Change search
ReferencesLink to record
Permanent link

Direct link
Connecting digital cancer model repositories with markup: introducing TumorML version 1.0
Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
2013 (English)In: ACM SIGBioinformatics Record, ISSN 2331-9291, Vol. 3, no 3, 5-11 p.Article in journal, Meeting abstract (Refereed) Published
Abstract [en]

The cancer research community requires a standardized way of describing mathematical and computational models to enable interoperation between systems, repositories, and between the models themselves. In this paper we describe a new markup language, TumorML, for describing computational models that fall within the domain of cancer. TumorML is an XML-based markup language that wraps existing cancer model implementations with metadata for model curation, parametric interface description, implementation description, and compound model linking.

In this paper we first introduce the rationale for a new markup language for computational cancer model description based on our experiences and requirements from the European Commission's 'Transatlantic Tumor Model Repositories' project. The aim of the project is to develop a European-based digital cancer model repository to link and interoperate with a similar established repository based in the United States. TumorML was developed to enable this interoperation between repositories. We introduce the language and describe the main features of the specification and go on to describe a real application of TumorML where a molecular pathway model has been packaged using the new markup language.

Place, publisher, year, edition, pages
New York: Association for Computing Machinery (ACM), 2013. Vol. 3, no 3, 5-11 p.
Keyword [en]
Cancer, Models, Repositories, Mark-up, Tumor-ML
National Category
Bioinformatics (Computational Biology) Software Engineering
Research subject
Computer Science
URN: urn:nbn:se:uu:diva-211543DOI: 10.1145/2544063.2544064OAI: diva2:667375
Available from: 2013-11-26 Created: 2013-11-26 Last updated: 2013-11-28Bibliographically approved

Open Access in DiVA

ConnectingCancerModels(185 kB)33 downloads
File information
File name FULLTEXT01.pdfFile size 185 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
McKeever, Steve
By organisation
Department of Informatics and Media
Bioinformatics (Computational Biology)Software Engineering

Search outside of DiVA

GoogleGoogle Scholar
Total: 33 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 217 hits
ReferencesLink to record
Permanent link

Direct link