Changes between Version 9 and Version 10 of SystemsBiologySBML

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Timestamp:
2010/02/12 19:43:45 (15 years ago)
Author:
ogishima
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  • SystemsBiologySBML

    v9 v10  
    11= SystemsBiologySBML = 
    2  
    32[[PageOutline]]  
    43 
    5 In systems biology field, most curated models are developed by for example [http://www.celldesigner.org/ CellDesigner], and are described in SBML format. Each model is publised in each paper, and in each SBML file. To integrate published models,  semantic web approach is very useful. BioPAX provides a common exchange format for biological pathways and models in OWL. http://www.biopax.org/ Please see usecase (goal) as described below. 
     4In systems biology field, most curated models are developed by for example [http://www.celldesigner.org/ CellDesigner], and are described in [http://sbml.org/Main_Page SBML] format. Each model is publised in each paper, and in each SBML file. To integrate published models,  semantic web approach is very useful. BioPAX provides a common exchange format for biological pathways and models in OWL. http://www.biopax.org/ Please see usecase (goal) as described below. 
     5 
     6= Goal = 
     7Goal is first of all an integration of curated models, in other words, pathways. As described above, each pathway is publised in each paper, and in each SBML file. However, as you know, pathways are closely related each other. If we can integrate these curated pathways, we can overview pathways and search pathways to find novel hypothesis. It will be very helpful for us to obtain novel insight and hypothesis. 
     8 
     9= Usecase - Alzheimer disease pathway = 
     10One usecase is Alzheimer disease study. We has developed a pathway database for Alzheimer disease named AlzPathway. AlzPathway collects signaling and metabolic pathways relevant to Alzheimer disease. By only AlzPathway, we already have discovered novel hypothesis of relationships between amyloid beta and tau phosphorylation pathways.  
     11 
     12Importantly, pathways relevant to Alzheimer disease are not exclusively relevant to Alzheimer disease. For example, Alzheimer disease pathway is closely related to apoptosis pathway, and if someone published a model for apoptosis, an integration of AlzPathway and apoptosis pathway will be very helpful for researchers in Alzheimer disease to obtain novel insight and hypothesis about relationships between Alzheimer disease and apoptosis. 
    613 
    714= Datasets = 
    … …  
    3340{{{ 
    3441$ wget http://www.ebi.ac.uk/compneur-srv/sbml/convertors/sbml2biopax-1.3.tar.gz 
    35 $ tar xvfz sbml2biopax-1.3.tar.gz; cd sbml2biopax-1.3; cp ~/mymodel.xml . 
    36 $ sh sbml2biopax.sh mymodel.xml 
     42$ tar xvfz sbml2biopax-1.3.tar.gz; cd sbml2biopax-1.3; cp ~/alzpathway.xml . 
     43$ sh sbml2biopax.sh alzpathway.xml 
    3744}}} 
    3845 
    … …  
    53604store[2577]: backend-setup.c:301 created RDF metadata for KB biopax_lv2 
    5461$ 4s-backend biopax_lv2 
     62$ 4s-import -v biopax_lv2 alzpathway.owl  
    5563$ 4s-import -v biopax_lv2 Oda_EGFR_2005.owl  
    5664removing old data 
    … …  
    95103SPARQL end point is now under construction, and will appear soon. :-) 
    96104 
    97 = Usecase (goal) = 
    98 Usecase is an integration of models, in other words, pathways. Each pathway is in each SBML file. However, as you know, pathways are closely related each other. For example, TMD systems biology group (http://bioinfo.tmd.ac.jp/sysbio/) has developed a database for Alzheimer disease named AlzPathway. AlzPathway collects signaling pathways relevant to Alzheimer disease, however, these pathways are not exclusively relevant to Alzheimer disease; Alzheimer disease pathway is closely related to apoptosis pathway, and if someone published a model for apoptosis, an integration of AlzPathway and apoptosis pathway will be very helpful for researchers in Alzheimer disease to obtain novel insight and hypothesis. 
    99  
    100105= Problems & ToDo = 
    101106 * BioPAX OWL might be too complicate to archive the above usecase (goal). SPARQL search might took so much time to return results. Appropriate reduction of information of SBML model is required to convert from SBML to RDF (not OWL). 
    … …  
    108113 
    109114= Members = 
    110  * Soichi Ogishima (BioCichlid, AlzPathway @ TMD systems biology group, JAPAN) 
     115 * Soichi Ogishima (AlzPathway, BioCichlid @ TMD systems biology group, JAPAN) 
    111116 * Ryosuke Ishiwata (BioCichlid @ TMD systems biology group, JAPAN) 
    112117