| | 1 | = SystemsBiologySBML = |
| | 2 | |
| | 3 | [[PageOutline]] |
| | 4 | |
| | 5 | In 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 === |
| | 25 | No convertor now. |
| | 26 | |
| | 27 | === BioPAX Level 2 === |
| | 28 | The 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 | |
| | 31 | The 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 | |
| | 46 | The sbml2biopax generate BioPAX Level 2 OWL file from given SBML file. |
| | 47 | |
| | 48 | = Store = |
| | 49 | === 4store === |
| | 50 | {{{ |
| | 51 | $ 4s-backend-setup biopax_lv2 |
| | 52 | 4store[2577]: backend-setup.c:176 erased files for KB biopax_lv2 |
| | 53 | 4store[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 |
| | 56 | removing old data |
| | 57 | Reading <file:///Users/ogishima/.../Oda_EGFR_2005.owl> |
| | 58 | Pass 1, processed 4951 triples (4951) |
| | 59 | Pass 2, processed 4951 triples, 61233 triples/s |
| | 60 | Updating index |
| | 61 | Index update took 2.412844 seconds |
| | 62 | Imported 4951 triples, average 1985 triples/s |
| | 63 | $ 4s-import -v biopax_lv2 Oda_TLR_2006.owl |
| | 64 | removing old data |
| | 65 | Reading <file:///Users/ogishima/.../Oda_TLR_2006.owl> |
| | 66 | Pass 1, processed 10087 triples (10087) |
| | 67 | Pass 2, processed 10087 triples, 78545 triples/s |
| | 68 | Updating index |
| | 69 | Index update took 0.605142 seconds |
| | 70 | Imported 10087 triples, average 13330 triples/s |
| | 71 | }}} |
| | 72 | |
| | 73 | === Virtuoso === |
| | 74 | Coming soon. |
| | 75 | |
| | 76 | = Query = |
| | 77 | === 4store === |
| | 78 | {{{ |
| | 79 | $ 4s-query biopax_lv2 |
| | 80 | 4store>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 | ... |
| | 86 | results.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 === |
| | 92 | Coming soon. |
| | 93 | |
| | 94 | = SPARQL end point = |
| | 95 | SPARQL end point is now under construction, and will appear soon. :-) |
| | 96 | |
| | 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 | |
| | 100 | = Problems & ToDo = |
| | 101 | 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 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]. |
