Incremental Export of Relational Database Contents into RDF Graphs

Incremental Export of Relational
Database Contents into RDF Graphs
Nikolaos Konstantinou, Dimitris Kouis, Nikolas Mitrou
By Dr. Nikolaos Konstantinou
National Technical University of Athens
School of Electrical and Computer Engineering
Multimedia, Communications & Web Technologies
4th International Conference on Web Intelligence, Mining and Semantics

Outline
• Introduction
• Proposed Approach and Measurements
• Discussion and Conclusions

Introduction
• Information collection, maintenance and update is not always taking
place directly at a triplestore, but at a RDBMS
• Triplestores are often kept as an alternative content delivery channel
• It can be difficult to change established methodologies and systems
• Newer technologies need to operate side-by-side to existing ones
before migration

Mapping Relational Data to RDF
• No one-size-fits-all approach
• Synchronous Vs Asynchronous RDF Views
• Real-time Vs Ad hoc RDF Views
• Real-time SPARQL-to-SQL Vs Querying the RDF dump using SPARQL
• Queries on the RDF dump are faster in certain conditions, compared to
round-trips to the database
• Difference in the performance more visible when SPARQL queries involve numerous
triple patterns (which translate to expensive JOIN statements)
• In this paper, we focus on the asynchronous approach
• Exporting (dumping) relational database contents into an RDF graph

Incremental Export into RDF (1/2)
• Problem
• Avoid dumping the whole database contents every time
• In cases when few data change in the source database, it is not necessary to
dump the entire database
• Approach
• Every time the RDF export is materialized
• Detect the changes in the source database or the mapping definition
• Insert/delete/update only the necessary triples, in order to reflect these changes in the
resulting RDF graph

Incremental Export into RDF (2/2)
• Incremental transformation
• Each time the transformation is executed, not all of the initial information
that lies in the database should be transformed into RDF, but only the one
that changed
• Incremental storage
• Storing (persisting) to the destination RDF graph only the triples that were
modified and not the whole graph
• Only when the resulting RDF graph is stored in a relational database or using
Jena TDB
• Regardless to whether the transformation took place fully or incrementally

R2RML and Triples Maps
• RDB to RDF Mapping Language
• A W3C Recommendation, as of 2012
• Triples Map: a reusable mapping
definition
• Specifies a rule for translating each row of
a logical table to zero or more RDF triples
• A logical table is a tabular SQL query result
set that is to be mapped to RDF triples
• Execution of a triples map generates the
triples that originate from a specific result
set (logical table)

The R2RML Parser
• An R2RML implementation
• Command-line tool that can export relational database contents as
RDF graphs, based on an R2RML mapping document
• Open-source (CC BY-NC), written in Java
• Publicly available at https://github.com/nkons/r2rml-parser
• Tested against MySQL and PostgreSQL
• Output can be written in RDF/OWL
• N3, Turtle, N-Triple, TTL, RDF/XML notation, or Jena TDB backend
• Covers most (not all) of the R2RML constructs (see the wiki)
• Does not offer SPARQL-to-SQL translations

Outline
• Introduction

Information Flow
• Parse the source database contents into result sets
• According to the R2RML Mapping File, the Parser generates a set of
instructions to the Generator
• The Generator instantiates in-memory the resulting RDF graph
• Persist the generated RDF graph into
• An RDF file in the Hard Disk, or
• In Jena’s relational database, or
• In Jena’s TDB (Tuple Data Base, a custom implementation Of B+ Trees)
• Log the results
Parser Generator
Mapping
fileSource database
RDF graph Hard Disk
Target database
TDB
R2RML Parser

Incremental RDF Triple Generation
• Basic challenge
• Discover, since the last time the incremental RDF
generation took place
• Which database tuples were modified
• Which Triples Maps were modified
• Then, perform the mapping only for this altered subset
• Ideally, we should detect the exact changed
database cells and modify only the respectively
generated elements in the RDF graph
• However, using R2RML, the atom of the mapping
definition becomes the Triples Map
a b c d e
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
s p O
. . .
. . .
. . .
.
. . .
. . .
. . .
. . .
. . .
. . .
Triples Map
Result
set
Triples
11

Keeping Track
• Reification
• Allows assertions about RDF statements
• “Reified” model
• A model that contains only reified
statements
• Stores the Triples Map URI that produced
each triple
• Logging
• Store MD5 hashes of
• Triples Maps, SELECT queries, Result sets
• A change in any of the hashes triggers
execution of the Triples Map
subject property object
subject
property
object
blank
node
rdf:subject
rdf:type
rdf:predicate
rdf:object
rdf:Statement
dc:source Triple Map URI
<http://data.example.org/repository/person/1>
foaf:name "John Smith" .
[] a rdf:Statement ;
rdf:subject
<http://data.example.org/repository/person/1> ;
rdf:predicate foaf:name ;
rdf:object "John Smith" ;
dc:source map:persons .

