=Paper=
{{Paper
|id=None
|storemode=property
|title=Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM
|pdfUrl=https://ceur-ws.org/Vol-698/poster12.pdf
|volume=Vol-698
|dblpUrl=https://dblp.org/rec/conf/swat4ls/Lopez-Garcia10
}}
==Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM==
https://ceur-ws.org/Vol-698/poster12.pdf
Are SNOMED CT Browsers Ready for
Institutions? Introducing MySNOM
Pablo López-Garcı́a
Faculty of Computer Science, University of the Basque Country
Paseo Manuel de Lardizábal 1, Donostia-San Sebastián, Spain
pablo.lopez@ehu.es
http://bdi.si.ehu.es
Abstract. SNOMED Clinical Terms (SNOMED CT) is one of the most
widespread ontologies in the life sciences, with more than 300,000 con-
cepts and relationships, but is distributed with no associated software
tools. In this paper we present MySNOM, a web-based SNOMED CT
browser. MySNOM allows organizations to browse their own distribution
of SNOMED CT under a controlled environment, focuses on navigating
using the structure of SNOMED CT, and has diagramming capabilities.
Keywords: SNOMED CT, Terminologies, Ontologies, Browser
1 Introduction
The Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT)
has become a reference terminology [1] and an active research topic in both the
healthcare and the Semantic Web communities [2] [3]. An effective way to ad-
vance research in ontologies for the life sciences in general, and in SNOMED CT
in particular, is by providing appropriate software to researchers and practition-
ers. In particular, visualization and browsing tools can provide a better under-
standing of the structure and complexity of a biomedical terminology. There are
lists of existing browsers, such as the ones provided by The National Library of
Medicine of the United States1 and the United Kingdom’s National Health Ser-
vice2 , in order to provide researchers and practitioners with a reference. These
lists, however, are not comprehensive, not up to date, and have not been fully
ranked or evaluated. These lists can also be misleading for practitioners: as an
example, Protégé3 is listed as a SNOMED CT browser. In 2008, Rogers [4]
performed a study of existing SNOMED CT browsers and developed a general
catalog of desirable browsing features.
In this paper we present a SNOMED CT web-based browser called MySNOM,
aiming at showing the structure of SNOMED, with support for rich diagrams.
1
www.nlm.nih.gov/research/umls/Snomed/snomed_browsers.html
2
www.connectingforhealth.nhs.uk/systemsandservices/data/snomed/browser
3
protege.stanford.edu
2 Pablo López-Garcı́a
2 Architecture Overview
MySNOM is a web application following a layered approach to decouple orthog-
onal functionalities such as access control, graphical interface, business logic and
persistence. The architecture is shown in Figure 1.
HTTP Digest Authentication
Access Control Layer
XHTML + CSS + Embedded Ruby CGI (ERB)
Presentation Layer
Ruby Scripts
Search Browse Diagram GraphViz
Business Logic Layer
SNOMED CT
SQLite Embedded RDBMS Distribution Files
Persistence Layer
Fig. 1. MySNOM architecture.
MySNOM is hosted in a CGI-enabled web server and accessed using a web
browser. It relies on the lightweight and standard HTTP Digest protocol [5] for
authentication of users, and SQLite4 to provide fast access to the terminology.
3 User Interface and Diagramming Support
MySNOM uses a clean interface to explore all the relationships related to a
given concept, including reverse relationships. It places the current concept in
the middle of the screen, with referring concepts on the left and referred concepts
on the right. This structure follows the extended left-to-right direction of flow
and shows the natural directed graph structure of SNOMED CT. Every concept
and relationship is clickable. Each clicked concept or relationship leads to a new
screen, becoming the current term. The current concept is shown only once on
screen. Users can hover their mouse over any given concept to further inspect the
concept (e.g. see the SNOMED CT code). A screenshot of MySNOM browsing
the term ‘chronic disease’ is shown in Figure 2.
MySNOM supports the generation of diagrams that might clarify the context
of a given concept or serve as a graphic resource to be embedded in SNOMED
4
www.sqlite.org
Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM 3
Fig. 2. MySNOM browsing the term ‘chronic disease’.
CT-related documents. It uses different colors to emphasize several concepts:
the main concept is marked in yellow and hierarchy relationships are colored
in red. The diagramming module creates an intermediate representation of the
browsed concept using the DOT language [6]. The DOT language is a plain text
description that can be read by humans and processed by visualization tools.
MySNOM uses Graphviz [7], an Open Source, fast, graph generation software,
to generate the final diagram. Generated diagrams reflect the ontological nature
of SNOMED CT, as a directed graph, showing all concepts and relationships of
a given concept. A sample diagram is shown in Figure 3.
Fig. 3. Diagram generated by MySNOM when browsing the concept ‘asthma’.
4 Pablo López-Garcı́a
4 Conclusion and Future Work
We have presented an access-controlled, web-based, lightweight browser in order
to provide structural navigation and concise diagrams for SNOMED CT, using
an authorized standard distribution of SNOMED CT. The browser can be viewed
and tested at [8] and freely obtained by contacting the author. As future work we
plan to improve the prototype and add modularization support. Modularization
support will let a user store and export selected portions of SNOMED CT by
using ontology modularization techniques [9]. A tool with these characteristics
will allow a deep research of SNOMED CT’s structure and capabilities.
Acknowledgments. Thanks to Arantza Illarramendi, Jesús Bermúdez and
Idoia Berges for their support, inquiries and feedback about MySNOM. Thanks
to Stefan Schulz and Martin Boeker at IMBI Freiburg for their feedback and sug-
gestions. This work is supported by grant TIN2007-68091-C02-01 from Ministerio
de Ciencia e Innovación (MICINN) of the Spanish Government.
References
1. Freitas, F., Shulz, S.: Survey of current terminologies and ontologies in biology and
medicine: Elect. J. Commun. Inf. Innov. Health vol. 3, no. 1, pp. 7–18. (2009)
2. Spackman, K., Reynoso, G.: Examining SNOMED from the perspective of formal
ontological principles: Some preliminary analysis and observations. In: Proceedings
of the 1st International Workshop on Formal Biomedical Knowledge Representation,
pp. 81-87. (2004)
3. Héja, G., Surján, G., Varga, P.: Ontological analysis of SNOMED CT: BMC Medical
Informatics and Decision Making vol. 8, suppl. 1, S8. (2008)
4. Rogers, J., Bodenreider, O.: SNOMED CT: Browsing the Browsers. In: Proceedings
of the 3rd International Conference on Knowledge Representation in Medicine, pp.
30–36. (2008)
5. Franks, J., Hallam-Baker, P., Hostetler, J., Leach, P., Luotonen, A., Sink, E.,
Stweart, L. RFC2069: An Extension to HTTP : Digest Access Authentication. RFC.
(1997)
6. Eleftherios Koutsofios, E., North, S. C.: Drawing Graphs With Dot (1996)
7. Ellson, J., Gansner, E., Koutsofios, L., North, S., Woodhull, G.: Graphviz Open
Source Graph Drawing Tools. In: Mutzel, Petra and Jnger, Michael and Leipert,
Sebastian (eds.). LNCS, vol. 2265, pp. 594–597. Springer, Heidelberg (2002)
8. BDI Group, MySNOM SNOMED CT Browser demo,
http://bdi.si.ehu.es/mysnom/ (user: demo, password: demo).
9. Stuckenschmidt et al.: Modular Ontologies: Concepts, Theories and Techniques for
Knowledge Modularization: LNCS. Springer, Heidelberg (2009)