Changes between Initial Version and Version 1 of SystemsBiologySBML

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2010/02/12 17:01:41 (13 years ago)
Author:
ogishima
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  • SystemsBiologySBML

    v1 v1  
     1= SystemsBiologySBML = 
     2 
     3[[PageOutline]]  
     4 
     5In systems biology field, most curated models are described in SBML format by using for example CellDesigner, and each model is 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. 
     6 
     7= Datasets = 
     8 * BioPAX http://www.biopax.org/ 
     9  * Level 3 (RC3): BioCyc, HumanCyc 
     10  * Level 2: Reactome, BioCyc, INOH, Nature/NCI Pathway Interaction Database, Cancer Cell Map, Pathway Commons 
     11  * Level 1: BioCyc, KEGG 
     12 
     13 * BioModels Database (EMBL-EBI) http://www.ebi.ac.uk/biomodels/ 
     14   stores over 400 published systems biology models in not only SBML and but also BioPAX Level 2 OWL. 
     15 
     16 * Mol Syst Biol - Structural Data Archive (in SBML) http://www.nature.com/msb/sdata/index.html 
     17 
     18 * E-cell Model Repository - SBML Models http://www.e-cell.org/ecell-models/repository/SBML 
     19 
     20 * Model Format OWL (MFO) http://cisban-silico.cs.ncl.ac.uk/MFO/ is an alternative OWL. 
     21  * BioPAX problems are described in [http://themindwobbles.wordpress.com/tag/semantic-data-integration/ ESBML in OWL: some thoughts on Model Format OWL (MFO)] 
     22 
     23= Convertor =  
     24=== BioPAX Level 3 === 
     25No convertor now. 
     26 
     27=== BioPAX Level 2 === 
     28The convertor sbml2biopax from SBML to BioPAX OWL is provided by BioModels Compneur Group. 
     29 * http://www.ebi.ac.uk/compneur-srv/sbml/convertors/SBMLtoBioPax.html 
     30 
     31The sbml2biopax requires [http://sbml.org/Software/libSBML libSBML], and it works with the latest libSBML (libsbml.4.0.1). 
     32 
     33{{{ 
     34$ 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 
     37}}} 
     38 
     39{{{ 
     40$ wget http://www.nature.com/msb/journal/v1/n1/extref/msb4100014-s3.xml -O Oda_EGFR_2005.xml 
     41$ sh sbml2biopax.sh Oda_EGFR_2005.xml 
     42$ wget http://www.nature.com/msb/journal/v1/n1/extref/msb4100057-s1.xml -O Oda_TLR_2006.xml 
     43$ sh sbml2biopax.sh Oda_TLR_2006.xml 
     44}}} 
     45 
     46The sbml2biopax generate BioPAX Level 2 OWL file from given SBML file. 
     47 
     48= Store = 
     49=== 4store === 
     50{{{ 
     51$ 4s-backend-setup biopax_lv2 
     524store[2577]: backend-setup.c:176 erased files for KB biopax_lv2 
     534store[2577]: backend-setup.c:301 created RDF metadata for KB biopax_lv2 
     54$ 4s-backend biopax_lv2 
     55$ 4s-import -v biopax_lv2 Oda_EGFR_2005.owl  
     56removing old data 
     57Reading <file:///Users/ogishima/.../Oda_EGFR_2005.owl> 
     58Pass 1, processed 4951 triples (4951) 
     59Pass 2, processed 4951 triples, 61233 triples/s 
     60Updating index 
     61Index update took 2.412844 seconds 
     62Imported 4951 triples, average 1985 triples/s 
     63$ 4s-import -v biopax_lv2 Oda_TLR_2006.owl 
     64removing old data 
     65Reading <file:///Users/ogishima/.../Oda_TLR_2006.owl> 
     66Pass 1, processed 10087 triples (10087) 
     67Pass 2, processed 10087 triples, 78545 triples/s 
     68Updating index 
     69Index update took 0.605142 seconds 
     70Imported 10087 triples, average 13330 triples/s 
     71}}} 
     72 
     73=== Virtuoso === 
     74Coming soon. 
     75 
     76= Query = 
     77=== 4store === 
     78{{{ 
     79$ 4s-query biopax_lv2 
     804store>SELECT * WHERE {?s ?p ?o} 
     81   >#EOQ 
     82?s      ?p      ?o 
     83<http://www.ebi.ac.uk/biomodels/biopax.owl#c3>  <http://www.biopax.org/release/biopax-level2.owl#TERM>  "late_br_endsome" 
     84<http://www.ebi.ac.uk/biomodels/biopax.owl#c2>  <http://www.biopax.org/release/biopax-level2.owl#TERM>  "recycling_br_endsome" 
     85... 
     86results.c:1655 hit soft limit 2 times 
     87# hit complexity limit 2 times, increasing soft limit may give more results 
     88#EOR 
     89}}} 
     90 
     91=== Virtuoso === 
     92Coming soon. 
     93 
     94= SPARQL end point = 
     95SPARQL end point is now under construction, and will appear soon. :-) 
     96 
     97= Usecase (goal) = 
     98Usecase 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 
     100= Problems & ToDo = 
     101BioPAX 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 generate not OWL but simple RDF files. 
     102 
     103= Visualization =  
     104 * RelFinder in Virtuoso 
     105 * Cytoscape: [http://chianti.ucsd.edu/Cyto-2_7-beta/ Cytoscape 2.7.0 beta] supports BioPAX Level 3 by Ono-san.  See [wiki:VisualizationAndInteraction].