=Paper=
{{Paper
|id=None
|storemode=property
|title=OpenDrugWiki – Using a Semantic Wiki for Consolidating, Editing and Reviewing of Existing Heterogeneous Drug Data
|pdfUrl=https://ceur-ws.org/Vol-632/paper16.pdf
|volume=Vol-632
|dblpUrl=https://dblp.org/rec/conf/semwiki/KostlbacherMHHH10
}}
==OpenDrugWiki – Using a Semantic Wiki for Consolidating, Editing and Reviewing of Existing Heterogeneous Drug Data ==
https://ceur-ws.org/Vol-632/paper16.pdf
OpenDrugWiki – Using a Semantic Wiki for
Consolidating, Editing and Reviewing of Existing
Heterogeneous Drug Data
Anton Köstlbacher1, Jonas Maurus1, Rainer Hammwöhner1,
Alexander Haas2, Ekkehard Haen2, Christoph Hiemke3
1
University of Regensburg, Information Science
Universitätsstr. 31, 93053 Regensburg, Germany
2
University of Regensburg, Clinical Pharmacology, Department of Psychiatry
Universitätsstr. 31, 93053 Regensburg, Germany
3
University of Mainz, Neurochemical Laboratory, Department of Psychiatry
Untere Zahlbacher Str. 8, 55131 Mainz, Germany;
anton.koestlbacher@sprachlit.uni-r.de; rainer.hammwoehner@sprachlit.uni-r.de;
jonas@maurus.net; ekkehard.haen@klinik.uni-regensburg.de;
hiemke@mail.uni-mainz.de
Abstract. The ongoing project which is described in this article pursues the
integration and consolidation of drug data available in different Microsoft
Office documents and existing information systems. An initial import of
unstructured data out of five heterogeneous sources into a semantic wiki was
performed using custom import scripts. Using Semantic MediaWiki and the
Semantic Forms extension, we created a convenient wiki-based system for
editing the merged data in one central application. Revised and reviewed data is
exported back into production systems on a regular basis.
Keywords: drug database, medical information system, semantic wiki, data
conversion
1 Introduction
PsiacOnline1, a drug interaction database for psychiatry in German speaking
countries, was released in 2006. As of 2010 it contains over 7000 drug interactions
with comprehensive information on pharmacological mechanisms, effects and
severity of each interaction. Strong emphasis lies on guidance how to handle
interactions in practice. [1]
1 PsiacOnline is an online service offered by SpringerMedizin: http://www.psiac.de
Built on top of the component-based and event-driven prado2 framework
PsiacOnline features an easy to use authoring tool for drug data. It also provides a
simple XML interface for reusing data in other information systems, particularly
Laboratory Information Systems (LIS).
After the system’s introduction, we identified several additional data sources that
are frequently used at the affiliated research institutes3, providing content for
PsiacOnline. These data sources consisted of different document types like Microsoft
Excel sheets, Word documents, CSV data and relational databases. For example,
biological pathway information for psychiatric drugs was kept in a Word document of
which new versions were distributed to the lab staff via email. The staff also used
relational databases with pharmacokinetic data that were part of a LIS system used for
managing lab workflow. [2]
Other examples were manually edited Excel sheets with brand names and drug
names or international non proprietary names (INN4) and ATC5 code tables. They
were distributed through an informal email based workflow in the lab.
Analysis of the various documents and their content showed that all content should
be integrated into the existing dataset of PsiacOnline. This was the starting point of
the OpenDrugWiki project, which now combines the converted and imported data
sources with the existing PsiacOnline dataset. It offers an easy-to-use interface for
collaborative editing of the unified data in one place.
The article shows a use case for semantic wikis in production environments in the
field of professional pharmacological information in psychiatry. It describes why we
chose a semantic wiki, how the import of the data is done, what the editing and
review process looks like and how the data can be reused in existing and future
software systems.
2 Why Use a Semantic Wiki?
Instead of trying to convert the data and thus expanding PsiacOnline and importing
the data directly, we chose an approach that uses a semantic wiki as an intermediate
system. This semantic wiki also provides a full replacement for PsiacOnline’s
authoring system. The decision for a semantic wiki was in fact not a single one, it was
based on three decisions to the following questions: Why use a wiki? Why use
semantic web technologies? And why use the combination of both?
