Samuel Lampa presented his MSc thesis on integrating SWI-Prolog as a semantic querying tool in Bioclipse. He demonstrated [1] how SWI-Prolog can be used for semantic querying of biological data in RDF format within Bioclipse, [2] examples of SPARQL and Prolog code used to perform semantic queries, and [3] benchmarking of Prolog's performance as a semantic querying tool. The work adds new semantic querying functionality to Bioclipse using SWI-Prolog and demonstrates its ability to efficiently query biological data.

1. MSc Thesis presentation:
SWI-Prolog as a Semantic Web tool for
semantic querying in Bioclipse:
Integration and performance benchmarking
Samuel Lampa <http://saml.rilspace.org>
Supervisor: Egon Willighagen <http://chem-bla-ics.blogspot.com>
Bioclipse & Proteochemometric group (Prof. Jarl Wikberg)
Department of Pharmaceutical Bioinformatics
Uppsala University
2010-06-18

3. What is Bioclipse?

6. What is the
Semantic Web?

7. What is the Semantic Web?

9. RDF Example (In Notation 3 format)
@prefix
: <http://www.nmrshiftdb.org/onto#> .
xsd: <http://www.w3.org/2001/XMLSchema#> .
nmr: <http://pele.farmbio.uu.se/nmrshiftdb/?>
nmr:moleculeId=234 :hasSpectrum nmr:spectrumId=4735 ;
:moleculeId "234" .
nmr:spectrumId=4735 :hasPeak nmr:s4735p0 ,
nmr:s4735p1 ,
nmr:s4735p2 .
nmr:s4735p0 :hasShift "17.6"^^xsd:decimal .
nmr:s4735p1 :hasShift "18.3"^^xsd:decimal .
nmr:s4735p2 :hasShift "22.6"^^xsd:decimal .

10. SPARQL Example
PREFIX fn: <http://www.w3.org/2005/xpath-functions#>
PREFIX nmr: <http://www.nmrshiftdb.org/onto#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT ?s
WHERE {
?s nmr:hasPeak [ nmr:hasShift ?s1 ] ,
[ nmr:hasShift ?s2 ] ,
[ nmr:hasShift ?s3 ] .
FILTER ( fn:abs(?s1 - 17.6) < 0.3 ) .
FILTER ( fn:abs(?s2 - 18.3) < 0.3 ) .
FILTER ( fn:abs(?s3 - 22.6) < 0.3 ) . }

11. What is Prolog?

12. Prolog: Fewer technical layers
Conventional software Prolog

13. % === SOME FACTS ===
Prolog code example hasHBondDonorsCount( substanceX, 3 ).
hasHBondDonorsCount( substanceY, 5 ).
hasHBondDonorsCount( substanceZ, 7 ).
hasHBondAcceptorsCount( substanceX, 7 ).
hasHBondAcceptorsCount( substanceY, 10 ).
hasHBondAcceptorsCount( substanceZ, 13 ).
hasMolecularWeight( substanceX, 320 ).
hasMolecularWeight( substanceY, 500 ).
hasMolecularWeight( substanceZ, 500 ).
% === A RULE ("RULE OF FIVE" ÀLA PROLOG) ===
isDrugLike( Substance ) :-
hasHBondDonorsCount( Substance, HBDonors ),
HBDonors <= 5,
hasHBondAcceptorsCount( Substance, HBAcceptors ),
HBAcceptors <= 10,
hasMolecularWeight( Substance, MW ),
MW < 500.
% === QUERYING THE RULE ===
?- isDrugLike(substanceX)
true.
?- isDrugLike(X)
X = substanceX ;
X = substanceY.

14. % === SOME FACTS ===
Prolog code example hasHBondDonorsCount( substanceX, 3 ).
hasHBondDonorsCount( substanceY, 5 ).
hasHBondDonorsCount( substanceZ, 7 ).
hasHBondAcceptorsCount( substanceX, 7 ).
hasHBondAcceptorsCount( substanceY, 10 ).
hasHBondAcceptorsCount( substanceZ, 13 ).
hasMolecularWeight( substanceX, 320 ).
hasMolecularWeight( substanceY, 500 ).
hasMolecularWeight( substanceZ, 500 ).
Implication (“If [body] then [head]”)
Head A RULE ("RULE OF FIVE" ÀLA PROLOG) ===
% ===
isDrugLike( Substance ) :-
hasHBondDonorsCount( Substance, HBDonors ),
HBDonors <= 5,
hasHBondAcceptorsCount( Substance, HBAcceptors ),
HBAcceptors <= 10,
hasMolecularWeight( Substance, MW ),
MW < 500.
Body
% === QUERYING THE RULE ===
?- isDrugLike(substanceX)
Comma means
true. conjunction (“and”)
?- isDrugLike(X)
X = substanceX ; Capitalized terms are always variables
X = substanceY.

15. % === SOME FACTS ===
Prolog code example hasHBondDonorsCount( substanceX, 3 ).
hasHBondDonorsCount( substanceY, 5 ).
hasHBondDonorsCount( substanceZ, 7 ).
hasHBondAcceptorsCount( substanceX, 7 ).
hasHBondAcceptorsCount( substanceY, 10 ).
hasHBondAcceptorsCount( substanceZ, 13 ).
hasMolecularWeight( substanceX, 320 ).
hasMolecularWeight( substanceY, 500 ).
hasMolecularWeight( substanceZ, 500 ).
% === A RULE ("RULE OF FIVE" ÀLA PROLOG) ===
isDrugLike( Substance ) :-
hasHBondDonorsCount( Substance, HBDonors ),
HBDonors <= 5,
hasHBondAcceptorsCount( Substance, HBAcceptors ),
HBAcceptors <= 10,
hasMolecularWeight( Substance, MW ),
MW < 500.
% === QUERYING THE RULE ===
Testing a specific atom
?- isDrugLike(substanceX)
(“sutstanceX”)
true.
?- isDrugLike(X) By submitting a variable “X”,
X = substanceX ; it will be populated with all
instances which satisfies
X = substanceY.
the “isDrugLike” rule

16. Prolog: Fewer technical layers
Conventional software Prolog

17. What was done
in this project?

18. The work done (New functionality in dashed lines)

19. SWI-Prolog in action in Bioclipse

20. SPARQL Code used

21. Prolog code used (1)

24. Prolog code
used (2)

27. Thank you!
Samuel Lampa <http://saml.rilspace.org>
Supervisor: Egon Willighagen <http://chem-bla-ics.blogspot.com>
Bioclipse & Proteochemometric group (Prof. Jarl Wikberg)
Department of Pharmaceutical Bioinformatics
Uppsala University
2010-06-18