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Error in sbmlimport - Conversion from SBML/XML to stochiometric matrix

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Namrata Tomar
Namrata Tomar 2015년 6월 19일
댓글: Ingrid Tigges 2015년 9월 7일
I am using sbmlimport function to convert KEGG pathway SBML (KGML) file into stochiometric matrix. It has .xml extension, but getting this error -- Error using SimBiology.SBMLReadWrite/sbmlread. A fatal error occurred reading in this file. Error in privatesbmlio (line 26). Error in sbmlimport (line 62) ret = privatesbmlio('read',nargout,{fullfilename, varargin});
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Namrata Tomar
Namrata Tomar 2015년 6월 24일
편집: Walter Roberson 2015년 8월 18일
Hello,
  1. I am using Matlab 2014a.
  2. example, m = sbmlimport('lotka.xml'); [M,objSpecies,objReactions] = getstoichmatrix(m1); is working but not for my Kegg Pathway.
  3. I downloaded a kegg pathway- http://www.genome.jp/kegg-bin/show_pathway?map=hsa05230&show_description=show. Code is m = sbmlimport('hsa.xml') but it is giving error.
Ingrid Tigges
Ingrid Tigges 2015년 9월 7일
Can you post your file hsa.xml here?

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답변 (1개)

Ingrid Tigges
Ingrid Tigges 2015년 6월 25일
Hi Namrata,
The files from KEGG are not in the SBML format but in the KGML format (see KGML specification information ). SimBiology cannot read in KGML files. There are however tools available on the internet, for example this tool which allow the conversion of KGML files into the SBML format.
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Namrata Tomar
Namrata Tomar 2015년 8월 18일
Thanks .. Can you please let me know how to use it - I have downloaded kgtrans.jnlp. Now how should I proceed?

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