Download SWAT4LS 2008, November 28 e- Science Institute, Edinburgh, Scotland, UK

KASBi: Knowledge-Based Analysis in Systems
Biology
SWAT4LS 2008, November 28 eScience Institute, Edinburgh,
Scotland, UK
Dr. José F. Aldana Montes ([email protected])
Ismael Navas Delgado ([email protected])
María del Mar Roldán-García
Amine Kerzazi
Othmane Chniber
Joaquín Molina
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Introduction
Ohhh
great,
i’ve
And
Brenda
Ohhh
great,
i’ve
And
Brenda
Uuf,
Nothing.
Uuf,
Nothing.
Let’s
look
in
BioMedNet,
And
Let’s look
in
BioMedNet,
Ufff,
And
Ufff, many
many biological
biological database.
database.
found
something.
this
http://www.brendafound
something.
this
http://www.brendaLet’s
search
Let’s
search
see
was
dd anymore
Let’s
see in
inItItthe
the
wasAnd
ititLet’s
was
this
was
II can’t
this
n
can’t
anymore
n
But
this
not
all
one?
enzymes.info/
u
And
But
this
not
all
one?
enzymes.info/
u
in
And
in this
this
o
And
o
f
other
database
http://www.brendaf
otherhttp://www.brendadatabase
http://www.bmn.com
one?
tt
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one?
o
this
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looking
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database that
that
this
enzymes.info/
enzymes.info/
aa n
t
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one?
a
for!!!!
Kegg
one? DD
a
for!!!!one?
they
told
they
told me
me
one?
And
And
And
And
http://www.genome.jp/kegg/
http://www.genome.jp/kegg/
this
this
this
this
one?
one?
one?
one?
Modeller
Modeller
Data
found
Data
found
http://www.salilab.org/modeller/
http://www.salilab.org/modeller/
Prosite
Prosite
http://www.expasy.ch/prosite
http://www.expasy.ch/prosite
Swiss-prot
Swiss-prot
http://www.expansy.org/sprot/
http://www.expansy.org/sprot/
Introduction
Let’s
Let’s see
see ifif we
we
find
find something
something
about
about this
this
Data Integration System
Data
Data found
found
Stream
Stream requests
requests
Stream
Stream answers
answers
Introduction
What
What can
can II do
do
with
with all
all this
this
“Semantics”?
“Semantics”?
<?xml version="1.0"?><rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cd="http://www.recshop.fake/cd#"> <rdf:Description
rdf:about="http://www.recshop.fake/cd/Empire Burlesque">
<cd:artist>Bob Dylan</cd:artist>
<cd:country>USA</cd:country>
<cd:company>Columbia</cd:company>
<cd:price>10.90</cd:price> <cd:year>1985</cd:year>
</rdf:Description><rdf:Description
rdf:about="http://www.recshop.fake/cd/Hide your heart">
<cd:artist>Bonnie Tyler</cd:artist>
<cd:country>UK</cd:country> <cd:company>CBS
Records</cd:company> <cd:price>9.90</cd:price>
<cd:year>1988</cd:year> </rdf:Description> . . . </rdf:RDF>
Introduction
A semantic reasoner, reasoning engine, rules engine, or
simply a reasoner, is a piece of software able to infer
logical consequences from a set of asserted facts or
axioms.
Wikipedia
Introduction
We need (efficient and scalable) TOOLS for
storing and querying OWL ontologies
Databases
DL Systems
Integration not trivial
Study how different logical and physical (persistent)
storage models influence on the querying
reasoning performance
and
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
KOMF
Planner mechanism
User
User query
query expressed
expressed in
in
Conjunctive
Conjunctive predicates
predicates (Q,O)
(Q,O)
Query
Query plan
plan execution
execution
Mappings
Mappings search.
search.
Resources
Resources search.
search.
Query solver mechanism
Query
Query plan
plan from
from the
the
query
query planner
planner
Ontology
Ontology instances
instances
XML Result
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Related Works
Arquitecture
User
OWL
1
Hierachies
Ontology structure
information
Ontology
parser
Instances
Properties
hierarchy
Classes
hierarchy
Ontology Tbox
Ontology
structure
information
DL reasoner
2
DBMS Oracle
3
DBOWL
database
Storage
Inferred instances
Instaces
DBOWL
Reasoner
Result
Arquitecture
SQL
query
Result
Reasoning and Querying
Reasoning (II)
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Tool Steps
Tool Steps
Tool Steps
Domain
Ontology
mappings
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Case Studies
• Protein Bindings
• Ans(P) :- Protein(P1), name(P1,name), Protein(P),
bindsTo(P1,P);
• Organism identification
• Ans(P) :- Pathway(P), BioSource(O),
name(O,name), organism(P,O);
Case Studies
• Protein Bindings
• Ans(P) :- Protein(P1), name(P1,name), Protein(P),
bindsTo(P1,P);
• Organism identification
• Ans(P) :- Pathway(P), BioSource(O),
name(O,name), organism(P,O);
Case Studies
Case Studies
Case Studies
Case Studies
• Protein Bindings
• Ans(P) :- Protein(P1), name(P1,name), Protein(P),
bindsTo(P1,P);
• Organism identification
• Ans(P) :- Pathway(P), BioSource(O),
name(O,name), organism(P,O);
Case Studies
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Conclusions
• The life science domain has to face a new era in
which the integration of information is an
important issue
• This paper presents a tool that has two main
pillars: an ontology-based mediator (KOMF) and
a persistent reasoner (DBOWL).
– The use of KOMF enables the retrieval of information
useful for end users
– DBOWL is used to create knowledgebases based on
the user query (for making persistent the information
that the user wants to analyze in more sophisticated
ways). It is used to discover new knowledge and even
inconsistencies between different databases.
• Two (three in the paper) use synthetic cases are
shown to demonstrate the need for a reasoner to
find implicit knowledge and inconsistencies.
Index
• Introduction
• Previous Works
– KOMF
– DBOWL
• System
– Architecture
– Case Studies
• Conclusions
• Future Work
Future Work
• Real applications are being developed under de
Amine System Project (http://asp.uma.es).
• The AMMO-Prot 3D Model Finder
(http://asp.uma.es/WebMediator)
• The Systems Biology Metabolic Modeling
Assistant (http://sbmm.uma.es)
• The system will be published
(http://khaos.uma.es/KASBi). Now there is a demo
Video and an online version will be available before
Christmas.
• The most recent improvements in each of its
components will be made available at
http://khaos.uma.es/KASBi.
Contact
KHAOS
KOMF
DBOWL
Dr. José F. Aldana Montes ([email protected])
Ismael Navas Delgado ([email protected])
Amine Kerzazi([email protected])
Othmane Chniber([email protected])
Maria del Mar Roldán-García ([email protected])
Joaquín Molina ([email protected])
KASBi (updated advances)
http://khaos.uma.es/KASBi/
Thanks