=Paper=
{{Paper
|id=Vol-1320/paper_3
|storemode=property
|title=Publishing Diachronic Life Science Linked Data
|pdfUrl=https://ceur-ws.org/Vol-1320/paper_3.pdf
|volume=Vol-1320
|dblpUrl=https://dblp.org/rec/conf/swat4ls/GkirtzouVHSD14
}}
==Publishing Diachronic Life Science Linked Data==
https://ceur-ws.org/Vol-1320/paper_3.pdf
Publishing Diachronic Life Science Linked Data
Katerina Gkirtzou1 , Thanasis Vergoulis1 , Artemis Hatzigeorgiou3 , Timos
Sellis2 , and Theodore Dalamagas1
1
IMIS, Research Center “Athena”, Athens, Greece,
2
RMIT University, Melbourne, Australia
3
University of Thessaly, Volos, Greece
Abstract. The Linked Data paradigm involves practices to publish,
share, and connect data on the Web. Thus, it is a compelling approach
for the dissemination and re-use of scientific data, realizing the vision
of the so-called Linked Science. However, by just converting legacy sci-
entific data as Linked Data, we do not fully meet the requirements of
data re-use. Scientific data is evolving data. To ensure re-use and allow
exploitation and validation of scientific results, several challenges related
to scientific data dynamics should be tackled. In this paper, we deal
with the publication of diachronic life science linked data. We propose a
change model based on RDF to capture versioned entities. Based on this
model we convert legacy data from biological databases as diachronic
linked data. Our linked data server can assist biologists to explore bio-
logical entities and their evolution by either using SPARQL queries or
navigating among entity versions. All services are publicly available at
http://diana.imis.athena-innovation.gr/lod.
Keywords: microRNA, RDF, LD
1 Introduction
As technology advances in scientific hardware (e.g., sequencers), easing the cre-
ation and consumption of large volumes of scientific data, and as more scientific
datasets are published and become available for potential data users, the cur-
rent trend moves towards open science data. Linked Data is a powerful and
compelling approach for spreading and consuming scientific data, involves prac-
tices how to publish, share, and connect data on the Web, and offers a new way
of data integration and interoperability. The driving force to implement Linked
Data spaces is the RDF technology1 . The basic principles of the Linked Data
paradigm is (a) use the RDF data model to publish structured data on the Web,
and (b) use RDF links to interlink data from different data sources. Linked Data
technologies have given rise to the Web of Data: “a Web of things in the world,
described by data on the Web” [2].
However, by just converting legacy scientific data to Linked Data (LD), we
do not fully meet the requirements of data re-use. To ensure the efficiency in data
1
http://www.w3.org/RDF/
2
re-use and allow both the exploitation and validation of scientific results, several
challenges related to the dynamics of scientific data must be tackled. Scientific
data is diachronic data. Thus, users (a) should have access not only to up-to-date
scientific LD, but to any of the previous versions and (b) should also be able to
track the changes among versions, as well as their causes and effects. In this
paper, we describe our work on publishing diachronic life science data, and more
specifically, genomic, experimental and bibliographic data related to miRNA
molecules. We have integrated data from well-known databases, tracked their
evolution, and published them as diachronic linked data. We propose a change
model based on RDF to capture versioned entities. Our linked data server can
assist biologists to explore biological entities and their evolution.
2 Background
MicroRNAs The discovery of microRNAs (miRNAs) in early 2000s has dra-
matically changed the view of biologists about the role of the so-called junk DNA.
miRNAs bind themselves to message RNA (mRNA) transcripts, called targets,
and regulate their expression. Knowledge of miRNA targets is very important for
therapeutic uses. For example, such knowledge could be used to down-regulate
genes by introducing artificial miRNAs into the cells. Since the terms “miRNA”
is nowadays used in a wide scope, it is common to distinguish between hairpin
miRNAs and mature miRNAs, or just hairpins and matures from now on. The
former signifies a precursor of the latter. A hairpin can actually be processed
into several matures. Matures bind themselves to transcripts and prevent the
creation of functional ribosomes.
Diachronic miRNA data During the past years, we have developed DIANA
tools 2 , a set of advanced Web applications supporting a series of sophisticated
work-flows enabling users with no strong background in informatics to perform
advanced multi-step functional miRNA analysis. Under the hood of DIANA tools
lies a relational database storing information for key entities of the miRNA do-
main, such as hairpins, matures, transcripts, genes, KEGG pathways, and publi-
cations. Information has been aggregated from a variety of sources, i.e informa-
tion concerning the miRNAs comes from the miRBase database (up to v.18)3 ,
gene related information from the Ensembl database (v.69)4 and molecular in-
teraction and reaction networks from KEGG pathways database5 .
