* source code: rdffederator - Revision 192: /trunk/src

 http://code.google.com/p/rdffederator/

* step:

1. make the corresponding VoID files

• method 1:

1.1 data download:

drugbank:  http://download.bio2rdf.org/release/3/drugbank/ drugbank.nq.gz 19-Dec-2014 13:23 52M

omim:  http://download.bio2rdf.org/release/3/omim/ omim.nq.gz 11-Nov-2014 03:50 124M

pharmgkb:  http://download.bio2rdf.org/release/3/pharmgkb/ diseases.nq.gz genes.nq.gz rsid.nq.gz drugs.nq.gz offsides.nq.gz twosides.nq.gz 01-Jun-2014 17:54 2.4G or so

1.2 ./generate_void.sh ../data/drugbank.nq drugbank_void.n3

    counting triples and properties
    counting types and entities
    counting distinct objects
    counting distinct subjects

drugbank: time taken: 91 seconds

omim: time taken: 411 seconds

• method 2:

Made the void files with the statistics queries in the following page:  https://github.com/bio2rdf/bio2rdf-scripts/wiki/Bio2RDF-Release-3-Summary-Statistics

2. execute: ./SPLENDID.sh SPLENDID-config.n3 query/query1.txt

For the VoID files with method 1,the following errors occur:

20:13:36 [WARN ] [Rio error] Expected ':', found '>' (465, -1) (ParseErrorLogger
.java:28)
20:13:36 [WARN ] [Rio error] Namespace prefix 'LBSL' used but not defined (465,
-1) (ParseErrorLogger.java:28)
20:13:36 [ERROR] [Rio fatal] Not a valid (absolute) URI: null (465, -1) (ParseEr
rorLogger.java:32)
20:13:36 [ERROR] can not parse VOID file file:/opt/services/fsearch/app/splendid
/void/omim.n3: Not a valid (absolute) URI: null [line 465] (VoidStatistics.java:
407)

check the corresponding void files, and deal with the lines as follows. we simply do the following changes:

void:property fusion> => void:property <fusion>

Result:

Query\time(ms)	time 1	time 2	time 3	time 4	time 5
case1	6724	4763	4766	4765	4763