SPARQLeR: Extended Sparql for Semantic Association Discovery

1
SPARQLeR Extended Sparql for Semantic
Association Discovery

• Krzysztof Kochut and Maciej Janik

ESWC 2007, Innsbruck, Austria June 4, 2007
Work supported by the National Science Foundation
Grant No. IIS-0325464, entitled SemDIS
Discovering Complex Relationships in the Semantic
Web.
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Paths in RDF
child
child
older
works_for
child
Directed path
child
child
Undirected path, but with specific properties
and directionality
Undirected path
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Why are paths interesting ?

• A path describes how entities are related.
• Relationships on the path define meaning of this
  connection.
• Entities on the path specify the content.
• Do you have migraine? Try taking magnesium!
• Path discovered by Dr. D.R.Swanson from partial
  information available in PubMed publications
• stress can lead to loss of magnesium in the human
  body
• migraine patients seem to be experiencing stress
• thats why
• migraine could lead to a loss of magnesium, so
  take magnesium to fight migraine!

Swanson, R.D. Migraine and Magnesium Eleven
Neglected Connections. Perspectives in Biology
and Medicine, 31 (4). 526-557.
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Formally, what is a simple path ?

• Simple directed path between resources r0 and rn
  in a description base R
• sequence r0 p1 r1 p2 r2 , , pn-1 rn-1 pn rn
  (ngt0)
• r0 p1 r1, r1 p2 r2 , , rn-2 pn-1 rn-1, rn-1 pn
  rn (ngt0) are triples in R.
• all of the resources ri (0 i n) in the path
  are distinct
• Simple undirected path between resources r0 and
  rn in R
• sequence r0 p1 r1 p2 r2 , , pn-1 rn-1 pn rn
  (ngt0)
• for each ri-1 pi ri (0 lt i n) in the path,
  either ri-1 pi ri or ri pi ri-1 is a triple in R
• all of the resources ri (0 i n) in the path
  are distinct

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Paths and SPARQL

• SPARQL query can express only static graph
  patterns.
• Some flexibility is introduced by an OPTIONAL
  part, but it does not solve path problems.
• No support for flexible length path expressions.
• Glycan biosynthesis pathway in biology has a
  specific pattern (properties), but its length may
  be unknown.
• Path discovery may be of unknown length and
  pattern, like in Dr. Swansons example.

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What we need to discover paths?

• Knowledge discovery needs more flexible patterns.
• Patterns may be partially known or even unknown
  (unrestricted path).
• Properties on the path, their order and
  directionality create a specific meaning.
• Entities on the path provide content.
• Relationships to entities outside of the path
  give an additional context.

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Proposed extensions

• A path may have a flexible length
• For computational reasons, length is limited.
• Constraints on properties
• Specific properties must appear in the path.
• Their order and directionality is meaningful.
• They can form a repeating pattern.
• Constraints on resources
• Specific resources must be on the path.
• They can be anywhere on the path or at specific
  positions.

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SPARQLeR

• Extension of SPARQL for semantic association
  discovery.
• Seamlessly integrated into the SPARQL syntax.
• Graph patterns incorporating simple paths with
  constraints.
• Constraints are based on regular expressions over
  properties.

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What is a path in SPARQLeR ?

• Path is a meta-property that connects two
  resources.
• Defined as a sequence of interleaving properties
  and resources.
• Starts and ends with properties (endpoint
  resources are not included).
• A path of length 1 is a sequence with just one
  property.
• ltrdfClass rdfabout"http//meta.org/rdf-meta-sch
  emaPath"gt
• ltrdfsisDefinedBy rdfresource"http//meta.org/r
  df-meta-schema"/gt
• ltrdfssubClassOf rdfresource"http//www.w3.org
  /1999/02/22-rdf-syntax-nsProperty"/gt
• ltrdfssubClassOf rdfresource"http//www.w3.org
  /1999/02/22-rdf-syntax-nsSeq"/gt
• ltrdfslabelgtPathlt/rdfslabelgt
• ltrdfscommentgtThe class of RDFMS
  paths.lt/rdfscommentgt
• lt/rdfClassgt