Proposed Approach
• For each Triples Map in the Mapping Document
• Decide whether we have to produce the resulting triples, based on the logged
MD5 hashes
• Dumping to the Hard Disk
• Initially, generate a number of RDF triples
• RDF triples are logged as reified statements, followed by a provenance note
• Incremental generation
• In subsequent executions, modify the existing reified model, by reflecting only the
changes in the source database
• Dumping to the Database or TDB
• No log is needed, storage is incremental by default

Measurements Setup
• An Ubuntu server, 2GHz dual-core, 4GB RAM
• Oracle Java 1.7, Postgresql 9.1, Mysql 5.5.32
• 7 DSpace (dspace.org) repositories
• 1k, 5k, 10k, 50k, 100k, 500k, 1m items, respectively
• A set of complicated, a set of simplified, and a set of simple queries
• In order to deal with database caching effects, the queries were run several
times, prior to performing the measurements

Query Sets
• Complicated
• 3 expensive JOIN conditions
among 4 tables
• 4 WHERE clauses
• Simplified
• 2 JOIN conditions among 3
tables
• 2 WHERE clauses
• Simple
• No JOIN or WHERE conditions
SELECT i.item_id AS item_id, mv.text_value AS text_value
FROM item AS i, metadatavalue AS mv,
metadataschemaregistry
AS msr, metadatafieldregistry AS mfr WHERE
msr.metadata_schema_id=mfr.metadata_schema_id AND
mfr.metadata_field_id=mv.metadata_field_id AND
mv.text_value is not null AND
i.item_id=mv.item_id AND
msr.namespace='http://dublincore.org/documents/dcmi-
terms/'
AND mfr.element='coverage'
AND mfr.qualifier='spatial'
SELECT i.item_id AS item_id, mv.text_value AS text_value
FROM item AS i, metadatavalue AS mv,
metadatafieldregistry AS mfr WHERE
mfr.metadata_field_id=mv.metadata_field_id AND
i.item_id=mv.item_id AND
mfr.element='coverage' AND
mfr.qualifier='spatial'
SELECT "language", "netid", "phone",
"sub_frequency","last_active", "self_registered",
"require_certificate", "can_log_in", "lastname",
"firstname", "digest_algorithm", "salt", "password",
"email", "eperson_id"
FROM "eperson" ORDER BY "language"

Measurements (1/3)
• Export to the Hard Disk
• Simple and complicated queries,
initial export
• Initial incremental dumps take
more time than non-incremental,
as the reified model also has to be
created
0
100
200
300
400
500
600
700
1000 5000 10000
source database rows
non-ncremental
incemental
0
5
10
15
20
25
30
35
40
3000 15000 30000 150000 300000
result model triples
non-incremental
incremental

Measurements (2/3)
• 12 Triples Maps
a. non-incremental mapping
transformation
b. incremental, for the initial time
c. 0/12
d. 1/12
e. 3/12
f. 6/12
g. 9/12
h. 12/12
0
100
200
300
400
500
600
700
a b c d e f g h
1000 items 5000 items 10000 items
0
50
100
150
200
250
300
350
a b c d e f g h
complicated mappings simpler mappings
Data change

Measurements (3/3)
• Similar overall behavior in cases of up
to 3 million triples
• Poor relational database performance
• Jena TDB is the optimal approach
regarding scalability
0
100
200
300
400
500
600
700
800
900
a b c d e f g h
RDF file database jena TDB
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
b c d e f g h
database jena TDB
~180k triples
~1.8m triples

Outline
• Introduction

Discussion (1/2)
• The approach is efficient when data freshness is not crucial and/or
selection queries over the contents are more frequent than the updates
• The task of exposing database contents as RDF could be considered
similar to the task of maintaining search indexes next to text content
• Third party software systems can operate completely based on the
exported graph
• E.g. using Fuseki, Sesame, Virtuoso
• Updates can be pushed or pulled from the database
• TDB is the optimal solution regarding scaling
• Caution is still needed in producing de-referenceable URIs

Discussion (2/2)
• On the efficiency of the approach for storing on the Hard Disk
• Good results for mappings (or queries) that include (or lead to) expensive SQL
queries
• E.g. with numerous JOIN statements
• For changes that can affect as much as ¾ of the source data
• Limitations
• By physical memory
• Scales up to several millions of triples, does not qualify as “Big Data”
• Formatting of the logged reified model did affect performance
• RDF/XML and TTL try to pretty-print the result, consuming extra resources, N-TRIPLES is
the optimal

Room for Improvement
• Hashing Result sets is expensive
• Requires re-run of the query, adds an “expensive” ORDER BY clause
• Further study the impact of SQL complexity on the performance
• Reification is currently being reconsidered in RDF 1.1 semantics
• Named graphs being the successor
• Investigation of two-way updates
• Send changes from the triplestore back to the database

Thank you for your attention!
Questions?

Incremental Export of Relational Database Contents into RDF Graphs

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