How to feed the Squerall with RDF and other data nuts?

Abstract

Advances in Data Management methods have resulted in a wide array of storage solutions having varying query capabilities and supporting different data formats. Traditionally, heterogeneous data was transformed off-line into a unique format and migrated to a unique data management system, before being uniformly queried. However, with the increasing amount of heterogeneous data sources, many of which are dynamic , modern applications prefer accessing directly the original fresh data. Addressing this requirement, we designed and developed Squerall, a software framework that enables the querying of original large and heterogeneous data on-the-fly without prior data transformation. Squer-all is built from the ground up with extensibility in consideration, e.g., supporting more data sources. Here, we explain Squerall's extensibility aspect and demonstrate step-by-step how to add support for RDF data, a new extension to the previously supported range of data sources.

Full text

How to feed the Squerall with RDF
and other data nuts?
Mohamed Nadjib Mami1,2, Damien Graux2,3, Simon Scerri1,2, Hajira Jabeen1,
S¨oren Auer4, and Jens Lehmann1,2
1Smart Data Analytics (SDA) Group, Bonn University, Germany
2Enterprise Information Systems, Fraunhofer IAIS, Germany
3ADAPT Centre, Trinity College of Dublin, Ireland
4TIB & L3S Research Center, Hannover University, Germany
{mami,scerri,jabeen,jens.lehmann}@cs.uni-bonn.de
damien.graux@iais.fraunhofer.de,auer@l3s.de
Abstract. Advances in Data Management methods have resulted in a
wide array of storage solutions having varying query capabilities and
supporting different data formats. Traditionally, heterogeneous data was
transformed off-line into a unique format and migrated to a unique data
management system, before being uniformly queried. However, with the
increasing amount of heterogeneous data sources, many of which are dy-
namic, modern applications prefer accessing directly the original fresh
data. Addressing this requirement, we designed and developed Squerall,
a software framework that enables the querying of original large and
heterogeneous data on-the-fly without prior data transformation. Squer-
all is built from the ground up with extensibility in consideration, e.g.,
supporting more data sources. Here, we explain Squerall’s extensibility
aspect and demonstrate step-by-step how to add support for RDF data,
a new extension to the previously supported range of data sources.
1 Introduction
Copyright 2019 for this paper by its authors. Use permitted under Creative Commons License
Attribution 4.0 International (CC BY 4.0).
The term Data Lake [1] denotes a repository of schema-less data stored in its
original form and format without prior transformations. We have built Squer-
all [2], a software framework implementing the so-called Semantic Data Lake
concept, which enables querying Data Lakes in a uniform manner using Semantic
Web techniques. In essence, Semantic Data Lake incorporates a ’virtual’ schema
over the schema-less data repository by mapping data schemata into high-level
ontologies, which then can be queried in a uniform manner using SPARQL.
The value of a Data Lake-accessing system lays in its ability to query as much
data as possible. For this sake, Squerall was built from the ground up with exten-
sibility in consideration, so to allow and facilitate supporting more data sources.
As we recognize the burden of creating a wrapper for every needed data source,
we resort to leveraging the wrappers that data source providers themselves offer
for many state-of-the-art processing engines. For example, Squerall uses Apache
Spark and Presto as underlying query engines, both of which benefit from a wide
range of connectors accessing the most popular data sources.

2 M. N. Mami et al.
In this demonstration, we complement the published5work about Squerall [3]
by (1) providing more details on the data source extensibility aspect, and (2)
demonstrating extensibility by supporting a new data source, RDF.
2 Squerall and its Extensibility
2.1 Squerall: a Semantic Data Lake
Squerall is an implementation of the Semantic Data Lake concept, i.e., query-
ing original large and heterogeneous data using established Semantic Web tech-
niques and technologies. It is built following the Ontology-Based Data Access
principles [5], where elements from the data schema (entities/attributes) are as-
sociated to elements from an ontology (classes/properties), by means of mapping
language, forming a virtual schema against which SPARQL queries can be posed.
2.2 Squerall Extensibility
As we recognize the burden of creating wrappers for the variety of data sources,
we chose not to reinvent the wheel and rely on the wrappers often offered by the
developers of the data sources themselves or by specialized experts. The way a
connector is used is dependent on the query engine:
– Spark: the connector’s role is to load a specific data entity into a DataFrame
using Spark SQL API. Its usage is simple, it only requires providing access
values to a predefined list of options inside a simple connection template:
s pa r k . re ad . f o rm a t ( s ou r ce T y pe ) . o pt i o ns ( o p ti o ns ). l oa d
Where sourceType designates the data source type to access, and options is
a simple key-value list storing e.g., username, password, host, cluster settings,
etc. The template is similar in most data source types. There are dozens
connectors6already available for a multitude of data sources.
– Presto: access options are stored in a plain text file in a key-value fashion.
Presto uses directly SQL interface to query heterogeneous data, e.g., SELECT
cassandra.cdb.product C JOIN mongo.mdb.producer M ON C.producerID
= M.ID, there is no direct interaction with the connectors. Presto internally
and transparently uses the access options to load necessary data on query-
time. Similarly, there are already several ready-to-use connectors for Presto7.
Hence, while Squerall supports by default MongoDB, Cassandra, Parquet,
CSV and various JDBC sources, interested users can easily provide access to
other data sources leveraging Spark and Presto connectors8.
5At ISWC-Resources track.
6https://spark-packages.org/
7https://prestosql.io/docs/current/connector.html
8Tutorial: https://github.com/EIS-Bonn/Squerall/wiki/Extending-Squerall

