2nd Status report of degree project

Integrating Blipkit/BioProlog for semantic reasoning in Bioclipse

Samuel Lampa, 2010-01-25Project blog: http://saml.rilspace.com

2nd Status report of degree project

Integrating Blipkit/BioProlog for semantic reasoning in Bioclipse

Samuel Lampa, 2010-01-25Project blog: http://saml.rilspace.com

Some background...Some background...

What is “Semantic Web”?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 →

What is Semantic Web?What is Semantic Web?

This project compares two reasoners: Pellet and Blipkit

This project compares two reasoners: Pellet and Blipkit

Research questionResearch question

How do biochemical questions

formulated as Prolog queries

compare to other solutions

available in Bioclipse in terms of

speed and expressiveness?

Research questionResearch question

● 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!

Semantic ReasonersSemantic Reasoners

What is Prolog?What is Prolog?

● State facts and rules● Execute by running queries over these

facts and rules

● Unique features:● Backtracking● “Closed-world assumption”

What is Prolog?What is Prolog?

Prolog code exampleProlog 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.

Prolog code exampleProlog 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.

Prolog code exampleProlog code example

Body

Head Implication (“If [body] then [head]”)

Comma means conjunction (“and”)

Capitalized terms are always variables

% === 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.

Prolog code exampleProlog code example

By submitting a variable (“X”), it will be populated with all instances which satisfies the “isDrugLike” rule

Testing a specific atom (“sutstanceX”)

Where are we now?Where are we now?

Project planProject plan

What is done so far?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)

What is What is donedone so far? so far?

What is left?What is left?

● 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)

What remains to be done?What remains to be done?

Example Bioclipse / Prolog script

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 arrayvar resultList =blipkit.queryProlog(["hasPeak","10","Subject","Predicate"]);

Example Bioclipse/Prolog scriptExample 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 arrayvar resultList =blipkit.queryProlog(["hasPeak","10","Subject","Predicate"]);

Example Bioclipse/Prolog scriptExample Bioclipse/Prolog script

Prolog rule to load into prolog engine

Prolog method to callLimit the number of results Prolog variables

Current status of research questionCurrent 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?

Current status of research questionCurrent status of research question

Project planProject plan

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

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

Project plan – Current versionProject plan – Current version

Project plan – Proposed versionProject plan – Proposed version