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Path patterns in SPARQLeR

• Meta-property similar concept to a property
• Resource property? Resource
• Resource path? Resource
• Path as a Sequence
• Test if a resource is in the path
• rdfsmember
• Test if a resource is at a specific position in
  the path
• rdf_2, rdf_4, ...
• SPARQLeR-specific path properties
• Test all resources or all properties in the path
• rdfmsentityResource and rdfmspropertyResource
• Example all resources on a path must be of type
  fooPerson

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Path pattern anatomy
p1
p1
p2
p3
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Path types in SPARQLeR

• Directionality of relationships in the path
  defines its specific semantics.
• SPARQLeR allows definition of the following path
  types
• As defined in graph theory
• Directed
• Undirected
• SPARQLeR specific extension
• Defined directionality path (includes directed
  path)

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Directionality of properties in path

• Defined directionality paths
• Neither directed nor undirected
• Each property in a path has a specified
  directionality
• Example simple graph with p relationship
• (a) X p Y, directed path
• (b) X p Y, undirected path
• (c) X ( p p-1 ) Y, directional path

(a)
(b)
(c)
p
p
p
p
X
Y
p
p
p
p
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Inverse property operator

• In standard SPARQL there is no need for inverse
  property operator
• Pattern syntax is based on individual statements,
  so it is easy to reverse direction.
• Defining path constraints requires the inverse
  operator
• A pPath expression defines constraints on
  properties, not on individual statements.
• Without the inverse property operator some paths
  constraints would be impossible to express (as
  shown in the previous example).

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RegExp in path constraints

• Path constraints on properties are based on
  regular expressions
• Uses syntax similar to lex
• Easy for grep users
• Examples
• a c d a (bc) a
• abc c? d ( b a-1 ) c

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Path constraints in SPARQLeR

• Defined as regular path expressions
• Can specify patterns of properties in the path
• Directionality requirement needs the inverse
  operator ? (- minus) p
• Supported regular expressions
• p (single property)
• -p (the inverse of p)
• p1 p2 ... pn (class of properties)
• -p1 p2 ... pn (class of inverse properties)
• p1 p2 .. pn (complement of properties)
• -p1 p2 .. pn (inverse of complement of
  properties)

. (wildcard) x y (alternative) xy
(concatenation) x (Kleene star) x (one or more
repetition) (x) (match a path matched by x)
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Path constraints (contd)

• Class of properties and inverse operator
• Complement operator can be applied only to
  defined properties, not their inverses
• Inverse operator
• Not allowed inside class of properties
• Inverses set created from defined properties
• Example
• properties q r s t
• rt ? q s
• qr ? t-1 s-1 (inverses)
• (st t) ? q r q-1 r-1 s-1

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Integrating paths into SPARQL

• Path variable binds a path
• Name begins with instead of ?
• Simple patterns path between two resources
• SELECT ?prop WHERE ltrgt ?prop ltsgt
• SELECT path WHERE ltrgt path ltsgt
• Single source path
• SELECT path, ?res WHERE ltrgt path ?res

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Integrating paths into SPARQL

• Resources on the path
• SELECT path WHEREltrgt path ltsgt . path
  rdfsmember ltegt
• SELECT path WHEREltrgt path ltsgt . path rdf_1
  ltpgt
• Listing path elements list operator
• SELECT list(path) WHERE ltrgt path ltsgt

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Expressing path constraints

• Bounded path length
• only constants allowed
• FILTER(length(path)lt5)
• FILTER(length(path)gt3 length(path)lt7)

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Expressing path constraints

• Constraints added as a regular expression filter
  (existing syntax in SPARQL)
• regex( pathvariable, pathexpr, pathflags )
• FILTER(regex(path,.fooprop.,uis))
• Flags i (instances) s (schema) l (literals)
  h (match using hierarchy) d (set
  directionality) u (undirected)
• Default flags d i

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Some examples

• SELECT list(path), ?res WHERE
• ltrgt path ?res .
• path rdfsmember ?x .
• ?x foolocatedIn wikiEurope
• FILTER(regex(path,fooprop)
• SELECT list(path) WHERE
• ltrgt path ltsgt .
• path rdfmsentityResource ?x .
• ?x rdftype fooPerson
• FILTER(regex(path,(foopropfoorel),u)
• SELECT list(path) WHERE
• ltrgt path ltsgt
• FILTER(length(path)lt6 length(path)gt4
• regex(path,(fooprop -foorel))

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SPARQLeR Prototype Implementation

• Prototype implementation is based on BRAHMS
  RDF/S main memory storage.
• Path search based on a bi-directional BFS for
  simple paths.
• Checking of path constraints in regex is
  implemented as a simulation of DFAs.

