The document discusses using Resource Description Framework (RDF) to represent biological data from sources like UniProt, PDBJ, and KEGG. It provides examples of SPARQL queries that can be used to query and analyze relationships within and across RDF datasets, such as finding gene families present in multiple cyanobacterial species or linking genes to biological pathways and literature citations. Large public RDF datasets are described along with Semantic Web technologies for publishing and querying linked open data.

1. RDF

2. •
•
etc
•
•

3. B=
150B
113B
75B
38B
B
1982 1986 1990 1994 1998 2002 2006 2010

7. ID
Gene Ontology, EC etc

9. RDF
•
• UniProt
• PDBJ DDBJ
•Bio2RDF BioGateway
RDF

10. UniProt RDF
• UniProt
•
• UniProt RDF

11. UniProt
Name Description Source File size #triples
uniprot Protein annotation data UniProt consortium 14G 3.3 B
uniref Clusters of proteins with similar sequences UniProt consortium 7G 900M
uniparc Non-redundant archive of UniProt sequences UniProt consortium 65G 1B
citations Literature citations UniProt consortium 1355M 10,177,308
taxonomy Classification of organisms UniProt consortium 421M 5,041,437
journals Journals UniProt consortium 3M 34,850
pathways Pathways UniProt consortium 1000K 8,865
keywords Keywords UniProt consortium 940K 8,449
locations Subcellular locations UniProt consortium 468K 4,476
tissues TIssues UniProt consortium 572K 7439
components Cellular components (Organelles) UniProt consortium 6K 43
go Gene onotology SBI 25M 263,944
enzymes Classification of enzymes GO consortium 4M 4,476
core.owl Classes and properties for UniProt RDF UniProt consortium 152K

12. #triples
Sesame Java 70 M
4store C 15 B
5store C
Virtuoso C 15.4 B
Jena Java 1.7 B
Bigdata Java 12.7 B
ARC PHP
AllegroGraph Lisp 1B
http://esw.w3.org/LargeTripleStores

13. Protein UniProt
Components encodedIn
core.owl
<owl:ObjectProperty rdf:about="encodedIn">
<rdfs:label rdf:datatype="&xsd;string">encoded in</rdfs:label>
<rdfs:comment rdf:datatype="&xsd;string"
>The subcellular location where a protein is encoded.</rdfs:comment>
<rdfs:domain rdf:resource="Protein"/>
<rdfs:range rdf:resource="Subcellular_Location"/>
</owl:ObjectProperty>

14. RDF purl
http://purl.uniprot.org/{database}/{identifier}
UniProt
http://purl.uniprot.org/core/
Gene URI
http://purl.uniprot.org/core/Gene
type

15. PDBJ, DDBJ RDF
• PDBJ
47 4.7B
• http://www.pdbj.org/rdf ID
• DDBJ INSD: International Nucleotide
Sequence Database 1.2 76
7.6B
• mulgara (http://mulgara.org/)

16. RDF
KEGG Taxonomy 23,238
KEGG GENES Cyanobacteria 708,745
KEGG OC 10,384,602
hmmer Pfam-A vs Cyano 11,881,212
hmmer Pfam-B vs Cyano 7,007,154
Kazusa Annotatioin 2,807,879

17. 1
•
• Synechococcus
• 1.0e-20
• Pfam

18. 1 SPARQL
SPARQL
PREFIX hmmer: <http://hmmer.janelia.org/>
PREFIX kegg: <http://www.kegg.jp/>
PREFIX kg: <http://www.kegg.jp/entry/>
PREFIX pfam: <http://pfam.sanger.ac.uk/>
PREFIX kt: <http://www.kegg.jp/taxon/>
SELECT ?pfam1, ?pfam2, COUNT(DISTINCT(?org))
WHERE {
GRAPH <hmmer_pfam_a_cyano> {
?gene hmmer:hit ?n1 .
?gene hmmer:hit ?n2 .
?n1 pfam:pfam_id ?pfam1 .
?n1 hmmer:i-evalue ?eval1 .
?n2 pfam:pfam_id ?pfam2 .
?n2 hmmer:i-evalue ?eval2 .
}
GRAPH <http://www.kegg.jp/genes> {
?gene kegg:belongs_to ?org .
}
GRAPH <http://www.kegg.jp/taxonomy> {
?org kegg:belongs_to kt:Synechococcus .
}
FILTER (?eval1 < 1.0e-10 && ?eval2 < 1.0e-10 && ?pfam1 != ?pfam2)
};

19. 10
Domain I Domain II #genes #species
RNA_pol_Rpb2 RNA_pol_Rpb2 9 9
_3
G6PD_N _1
G6PD_C 9 9
5_3_exonuc_N 5_3_exonuc 9 9
HIT DcpS_C 9 9
Glyco_hydro_38 Glyco_hydro_38 9 9
C
RNA_pol_Rpb2 RNA_pol_Rpb2 9 9
_6
GARS_N _3
GARS_C 9 9
DSHCT DEAD 9 9
adh_short KR 12 9
EFG_C EFG_IV 10 9
.... 171 9 Synechococcus

20. 2
• KEGG OC
• Cyanobacteria
• Kazusa Annotation PumMed
• KO KEGG Othology

21. 2 SPARQL
SPARQL
PREFIX kegg: <http://www.kegg.jp/>
PREFIX kg: <http://www.kegg.jp/entry/>
PREFIX kt: <http://www.kegg.jp/taxon/>
PREFIX kns: <http://a.kazusa.or.jp/ns/>
SELECT ?oc, ?gene, ?ko, COUNT(DISTINCT(?pm))
WHERE {
GRAPH <http://www.kegg.jp/oc> {
?gene kegg:belongs_to ?oc .
}
GRAPH <http://www.kegg.jp/genes> {
?gene kegg:belongs_to ?taxon .
?gene kegg:linked_to ?cb_gene .
OPTIONAL {
?gene kg:ortholog ?ko .
}
}
GRAPH <http://www.kegg.jp/taxonomy> {
?taxon kegg:belongs_to kt:Cyanobacteria .
}
GRAPH <http://kazusa.or.jp/cyanobase> {
?cb_gene ?p1 ?bm .
?bm ?p2 ?pm .
}
};

22. PumMed ID 10
OC #gene with PMID #PMID
Genes_537709 3 1296
Genes_565278 3 761
Genes_710476 2 527
Genes_189668 1 497
Genes_710587 1 479
Genes_710480 1 416
Genes_711471 1 407
Genes_71824 1 393
Genes_75617 5 381
Genes_711511 1 376

23. Semantic Web
• URI
•
•
• W3C

24. Semantic Web
• SPARQL
->
• ->
•
• ->