The document is a status report on a degree project that integrates blipkit/bioprolog for semantic reasoning in Bioclipse. It compares two reasoners, Pellet and Blipkit, focusing on biochemical questions formulated as Prolog queries in terms of speed and expressiveness. The project has successfully integrated Blipkit, conducted initial performance testing, and outlines further tasks including NMR spectrum similarity search and further comparisons between Prolog and Pellet.

1. nd
2 Status report of degree project
Integrating Blipkit/BioProlog
for semantic reasoning in Bioclipse
Samuel Lampa, 2010-01-25
Project blog: http://saml.rilspace.com

2. Some background...

3. What is “Semantic Web”?

4. What is Semantic Web?
“Enabling more powerful use of information”
Main goals:
● Data availability (on the web)
● Machine-readability of data
● Knowledge integration
● Automatic “conclusion drawing”
● “Reasoning”, using Reasoners →

5. This project compares
two reasoners:
Pellet and Blipkit

6. Research question

7. Research question
How do biochemical questions
formulated as Prolog queries
compare to other solutions
available in Bioclipse in terms of
speed and expressiveness?

8. Semantic Reasoners
● Pellet/Jena
● Uses W3C languages
– OWL (Class definitions)
– RDF (Facts)
– SPARQL (Querying)
● Blipkit/BioProlog
● Uses Prolog, with W3C languages “on top”
– Class definitions, Facts and Queries either in
W3C languages (“on top” of prolog) or in pure
Prolog!

9. What is Prolog?

10. What is Prolog?
● State facts and rules
● Execute by running queries over these
facts and rules
● Unique features:
● Backtracking
● “Closed-world assumption”

11. Prolog code example

12. Prolog code example
% === SOME FACTS ===
hasHBondDonors( substanceX, 3 ). % “substance X has 3 H-bond donors”
% etc …
% === 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.

13. Prolog code example
% === SOME FACTS ===
hasHBondDonors( substanceX, 3 ). % “substance X has 3 H-bond donors”
% etc …
% === A RULE ("RULE OF FIVE" ÀLA PROLOG) ===
Head Implication (“If [body] then [head]”)
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 conjunction (“and”)
true.
?- isDrugLike(X)
X = substanceX ;
X = substanceY.
Capitalized terms are always variables

14. Prolog code example
% === SOME FACTS ===
hasHBondDonors( substanceX, 3 ). % “substance X has 3 H-bond donors”
% etc …
% === 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) Testing a specific atom (“sutstanceX”)
true.
?- isDrugLike(X)
X = substanceX ; By submitting a variable (“X”), it will be populated with all
instances which satisfies the “isDrugLike” rule
X = substanceY.

15. Where are we now?

16. Project plan

17. What is done so far?

18. What is done so far?
● Integration of Blipkit in Bioclipse
● Done: General purpose methods
● Done: Found usage strategy for combined use of
Bioclipse JS scripting and Prolog
● Comparing Prolog and Pellet
● Done: Simple performance testing
● Now: Stuck on NMR spectrum similarity search
– (No backtracking on arithmetic operators in
SPARQL)

19. What is left?

20. What remains to be done?
● Integration of Prolog / Blipkit
● Refinements?
● Comparing Prolog and Pellet
● NMR spectrum similarity search
– Investigate use of OWL in querying
– Other options? SWRL?
● ChEMBL data
● Toxicity data (opentox.org)

21. Example
Bioclipse / Prolog script

22. Example Bioclipse/Prolog script
blipkit.init();
blipkit.loadRDFToProlog("nmrshiftdata.100.rdf.xml");
// Define a “convenience prolog method”
blipkit.loadPrologCode("
hasPeak( Subject, Predicate ) :-
rdf_db:rdf( Subject,
'http://www.nmrshiftdb.org/onto#hasPeak',
Predicate ).
");
// Call the convenience method (which in turn executes it's
// “body”), and returns all mathing results as an array
var resultList =
blipkit.queryProlog(["hasPeak","10","Subject","Predicate"]);

23. Example Bioclipse/Prolog script
blipkit.init();
blipkit.loadRDFToProlog("nmrshiftdata.100.rdf.xml");
// Define a “convenience prolog method”
blipkit.loadPrologCode("
hasPeak( Subject, Predicate ) :-
rdf_db:rdf( Subject,
'http://www.nmrshiftdb.org/onto#hasPeak',
Predicate ).
"); Prolog rule to load into prolog engine
// Call the convenience method (which in turn executes it's
// “body”), and returns all mathing results as an array
var resultList =
blipkit.queryProlog(["hasPeak","10","Subject","Predicate"]);
Prolog method to call
Limit the number of results Prolog variables

24. Current status of
research question

25. Current status of research question
● Performance
● Prolog won so far. Exceptions?
● Usability
● Prolog very convenient for iterative
wrapping of complex logic.
Can RDF/OWL/SPARQL replicate this?
● Where do RDF/OWL/SPARQL excel?

26. Project plan

27. Thank you!
Project blog: http://saml.rilspace.com

28. Project plan – Current version

29. Project plan – Proposed version