2 http://www.pradosoft.com
3 University of Regensburg, Clinical Pharmacology, Department of Psychiatry; University of
Mainz, Department of Psychiatry; University of Regensburg, Department for Information
Science; Regional Hospital Kaufbeuren, Department of Psychiatry
4 INN: International Non Proprietary Name: Generic name of a pharmaceutical ingredient
issued by the World Health Organisation (WHO).
5 ATC: Anatomical Therapeutic Chemical Classification System, used to classify drugs and
other medical products, controlled by WHO Collaborating Centre for Drug Statistics
Methodology (WHOCC).
2.1 Why Use a Wiki?
The main reason for favoring a wiki is that we will invite more institutes and authors
to contribute to PsiacOnline, therefore supporting collaboration and versioning is of
great importance. Wikis are well known to be of great use for distributed text editing
and reviewing. This also applies to scientific communities. [3][4][5]
We wanted to replace the various inconvenient email based workflows by one
structured storage and workflow system. We anticipate time savings in the
participating organizations by centralizing and streamlining the editing and reviewing
process. Time savings are already confirmed by users and are mostly achieved by
discarding the inefficient email based workflows and by the possibility of editing all
data in one place as well as the ability to instantly see changes made by other users.
Eventually, the affiliated research institutes do not only want to use the new system
to publish information on drug interactions which is both, necessary and useful for
psychiatrists or family doctors, but they also need a central platform for exchange of
the underlying pharmacokinetic mechanisms which is important to motivate and
execute further research.
2.2 Why Use Semantic Web Technologies?
Semantic Web technologies provide standards-based data exchange (RDF/XML) and
storage methods (Triple Stores) and a powerful query language (SPARQL). This
makes it easy to export parts of the semantic data back into production systems like
PsiacOnline, LIS or other medical information systems (MIS) after they passed a
review process.
The possible integration of data from other existing pharmaceutical or biomedical
ontologies, for example the Open Biological and Biomedical Ontologies6 was another
reason to favor semantic technologies. Having the ability to provide data for services
like Linked Life Data7 or Linking Open Drug Data (LODD8) was additionally
convincing.
2.3 Why Use a Combination of Both?
Based on the above arguments, the decision for a semantic wiki was identified as the
best way to go forward. Both, wiki and semantic web technologies in combination,
together with using a triple store connected to the wiki support each other in
achieving the goals described above. Using a semantic wiki offers the possibility to
extend the underlying data model at any time without trouble. This is important, as
extensions will be needed when new data relevant for research becomes available.
6 http://www.obofoundry.org
7 http://linkedlifedata.com/
8 http://esw.w3.org/topic/HCLSIG/LODD
3 Semantic Wiki Evaluation
We evaluated four of the mature semantic wiki engines: IkeWiki [6], Semantic
MediaWiki [7] (with the Halo extension [8]), OntoWiki [9] and AceWiki [10]. Finally
Semantic MediaWiki was chosen to be the product best-suited for our purposes,
mainly because of its usability and the underlying MediaWiki [11] software, known to
have a broad developer and user base and a big variety of available extensions.
Further results of the evaluation, presented in a more general article, can be found in
[12].
4 Implementation Details
OpenDrugWiki is based on Semantic MediaWiki and extensively uses templates,
magic words9, and various extensions. These include the Parser Functions extension10,
Semantic Results Format11 and Semantic Forms12 for convenient editing. Attached to
the wiki we use the basic triple store for Semantic MediaWiki provided by Ontoprise
[13]. It is based on Jena [14] and allows querying the semantic data that is stored in
the wiki via a SPARQL [15] webservice. Having all semantic data available through a
standards-based remote interface makes it easy to integrate new applications and
gives us a way to bring it back into production systems.
4.1 Data Conversion and Importing
Converting and importing the various data sources proved not to be a trivial task.
While reading the SQL databases and Excel sheets is a solved problem, the Microsoft
Word documents are converted to Excel sheets using an add-in for Microsoft Word
that was developed for this specific task.
After preprocessing the various data sources into Excel files and relational
databases, the main import job is performed by a PHP CLI application. This
application processes all data by matching known terms to semantic classes (brand
names, drug interactions, INN etc) and merges duplicate entries coming from the
different sources (see Fig. 3). It also computes redirections for sameAs-relations,
based on the information provided in the legacy data sources. The import application
then generates articles which are directly imported into MediaWiki using the its
command line interface.