How to feed the Squerall with RDF and other data nuts? 3
3 Supporting a New Data Source: Case of RDF Data
In case no connector is found for a given data source type, we show in this section
the principles of supporting a new data source. The procedure concerns Spark
as query engine, where the connector’s role is to generate a DataFrame from an
underlying data entity. Squerall did not previously have a wrapper for RDF data.
With the wealth of RDF data available today as part of the Linked Data and
Knowledge Graph movements, supporting RDF data is paramount. Contrary to
the previously supported data sources, RDF does not require a schema, neither
fixed nor flexible. As a result, lots of RDF data is generated without schema.
In this case, it is required to exhaustively extract the schema from the data
on-the-fly during query execution. Also, as per the Data Lake requirements, it
is necessary not to apply any pre-processing, and to directly access the original
data. If an entity inside an RDF data is detected as relevant to (part of) a query, a
set of transformations are applied to flatten the (subject,property,object) triples
and extract the schema elements needed to generate the DataFrame(s). Full
procedure is shown in Figure 1 and is described as follows:
1. First, triples are loaded into Spark distributed dataset9of the schema (sub-
ject : String, property : String, object : String).
2. Using Spark transformations, we generate a new dataset. We map (s,p,o)
triples to pairs: (s,(p,o)), then group pairs by subject: (s,(p,o)+), then find
class from p ( p=rdf:type) and map the pairs to new pairs: (class,(s,(p,o)+])),
then group them by class (class, (s, (p, o)+)+). Each class has one or more
instances identified by ‘s’ and contains one or more (p, o) pairs.
3. The new dataset is partitioned into a set of class-based DataFrames, columns
of which are the properties and tuples are the objects. This corresponds to
the so-called property table partitioning [6].
4. The XSD data types, if present as part of the object, are detected and used
to type the DataFrame attributes, otherwise string is used.
5. Only the relevant entity/ies (matching their attributes against query prop-
erties) detected using the mappings is/are retained, the rest are discarded.
This procedure generates a (typed) DataFrame that can join DataFrames
generated using other data connectors from other data sources. The procedure
is part of our previously published effort: SeBiDa [4]. We made the usage of the
new RDF connector as simple as the other Spark connectors:
val rdf = n e w NTtoDF ()
df = r df . o pt i on s ( op t io n s ). r ea d ( f il eP at h , s pa r kU R I ). t oD F
Where NTtoDF is the connector’s instance, options are the access information
including RDF file path and the specific RDF class to load into the DataFrame.
9Called RDD: Resilient Distributed Dataset, a distributed tabular data structure.

4 M. N. Mami et al.
DS1
RDF Connector
(s1 , a, A)
(s1, p1, o1_t1)
(s1, p2, o2_t2)
…
(s2 , a, B)
(s2, pn,
on_t3)
(s2, pn+1,
on+1_t4)
...
...
Type A DataFrame (Relevant)
s2pnon_t3
...
ID: Str p1: t1 p2: t2
s1p1o1_t1
s1o1o2
... pm: str
... om
S: str P: str 0: str
Type B DataFrame (Irrelevant)
... ...
ID: Str pn: t3 pn+1: t4
s2onon+1
... pn+r: str
... on+r
s1p2o2_t2
s2pn+1 on+1_t4
DS2
DS1
Connector
DS2
Connector
DataFrame
Joins
Triples Dataset
RDF Triples
Fig. 1. RDF Connector. A and B are RDF classes, tndenote data types.
4 Conclusion
In this demonstration article10, we have described with more depth the extensi-
bility aspect of Squerall in supporting more data sources. We have demonstrated
extensibility principles by adding a support for RDF data. In the common ab-
sence of schema, RDF triples have to be exhaustively parsed and reformatted
into a tabular representation on query-time, which only then can be queried.
In the future, in order to alleviate the reformatting cost and, thus, accelerate
query processing time, we intend to implement a light-weight caching technique,
which can save the results of the flattening phase across different queries. Be-
yond Squerall context, we will investigate making the newly created connector
(currently supporting NTriples RDF) available in Spark Packages (connectors)
hub for the public to be able to process large RDF data using Apache Spark.
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10 Screencasts are publicly available from: https://git.io/fjyOO