We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.&#xd;&#xa

Christoph Grabm&#xfc

Dietrich Rebholz-Schuhmann

Samuel Croset

English

AbstractWe present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.</jats:p

Christoph Grabmüller

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A Semantic Model for Federated Queries Over a Normalized Corpus

EMBL- EBI 
Wellcome Trust Genome 
Campus
Hinxton 
Cambridge
CB10 1SD
UK
T +44 (0) 1223 494 444
F +44 (0) 1223 494 468
http://www.ebi.ac.uk
A Semantic Model for Federated Queries 
Over a Normalized Corpus
Samuel Croset (croset@ebi.ac.uk  - www.SamuelCroset.com), Christoph Grabmueller 
(grabmuel@ebi.ac.uk), Dietrich Rebholz­Schuhmann  (rebholz@ebi.ac.uk)
Semantic Model in Web Ontology Language (OWL)
Acknowledgements
This work was funded by the EU Support Action grant 231727 under the 7th EU Framework Programme within Theme “Intelligent Content and Semantics” (ICT 2007.4.2)
Samuel Croset
www.SamuelCroset.com
PhD Student
Rebholz Group
croset@ebi.ac.uk
European Bioinformatics Institute
Thing
Semantic_Type
DISO
Sentence
SPE
Corpus
Article
Non_Annotated_Sentence CALBC
“G-protein coupled receptor 3”
PRGE
CHED
Annotation
Annotated_Sentence
Annotation1
Sentence1
“Identification of a novel mechanism regulating
β-cell mass: neuronal relay from the liver to 
pancreatic β-cells.”
“Katagiri H.”
“Oka Y.”
http://www.ncbi.nlm.nih.gov/pubmed/21084852
http://dx.doi.org/10.4161/isl.1.1.8615
2008-11-21T00:00:00
Annotation2
“adrenaline ”
Sentence2
Article1
rdf:type
rdf:type
rdf:typerdf:type
rdf:type
rdf:type
rdf:type
rdf:type
rdf:type
calbc:has_annotaioncalbc:has_annotaion calbc:is_in
calbc:is_in
calbc:
is_in
calbc:is_in
ca
lbc
:is
_in
rd
fs
:s
ub
Cl
as
sO
f rdfs:subClassOf
rdfs:subCl
assOf
rdfs:subClassOf
rdfs:subClassOf
rdfs:subClassO
f
rdfs:sub ClassO
f
rd
fs
:s
ub
Cl
as
sO
f
rdfs:subClassOf
rd
fs
:s
ub
Cl
as
sO
f
rdfs:subClassO
f
dc
:ti
tle dc:identifier
dc:creator
dc:creatordc:
dat
eA
cce
pte
d
calbc:pubmed_URI
Gene OntologyInteraction Partners
Chemical Families
…
http://purl.org/obo/owl/CHEBI#CHEBI_33568
http://purl.uniprot.org/uniprot/P35413
calbc:has_string
calbc:has_string
calbc:
has_s
enten
ce
calbc:has_sentence
owl:Class
Resources
External ResourceIndividual from CALBC
Properties
rdfs:SubClassO
f
calbc:has_sentence
dc:dateAccepted
dc:title
dc:identifier
dc:creator
calbc:has_annotation
calbc:has_string
rdf:type
calbc:pubmed_URI
calbc:is_i
n
owl:Class owl:Class
owl:ClassResource
Sentence XArticle X
: Transitive property
Annotation X
“Literal”
Resource
Article X
“Literal”
Resource
“Literal”
“Date”
Local and Federated Queries Example - SPARQL
Sentence X
Annotation X
Article X
Model for a corpus
Which are  the articles where  the protein P35413  (Uniprot) 
has been identified? List the title of the articles.
Which  are  the  sentences  having  both  an  annotation  about  a 
chemical  and  an  annotation  about  a  protein?  List  only  the 
annotations.
Which  are  the  sentences  with  2  protein  annotations?  These 
proteins  have  to  be  known  to  interact  together  from  Uniprot. 
List these annotations and the sentences.
Article?
rdf:type
Article
Article?
dc:title
Title?
calbc:has_sentenc
eArticle? Sentence?
calbc:has_annotation
Sentence? Annotation?
Annotation?
rdf:type
uniprot:P35413
SELECT                     WHERE {Title?
}
calbc:has_annotation
Sentence?
Annotation1?
calbc:has_annotation
Sentence?
Annotation2?
rdf:type
Annotation1? PRGE
rdf:type
Annotation2? CHED
SELECT                              ,                              WHERE {
}
Annotation1?
Annotation2?
calbc:has_annotation
Sentence?
calbc:has_annotation
Sentence?
rdf:type
Annotation1? PRGE
rdf:type
Annotation2? PRGE
SELECT                           ,                         ,                      WHERE {
}
Annotation1?
Annotation2?
uniprot:Participant
Sentence?
We present here a model implemented in OWL which improves information 
retrieval and data integration of the corpus. The model is populated with entities 
from CALBC and some simple queries over it are presented.
Normalization
Annotation1? Annotation2?
rdf:type
Annotation1? UniprotEntry1?
rdf:type
Annotation2? UniprotEntry2?
UniprotEntry1? UniprotEntry2?
Default prefix:  calbc: http://www.ebi.ac.uk/Rebholz/core/calbc#
N
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Pr
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in
gs
 : 
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0.
10
38
/n
pr
e.
20
11
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82
3.
2 
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 M
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A Semantic Model for Federated Queries Over a Normalized Corpus

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