9 http://www.mediawiki.org/wiki/Manual:Magic_words
10 http://www.mediawiki.org/wiki/Extension:ParserFunctions
11 http://www.mediawiki.org/wiki/Extension:Semantic_Result_Formats
12 http://www.mediawiki.org/wiki/Extension:Semantic_Forms
For generating the articles we created boilerplates for each article class (brand
names, pharmaceutical ingredients, drug interactions, others) consisting of various
MediaWiki templates. Article boilerplates and templates were defined manually after
analysis of the available data. A simple mapping between columns in the relational
databases, the word and excel tables and the semantic properties is performed by the
import tool.
Using this method, we generated and imported about 15,000 articles, consisting of
about 3,000 brand name entries, 4,000 entries on pharmaceutical ingredients (INNs),
7,000 drug interactions and 1,000 other articles. All articles have data-type
information and semantic properties which results in about 150k RDF triples. Reading
and processing the data, generation of wiki articles and importing them into SMW
take about one hour altogether.
4.2 Editing and Reviewing
After having successfully imported all data, the semantic wiki is used for editing and
reviewing by the PsiacOnline authors as well as carefully selected associate authors.
Since there is no Semantic MediaWiki extension available which supports a
collaborative peer reviewed editing process, we are forced to manually track all
changes made to the wiki articles. This is done by the core authors of PsiacOnline
who immediately review all edits made by other authors. To control which data is
exported back to production systems we store the user name and the revision date of
each article as semantic properties. Only articles which were approved by one of the
core authors are imported into production systems. This means, that a reviewer who
checks edits of a normal author has to resave the edited articles, even if he himself
made no changes. This process works perfectly for the moment, but cannot be seen as
a long term solution.
4.3 Querying the Wiki
As a proof of concept and a useful application for the staff in the lab we created a
simple Ajax powered web interface to retrieve data from the wiki. Given a list of
drugs or brand names, it shows all drug interactions, the biological pathways involved
and the citations on which the displayed information is based (see Fig. 2). This tool
demonstrates the possibility to query the triple store attached to the wiki and can be
used completely independent from the wiki itself. Being in private beta phase at the
moment, it will be made publicly available, when the content is completely reviewed
and double checked.13
The tool uses a PHP proxy script which queries the SPARQL endpoint,
preprocesses returned data, and delivers it back to the Ajax application using JSON.
Preprocessing consists primarily of dealing with the returned XML and character-set
related quirks.
13 Project Website: http://www.opendrugwiki.org/wq
Fig. 1. Screenshot Wikiquery-tool (german)
4.4 Exporting Data
One of the crucial requirements for the project is the possibility to export data back
into production systems like PsiacOnline and the labs’ LIS software. Initial results
were easily achieved by retrieving data from the wiki using ASK or SPARQL via
JSON and XML interfaces. This results in structured data which is then synchronized
with the data in production systems (see Fig. 3).
Fig. 2. Graphical overview of the import and export process
5 Conclusion and Prospects
With the approach presented in this article we wanted to show that a semantic wiki is
an appropriate tool for consolidation of data with heterogeneous structure, sources
and quality. The next step in this ongoing research project is the evaluation of the
wiki’s suitability to support continuous editing and reviewing processes in the
different organizations, especially from a usability standpoint. We are anticipating
good results, as Semantic Forms provides an easy-to-use interface for most purposes.
Since Semantic MediaWiki by default only provides semantic data for the latest
revision of an article there is currently no easy way for integrating review processes.
As we are preparing to open the wiki up to more and more research organizations for
editing and contributing information on drugs and drug interactions, being able to
have a reviewed and officially approved state of an article is currently the most
important missing feature.
We would like to see the MediaWiki extension Flagged Revisions14 integrated with
Semantic MediaWiki, since this would help us to implement review processes and
subsequently have reviewed and approved semantic data available in the triple store.
A benefit wikis and semantic web technologies offer is the possibility to create a
multilingual information system by using interwiki links and semantic relations. A
future task will be the creation of multiple wikis that will allow us to connect terms,
drug names and drug interactions in different languages. Mapping classes and
properties to standard drug and biomedical ontologies is therefore an important task
either. In the near future we will integrate more data from new sources as they
become available and begin connecting other production systems to the wiki to
provide an efficient tool for researchers for editing drug data in one place.