The miRBase database is a searchable database of published miRNAs and
maintains information for 18, 589 hairpins and 21, 881 matures. It also maintains
a list of files that record successive versions along with the changes between
them. By examining all these files, a number of changes are observed. Ana-
lytically, we observe the following changes: (a) NAME/SEQUENCE : change
2
http://diana.imis.athena-innovation.gr/DianaTools/index.php
3
http://www.mirbase.org/
4
http://www.ensembl.org/index.html
5
http://www.genome.jp/kegg/pathway.html
3
over the values of name and sequence respectively for both hairpins and ma-
tures, (b) NEW/DELETE : creation and deletion of a hairpin/mature entry,
(c) FORWARD : merging of multiple hairpin entries into a single one, (d) ADD
HAIRPIN PARENT/REMOVE HAIRPIN PARENT : creation/deletion of the
relationship among a pair of hairpin and mature. Being able to track the changes
of the miRNA and having access to older versions it is a crucial information when
working with miRNAs. For example, the hairpin MI0001364 was introduced into
miRBase at v5.0 with name dre-mir-10b and at v7.0 its name changed to dre-mir-
10b-1. Having access to all possible names, allows us to better track bibliographic
references independent of its latest name.
3 Change model based on RDF
A challenging problem in LD publishing is how to deal with evolving data. In
the general case, changes are complex objects that interact with data objects,
they can have structural, temporal and probabilistic characteristics, thus they
cannot be handled as plain differences neither transformation operations between
datasets. This is evident especially in life science LD, since by just converting
legacy scientific data as LD, we do not fully meet the requirements of data re-
use. To support the above requirements, we adopt versioned RDF entities and
version properties, and we also model changes as first class citizens, i.e. RDF
resources, in the LD itself. Based on our approach, both query and navigation
services can be developed on top of diachronic LD sets.
3.1 Versioned entities and properties
To represent up-to-date RDF descriptions, we use a general URI that is based
on the class of the resource and an id that uniquely identifies the resource:
http://.../resource/class-name/resource-id. By using such URIs, one can
retrieve the RDF description for the current version of a requested RDF re-
source. To retrieve the RDF description for an RDF resource in a previous
version of the LD set, we use version timestamps to append the general URIs:
http://.../resource/class-name/resource-id/timestamp. For example, the
URI http://.../resource/matures/MIMAT0009477 retrieves the current ver-
sion of the mature with id MIMAT0009477, while http://.../resource/matures/
MIMAT0009477/17 the description of the same mature for v17.
While versioned URIs support the navigation among versioned entities by
following those URIs, we use four version properties to facilitate the querying
of diachronic LD set: (a) :label, with the constant value "now", (b) :version,
with version timestamp values, (c) :previousVersion, and (d) :nextVersion.
The first property can be used in SPARQL to provide access only to the current
version of the RDF resources, while the second can be used to form queries that
span several versions of the LD set. The other two properties are used to ease the
navigation among different resource’s versions back and forward, respectively.
4
Fig. 1. An RDF subgraph of the miRNA LD showing versioned RDF resources of the
hairpin miRNA MI0000095 and its produced mature miRNA MIMAT0004509 for the
miRBase v16, v17 and v18.
Figure 1 presents an RDF subgraph from the miRNA LOD published us-
ing our proposed method. At the left column from top to bottom, it shows
three RDF resources of the hairpin MI0000095 for miRBase versions 16, 17 and
18. Similarly at the right column, it shows the RDF resources of the mature
MIMAT0004509 for the same miRBase versions. The mature MIMAT000450
is produced by hairpin MI0000095, a relationship that is reflected in the RDF
graph via the property diana:producesMature. Figure 1 also shows some of
the properties related with the Hairpin and Mature class, such as diana:name
and diana:accession. The property diana:name represents the name of each
miRNA, a property that evolves over time, while diana:accession representing
the miRBase id of each miRNA, which remains unchanged over their lifespan.
3.2 Change Management
A key requirement for diachronic LD is the need to trace the origins of data and
transformations that occurred. Capturing the changes themselves and having
querying capabilities on them, actually give us the possibility to step back and
examine how and when the changes took place. In other words, it opens the key
challenging problem of preservation and provenance support. Our approach uses
the RDF schema itself to represent changes. We propose two different strategies
depending whether the change occurs in an RDF triple that involves a property
with a literal object or a property connecting two resources.
Property to Literal In this case, the literal value is substituted by a new value.
