Bilkent University
Department of Computer Engineering


Validation of Biological Maps in SBGN


Umut Utku Çalış
MS Student
Computer Engineering Department
Bilkent University

Systems Biology Graphical Notation (SBGN) is a graphical language for representing biological maps. LibSBGN is a library that deals with reading and writing of the SBGN-ML format ( XML-based format for description of SBGN maps ) and conversion to other formats. Hence, validation of this library is important for semantical and syntactical correctness of these processes. In Javascript version of this library, low level syntactic validation with certain XSD is also provided . As a high level symantic validation, schematron validation which includes xlst transformation and sax parsing is proposed in this work. We aimed that sax parsing and xlst transformation is added to Javascript version of this library for adding schematron validation to enable symantic correctness as well as syntatical correctness. We plan to turn this facility into a web service, which can be used by SBGN editors such as Newt.


DATE: 09 April, 2018, Monday, CS590 & CS690 presentations begin at @ 15:40