14 http://www.mediawiki.org/wiki/Extension:FlaggedRevs
6 References
1. Köstlbacher, A., Hiemke C., Haen E., Eckermann, G., Dobmaier, M., Hammwöhner R.,
PsiacOnline - Fachdatenbank für Arzneimittelwechselwirkungen in der psychiatrischen
Pharmakotherapie. In: Osswald, A., Stempfhuber, M., Wolff, C. (Hrsg.). Open Innovation.
Proc. 10 Internationales Symposium für Informationswissenschaft. Konstanz: UVK, 321-
326. (2007)
2. Köstlbacher, A.: Information Management In A Neurochemical Laboratory, In: Kuhlen, R.r
(Hrsg.) (2009). Information: Droge, Ware oder Commons? Proc. 11 Internationales
Symposium für Informationswissenschaft. Konstanz: UVK, 567-570.
3. Leuf, B., Cunningham, W.: The Wiki Way: Quick Collaboration on the Web. Addison-
Wesley, New York, 2001.
4. Hoffmann, R.: A wiki for the life sciences where authorship matters. Nature Genetics, Vol.:
40/9: 1047-1051 (2008)
5. Baumeister, J., Reutelshoefer, J., Nadrowski, K., Misok, A.: Using Knowledge Wikis to
Support Scientific Communities. In: Proceedings of 1st Workshop on Scientifc Communities
of Practice (SCOOP), Bremen, Germany (2007).
6. Schaffert, S.: IkeWiki: A semantic wiki for collaborative knowledge management. In:
Tolksdorf, R., Paslaru Bontas, E., Schild, K., editors, 1 st Int. Workshop on Semantic
Technologies in Collaborative Applications (STICA’06) Manchester, UK, (2006)
7. Krötzsch, M., Vrandečić, D., Völkel, M.: Semantic MediaWiki. In: Proceedings of the 5th
International Semantic Web Conference (ISWC’06). LNCS, vol. 4273, pp. 935-942.
Springer, Heidelberg (2006)
8. Friedland, N.S., Allen, P.G., Matthews, G., Witbrock, M., Baxter, D., Curtis, J., Shepard, B.,
Miraglia, P., Angele, J., Staab, S., Moench, E. Oppermann, H., Wenke, D. Israel, D.
Chaudhri, V., Porter, B., Barker, K., Fan, J. Chaw, S.Y., Yeh, P., Tecuci, D.: Project halo:
towards a digital Aristotle, AI Magazine, Winter 2004, (2004)
9. Auer S., Dietzold S., Riechert, T.: OntoWiki – A tool for social, semantic collaboration. In
Yolanda Gil, Enrico Motta, Richard V. Benjamins, and Mark Musen, editors, Proc. 5th Int.
Semantic Web Conference (ISWC’05), number 4273 in LNCS, pages 736–749. Springer,
(2006)
10.Kuhn, T.: AceWiki: A Natural and Expressive Semantic Wiki. In: Semantic Web User
Interaction at CHI 2008: Exploring HCI Challenges (2008)
11.MediaWiki contributors: MediaWiki, The Free Wiki Engine,
http://www.Mediawiki.org/w/index.php?title=Mediawiki&oldid=65192 (accessed March 3,
2010)
12.Köstlbacher, A., Maurus, J.: Semantische Wikis für das Wissensmanagement. Reif für den
praktischen Einsatz? In: DGI e.V./M. Heckner, C. Wolff (Ed.). Information Wissenschaft
und Praxis. Mai/Juni 2009, Dinges & Frick GmbH, Wiesbaden, pp. 225-231 (2009)
13.Ontoprise GmbH (Ed.): Basic Triplestore,
http://smwforum.ontoprise.com/smwforum/index.php/Help:Basic_Triplestore (accessed
March 3, 2010)
14.McBride, B.: Jena: A Semantic Web Toolkit. In: IEEE Internet Computing
November/December 2002, pp. 55-59. (2002)
15.Prud'hommeaux, E., Seaborne, A.: SPARQL Query Language for RDF. W3C
Recommendation 15 January 2008. http://www.w3.org/TR/rdf-sparql-query/ (accessed
March 3, 2010)