Are SNOMED CT Browsers Ready for Institutions? Introducing MySNOM

Abstract

SNOMED Clinical Terms (SNOMED CT) is one of the most widespread ontologies in the life sciences, with more than 300,000 concepts 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

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Introduction

Architecture Overview MySNOM is a web application following a layered approach to decouple orthogonal functionalities such as access control, graphical interface, business logic and persistence. The architecture is shown in Figure 1.

Access Control Layer Presentation Layer Business Logic Layer Persistence Layer

HTTP Digest Authentication

XHTML + CSS + Embedded Ruby CGI (ERB) Ruby Scripts

Search

Browse

Diagram

GraphViz SQLite Embedded RDBMS

SNOMED CT

Distribution Files

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

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.

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, Jesu´s Bermu´dez 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 suggestions. This work is supported by grant TIN2007-68091-C02-01 from Ministerio de Ciencia e Innovaci´on (MICINN) of the Spanish Government.

References

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