SADI for GMOD: An RDF/OWL Interface for GMOD

SADI for GMOD: An RDF/OWL Interface for GMOD

http://code.google.com/p/sadi/wiki/SADIforGMOD

RDF primer

What is SADI for GMOD?

What is the purpose of SADI for GMOD?

An RDF data set is a list of triples.

In RDF, each statement is encoded as a triple.

An RDF data set

can be visualized

as a graph.

N3 Format

• SADI stands for Semantic Automated Discovery and Integration; it's our standard for RDF web services (more info later)
• SADI for GMOD is a set of CGI scripts for accessing sequence feature data as RDF
• "DAS for RDF"

RDF/XML Format

• Provide an easy way for GMODs to share their data as RDF, using a standardized protocol (SADI)
• Provide infrastructure for data integration across GMODs and other biology resources
• Support development of smarter bioinformatics software:

Merging can also be visualized as the overlay of two graphs.

There is a simple, automated procedure for merging RDF data sets.

=> Distributed queries

=> Automated construction of web service workflows

=> Assembly of datasets from

multiple sources

Demo (distributed query)

What SADI for GMOD services are currently available?

How do I use the services?

(for GMOD users)

SHARE Query Resolution

To bootstrap participation, we are mirroring several GMODs (9 so far):

The SADI for GMOD services are in the public SADI registry.

• AmoebaDB -- E. histolytica
• CGD -- C. albicans
• CryptoDB -- C. hominis
• FlyBase -- D. melanogaster
• Gramene -- A. thaliana
• PlasmoDB -- P. falciparum
• SGD -- S. cerevisiae
• ToxoDB -- T. gondii (RH strain)
• TriTrypDB -- L. major

http://sadiframework.org/registry/services/

Demo Query

SADI for GMOD services are provided for each, e.g.

http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_feature_info

By the way, you can register your own SADI services here too.

"Find FlyBase genes that participate in

glycolysis and overlap genomic region

5,919,623..6,344,662 on chromosome 3L"

Wait a while...

PREFIX feature: <http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/feature?id=>

PREFIX range: <http://sadiframework.org/ontologies/GMOD/RangedSequencePosition.owl#>

PREFIX region: <http://sadiframework.org/ontologies/GMOD/BiopolymerRegion.owl#>

PREFIX strand: <http://sadiframework.org/ontologies/GMOD/Strand.owl#>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX owl: <http://www.w3.org/2002/07/owl#>

PREFIX sio: <http://semanticscience.org/resource/>

PREFIX pathway: <http://lsrn.org/KEGG_PATHWAY:>

SELECT ?flybase_gene_record ?startpos ?endpos ?strand_type

WHERE {

pathway:dme00010 sio:SIO_000132 ?kegg_gene_record . # SIO_000132 = 'has participant'

?kegg_gene_record owl:sameAs ?flybase_gene_record .

?flybase_gene_record sio:SIO_000332 ?flybase_feature . # SIO_000332 = 'is about'

?flybase_feature region:position [

range:coordinate [ rdf:type range:StartPosition; sio:SIO_000300 ?startpos ];

range:coordinate [ rdf:type range:EndPosition; sio:SIO_000300 ?endpos ];

range:in_relation_to [

sio:SIO_000210 [ # SIO_000210 = 'represents'

rdf:type ?strand_type;

sio:SIO_000093 feature:3L # SIO_000093 = 'is proper part of'

]

]

];

FILTER ((?endpos >= 5919623) && (?startpos <= 6344662))

FILTER ((?strand_type = strand:MinusStrand) || (?strand_type = strand:PlusStrand))

}

Submit the query to SHARE.

http://sadiframework.org/registry/register/

Future plans

Acknowledgements

How do I set up the services? (for GMOD providers)

• Chado support (soon!)
• add BLAST service (anything else that you want?)
• use cases and demos
• more GMOD mirrors
• page on GMOD wiki
• distribute with Tripal or GBrowse?

1

2

1

Ben Vandervalk*, Luke McCarthy, Edward Kawas, Michel Dumontier, Mark Wilkinson

James Hogg Research Institute, St. Paul's Hospital, University of British Columbia

Carleton University

*ben.vvalk@gmail.com

2

http://sadiframework.org/