTE: use all the three options of ga GUS::Common::Plugin::LoadTaxon --gencode, --names and --nodes at the same time/together
2) GenBank
e.g. Sres.ExternalDatabase
insert into sres.externaldatabase values('GenBank (nrdb)','genbank (nrdb)', SYSD ATE,1,1,1,1,1,0,6,3,2,1);
Sres.ExternalDatabaseRelease
insert into sres.externaldatabaserelease values(135,1,15-APR-03,'Tcruzi', SYSDATE,1,1,1,1,1,0,6,3,2,1);
and Dots.SequenceType (create a .sql script)
insert into Dots.sequencetype values (1,'DNA',null,null,1,1,'DNA', 'DNA,unkown standedness',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (2,'RNA',null,null,1,1,'RNA', 'RNA,unkown standedness',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (3,'DNA',null,'ds',2,1,'ds-DNA', 'double stranded DNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (4,'DNA',null,'ss',2,1,'ss-DNA', 'single stranded DNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (5,'DNA',null,'ss',2,2,'ss-RNA', 'single stranded RNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (6,'RNA',null,'ds',2,2,'ds-RNA', 'single stranded RNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (7,'RNA','mRNA','ss',3,5,'mRNA', 'mRNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (8,'RNA','est','ss',3,5,'EST', 'EST - could be mRNA, rRNA...',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (9,'RNA','tRNA','ss',3,5,'tRNA', 'tRNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (10,'RNA','rRNA','ss',3,5,'rRNA', 'rRNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (11,'unknown',null,null,1,11,'unknown', 'unkown',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (12,'RNA','predicted_mRNA','ss',2,1,'predicted_mRNA', 'mRNA sequence predicted by an algorithm from genomic DNA',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (13,'virtual',null,null,1,null,'virtual', 'virtual nuclieic acid sequence',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (14,'DNA','GSS','ds',3,3,'GSS', 'Genome Survey Sequence',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Dots.sequencetype values (15,'DNA','oligonucleotide','ss',3,4,'oligonucleotide', 'synthetic single stranded oligonucleotide ',SYSDATE,1,1,1,1,1,0,6,3,2,1);
3) GOOntology
e.g. SRes.ExternalDatabase
##These id values 92,93,94 are used because they were the next in order.. insert into Sres.Externaldatabase values(92,'GO Function','go function',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Sres.Externaldatabase values(93,'GO Component','go component',SYSDATE,1,1,1,1,1,0,6,3,2,1); insert into Sres.Externaldatabase values(94,'GO Process','go process',SYSDATE,1,1,1,1,1,0,6,3,2,1);
SRes.GORelationshiptype
insert into sres.GORelationshiptype values(1, 'isa',SYSDATE, 1,1,1,1,1,0,6,3,2,1); insert into sres.GORelationshiptype values(2, 'partof',SYSDATE, 1,1,1,1,1,0,6,3,2,1);
NOTE: Since we loaded GO data from scratch we encountered problems in ancestor_go_term_id in table SRes.GOTerm. Login as SReS in the database and modify as following:
alter table goterm modify (ancestor_go_term_id number(10) null);
NOTE: 05/22/2003
We had comment off line 500 to overcome an error but I guess in future this willgo away as GUS is constantly evolving.
(line 500 of LoadGoOntology.pm):
my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
go_id => $rootGoId,
external_database_release_id => $extDbRelId,
source_id => $rootEntry->getId(),
name => $rootEntry->getName(), #just the name
definition => $rootEntry->getName(),
minimum_level => 0,
maximum_level => 0,
number_of_levels => 1,
ancestor_go_term_id => $tempAncestorId, <=== COMMENT THIS LINE
} );
4) TIGR XML data
Under Construction