Janik, M. and Kochut, K., BRAHMS A WorkBench RDF
Store And High Performance Memory System for
Semantic Association Discovery. ISWC 2005
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Implementation details

• Each path expression (FILTER regex) is translated
  into a DFA.
• For path between two resources, partial
  constraints are checked while building the search
  trie from both endpoints forward and reverse
  DFAs
• When a path is connected,the forward DFA used
  to check the full (path) constraint.

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Experiments biology pathway

• Biosynthesis paths in biology (glycomics)
• How specific glyco peptide is created from a
  basic structure?
• Find pathway between dolichol phosphate and glyco
  peptide G00009
• Path has 15 reactions (30 hops, as each reaction
  is represented by its substrates and products)
• Only undirected path connects the endpoint
  resources, but a specific directionality pattern
  is present
• RDF representation sample reactions in
  the path

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Experiments biology pathway

• Functionality test - proof of concept
• N-glycan biosynthesis pathway

SELECT list(path) WHERE glycodolichol_phosph
ate path glycoglyco_peptide_G00009 . path
rdfsmember enzyoR05969 FILTER ( length(path)
lt 30 regex(path,
"((-glycohas_acceptor_substrate
-glycohas_reactant) glycohas_product)" ) )
Ontology GlycO Length 30 hops Consists
of 15 reactions Search time milliseconds (less
than 1 tick)...
courtesy of Dr. Alison Vandersall-Nairn,
University of Georgia
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Experiments

• Scalability
• Modified DBLP datasets in RDF (added random
  citations)
• Test on increasing dataset (adding older years of
  publications)
• Search for cited publications (transitive)
• PREFIX opus lthttp//lsdis.cs.uga.edu/projects/sem
  dis/opusgt
• SELECT ?end_publication WHERE
• lthttp//dblp.uni-trier.de/rec/bibtex/journals/ai/H
  uber06gtpath ?end_publication
• FILTER ( length(path)lt26 regex(path,
  "(opuscites_publication)" ) )

B. Aleman-Meza et. al. Semantic Analytics on
Social Networks Experiences in Addressing the
Problem of Conflict of Interest Detection.
(WWW2006)
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Experiments dataset characteristics
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Experiments results single source paths
Search paths up to length 26
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Experiments results two endpoint paths
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More complex uses of path expressions

• Discover connecting paths with a shared node
• Path between A and B, length up to 4
• Path between C and D, length up to 4
• Both paths have a shared resource

A path_1 B length(path_1) lt 4
?x
C path_2 D length(path_2) lt 4
path_1 rdfsmember ?x path_2 rdfsmember ?x
Potential subgraph discovery
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SPARQLeR summary

• Path expressions
• use of regular expressions over properties
• Flexible path specification
• Undirected
• Defined directionality paths
• Directed
• Length restricted
• Complex path patterns
• Test of resources and properties on the path
• Intersecting paths

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Conclusion and future work

• SPARQLeR extension fits seamlessly into the
  current SPARQL syntax.
• Performance of path queries is acceptable (if
  defined expression is highly selective).
• Optimization of path queries, complex expressions
  and multiple paths in query.
• Inclusion of context.

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SPARQLeR Krys Kochut, Maciej Janik

• Thank you

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Predicate Vs. Statement expressions

• Predicate alphabet
• p
• -p
• _ (wildcard)
• simplicity

• Statement alphabet
• s p o
• _ p o
• s _ o
• s p _
• _ _ o
• _ p _
• s _ _
• _ _ _

Additional rules Which statement pattern can
be connected withwhich one