We model this change by adding to the RDF schema an extra property :change,
which is a property to literal and describes the type of change. Figure 2 shows
an RDF subgraph of the miRNA LOD, where a change occurs to the property
diana:name of the hairpin MI0000069 at v2.0. On the left side, we see its RDF
resource at the previous miRBase v1.5, which also contains the old name value
5
Fig. 2. An RDF subgraph of the miRNA LD showing how a change in property
diana:name (property to Literal) is modeled.
Fig. 3. An RDF subgraph of the miRNA LD showing how a change in a property
connecting two resources, such as diana:producesMature, is modeled.
hsa-mir-15a (depicted in red), while on the right side we see the RDF resource
of the hairpin at miRBase version 2.0 with the new name value hsa-mir-15a
and the extra property diana:change with literal value the type of change –in
this case "NAME"– that models the change itself (depicted in green).
Property to Resource In this case, the change is an RDF resource itself
that links to the two resources of the property (the subject and the object)
that changed. This “change” resource apart from links to the corresponding re-
sources, it contains also a time property, showing at which time point the change
occurred. Other characteristics, like probabilistic ones, can easily be modeled by
adding extra properties to the “change” resource. Figure 3 shows an RDF sub-
graph of the miRNA LOD when a change occurs at property diana:producesMature
between the hairpin MI0000769 and the mature MIMAT0009199 at v17. At
the top of the Figure 3 we see the two connected RDF resources at the pre-
vious v16 (depicted in red). At the bottom, we see the two resources at v17
where the property diana:producesMature has been dropped. To proper model
proper this change, we extend the RDF graph with an instance of the class
RemoveHairpinParent (depicted in green) that contains links to the respective
resources at v17.
6
4 Publishing and exploring LD miRNA data
All the curated information related to miRNAs for DIANA tools is stored in a
relational database, but a Linked Data representation is necessary and useful for
biologists. Such a LD representation will be open and available to everyone for re-
use, exploration and validation. Moreover, it can be used for inference and can be
potentially be part of an automated interpretation tool of the role of non-coding
RNAs. Due to the internal relational storage of the data, we adopt the “virtual
RDF” approach: accessing a non-RDF database using an RDF view. Such an
approach enables the access of non-RDF, legacy databases without having to
replicate the whole database into RDF. We use the D2R server [3], a popular
tool that follows this approach.
In order to show the abilities of our proposed model and its flexibility, we
present a number of SPARQL queries. The queries are categorized into the fol-
lowing types: (a) retrieval of up-to-date entities, (b) retrieval of diachronic enti-
ties and (c) change exploration. The retrieval of up-to-date entities requires the
triple pattern ?e diana:label "now" as mentioned at Section 3.1. The follow-
ing SPARQL query is an example of this type, retrieving the targets of miRNAs
predicted by microT-ANN and showing the whole biogenesis path. Thus, we get
the hairpin’s URI, the URI of its produced mature and the transcript’s URI that
is targeted by the mature.
SELECT ?hairpin ?mature ?target WHERE
{
?hairpin rdf:type diana:Hairpin.
?hairpin diana:label "now".
?hairpin diana:producesMature ?mature.
?interaction rdf:type diana:Interaction.
?interaction diana:hasMature ?mature.
?interaction diana:hasTarget ?target.
?interaction diana:application "microT-ANN (v4.0)".
}
To retrieve diachronic data we need just to specify the period of interest. For
example, if we want to reproduce the previous query, but for a specified previous
miRBase version, e.g version 13.0, we have the following SPARQL query :
SELECT ?hairpin ?mature ?target WHERE
{
?hairpin rdf:type diana:Hairpin.
?hairpin diana:version "13.0".
?hairpin diana:producesMature ?mature.
?interaction rdf:type diana:Interaction.
?interaction diana:hasMature ?mature.
?interaction diana:hasTarget ?target.
?interaction diana:application "microT-ANN (v4.0)".
}
Finally we present two examples of SPARQL queries that show the evolution
of data. The first one retrieves the hairpins that changed their name throughout
their lifespan and returns the hairpin’s URI, the miRBase version the name
changed, the old name value and the new name value:
7
SELECT ?hairpin ?version ?old_name ?new_name WHERE
{
?hairpin rdf:type diana:Hairpin.
?hairpin diana:change "NAME".
?hairpin diana:version ?version.
?hairpin diana:name ?new_name.
?hairpin diana:previousVersion ?hairpin_prev.
?hairpin_prev diana:name ?old_name.
}
In order to retrieve the old name values of the Hairpins, we can access the previ-
ous version of the hairpin via the property diana:previousVersion. The second
one retrieves all currently not-related hairpin and mature pairs that used to be
related in the past and returns from left to right the hairpin’s URI, the miRBase
version the property diana:producesMature dropped and the mature’s URI :
SELECT DISTINCT ?hairpin ?version ?mature WHERE
{
?connection rdf:type diana:removeHairpinParent.
