Test Platform: Ubuntu 8.04 (Hardy Heron) CREATING OBD ...

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29 Νοε 2012 (πριν από 8 χρόνια και 8 μήνες)

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Test Platform: Ubuntu 8.04 (Hardy Heron)


CREATING OBD PHENOSCAPE DATABASE THROUGH THE PERL SCRIPTS


Command
:


perl obd
-
create
-
db.pl
-
d obdphenoscape
-
c ../conf/obd
-
phenoscape.conf


Perl Scripts are Available at:


http://www.bioontology.org/wiki/index.php/OBD:Main_Page#Project_Page


Changes to Perl Scripts for Ubuntu 8.04




obd
-
create
-
db.pl



Line 170: Changed run(“obd
-
create...”) to run(“
../scripts
/obd
-
create...”)




obd
-
r
easoner.pl



Line 76: Changed DBI
-
>connect(“dbi:Pg:dbname=$d”) to

DBI
-
> connect(“dbi:Pg:dbname=$d
;hostname=localhost;port=5433”, “<uid>”, “<pwd>”
)




obd
-
load
-
db
-
from
-
obo.pl



Line 60: Changed $d = "jdbc:postgresql://localhost:
5432
/$d" to

$d = "jdbc:postgres
ql://localhost:
5433
/$d"



Line 94: Changed my $nu=$1 to my $nu =”/
tmp/
$1”



Line 116: Changed run(“obo2database...”) to run(“
../launch_scripts/
obo2database...”)


Changes to pg_hba.conf to allow universal access



Changed Password parameter to trust for local a
ccess


LOADING DATA FROM Nexus FILES INTO OBD PHENOSCAPE DATABASE


This was accomplished by running OBDModelBridgeTest.java file from org.phenoscape.bridge
package from the Phenote project. Junit test invokes OBDModelBridge class from same package and
pro
ject.


Project is available at:


https://obo.svn.sourceforge.net/svnroot/obo


Changes to org.phenoscape.bridge.OBDModelBridg
e.java in Phenote project to disallow concepts
without proper valid names


Line 93: Added condition to check to disallow taxa without valid names to avoid
NullPointerExceptions


Loaded data from NeXML files




Toledo
-
Piza 2000



Fang 2003



Chen et al 1984*



Conw
ay Mayden 2007 Merged*



De Pinna 1996*



Lucena Menezes 1998*


* Indicates some states and qualities are missing valid names in the data. Loaded data may be


incomplete


Data from some NeXML files cannot be loaded. These are:




Buckup 1998



Vari 1995



Vari Har
old 2001



Lundberg 1992


QUERYING DATA FROM OBD PHENOSCAPE DATABASE


This is done by running OBDQueryTest.java from org.nescent.informatics package.


NOTES
: This was tested on PC running Ubuntu 8.04. (Hardy Heron) Perl Module dependencies were
imported fro
m http://CPAN.org and installed. Dependencies include:


1)

DBI
-
1.607

2)

DBIx::DBStag 0.10

3)

Data::Stag

0.11

4)

IO::String 1.08

5)

DBD::Pg 2.10.6

6)

DBIx::DBSchema 0.34

7)

XML::Parser::PerlSAX 0.08

8)

Parse::RecDescent

9)

FreezeThaw

10)

Version 0.76

11)

Ext::Utils
::MakeMaker 6.44