?connection diana:version ?version.
FILTER (?version <= "18").
?connection diana:hasHairpin ?hairpin.
?connection diana:hasMature ?mature.
}
Using the property diana:version in FILTER we can retrieve all changes in
the relationship between hairpin and mature miRNAs before that version. Note
also that since the property diana:producesMature connects two resources, a
change in that relationship-type property we model it as a new RDF class.
5 Related Work
This work is an extension of [5], which was our first attempt to publish legacy
miRNA data as LD. Compared to that work, (a) we use a different database
schema in order to support a wider range of diachronic queries, and (b) we have
integrated new miRNA-related datasets. Various approaches have been proposed
in the bibliography studying the problems of evolution, versioning and change
detection in the context of LD. The Memento framework [8] handles different
versions of LD by attaching time-specific attributes as global version indica-
tor. [9] focuses on monitoring and examining the dynamics of LD, a knowledge
that can be leveraged to optimize existing systems and algorithms, especially
indexing techniques. Other publications, such as [7] and [11], deal with changes
in the linkages between datasets and the problem of broken links. A comparative
study of tools and approaches that deal with the problems of LD dynamics has
also been presented in [10]. The survey studies the aspects of discovery, change
detection at several granularity level (i.e at the dataset level, at triple level, etc),
and description of the changes, as well as the detection algorithms and notifi-
cation mechanisms. Evolutionary Terminology Auditing (ETA) examines how
terminology changes reflect evolutions in the underlying domain. An example
8
of this work can be seen in the context of SNOMED CT in [1]. Finally, named
graphs [4], RDF graphs which are assigned a name in the form of a URIref, allow
easier provenance tracking and trustness warranties.
6 Conclusion - Future Work
In this paper we presented our work on the publication of diachronic life science
LD. More specifically, we aggregated data from well known databases related to
miRNA molecules and exported as LD. The curated data contains information
from experimental observations, as well as change and version information about
the miRNA entities. The miRNA LD server can assist biologists to explore bio-
logical entities, navigate between versions of the resources and via the SPARQL
endpoint it provides access to applications for querying historical miRNA data
and tracking their changes. As future work, we plan to interlink our linked data
set with the linked data provided by the EBI RDF Platform [6]. Futhermore, we
will focus on providing keyword search querying capabilities on LD.
Acknowledgments This study has been supported by LODGOV project, Research
Programme ARISTEIA (EXCELLENCE), General Secretariat for Research and Tech-
nology, Ministry of Education, Greece and the European Regional Development Fund.
References
1. Applying Evolutionary Terminology Auditing to SNOMED CT. In: AMIA 2010
Proceedings. pp. 96–100 (2010)
2. Bizer, C., Heath, T., Berners-Lee, T.: Linked data - the story so far. International
Journal on Semantic Web and Information Systems 5(3), 1–22 (2009)
3. Bizer, C., Cyganiak, R.: D2r server publishing relational databases on the semantic
web (2006)
4. Carroll, J.J., Bizer, C., Hayes, P., Stickler, P.: Named graphs. Web Semantics:
Science, Services and Agents on the World Wide Web 3(4), 247 – 267 (2005)
5. Dalamagas, T., Bikakis, N., Papastefanatos, G., Stavrakas, Y., Hatzigeorgiou,
A.G.: Publishing life science data as linked open data: the case study of mirbase.
In: WOD. pp. 70–77 (2012)
6. Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton,
A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S.M., Martin, M., Le Novre,
N., Parkinson, H., Birney, E., Jenkinson, A.M.: The EBI RDF Platform: Linked
Open Data for the Life Sciences. Bioinformatics (2014)
7. Popitsch, N., Haslhofer, B.: Dsnotify: handling broken links in the web of data. In:
WWW. pp. 761–770 (2010)
8. de Sompel, H.V., Sanderson, R., Nelson, M.L., Balakireva, L., Shankar, H.,
Ainsworth, S.: An http-based versioning mechanism for linked data. CoRR (2010)
9. Umbrich, J., Hausenblas, M., Hogan, A., Polleres, A., Decker, S.: Towards Dataset
Dynamics: Change Frequency of Linked Open Data Sources. In: LDOW (2010)
10. Umbrich, J., Villazn-Terrazas, B., Hausenblas, M.: Dataset dynamics compendium:
A comparative study. In: COLD. vol. 665 (2010)
11. Volz, J., Bizer, C., Gaedke, M., Kobilarov, G.: Discovering and maintaining links
on the web of data. In: ISWC 2009. pp. 650–665 (2009)