Open Flow Biological Network Initiative: Pathway map building, standards, simulation, and knowledge sharing

Transcription

1 Open Flow Biological Network Initiative: Pathway map building, standards, simulation, and knowledge sharing Hiroaki Kitano (1,2), Yukiko Matsuoka (1) (1) The Systems Biology Institute, (2) OIST 2009/04/07

2 Evolution of Pathway DB & Modeling 1 st Generation Isolated DB, domain specific models KEGG, Panther Pathway DB, Reactome, etc. 2 nd Generation Repository, Standard Formation (SBML, SBGN, MIRIAM..) such as Biomodels.net, Panther Community 3 rd Generation Integration, Web 2.0, Open Flow Payao, Next Generation Pathway DB Suite 4 th Generation Integration simulation, Plug-in Scalable System 5 th Generation Integrate with original resource banks

3 Pathway Map Building Infrastructure Model Representation Standard representation methods of biological models Modeling tools Databases CellDesigner BioPAX Curation Model sharing Jarnac Plot Gibson Simulation / Analysis tools

4 PAYAO platform for sharing models

5 PAYAO Community Tagging System to SBML models A community tool to work on the same pathway models simultaneously, insert tags to the specific parts of the model, exchange comments, record the discussions and eventually update the models accurately and concurrently. Reads SBML models, display them with CellDesigner

6 PAYAO: SBML Models Tagging System

7 PAYAO - Tags

8 PAYAO Tags expanded

9 PAYAO-PATHTEXT

10 PAYAO PathTEXT (1)

11 PAYAO PathTEXT (2)

12 Payao Client <Model ID="oda_nfkappab"> <Node ID="re1" Type="reaction"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> <Node ID="re2" Type="species"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> <Node ID="sa1" Type="species"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> <Node ID="sa2" Type="species"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> <Node ID="csa1" Type="complexspecies"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> <Node ID="csa2" Type="complexspecies"> <Link PMID=" " Type="textmining" Source="medie" MedlineDate=" "> <Link PMID=" " Type="annotation" Source="koda" MedlineDate=" "> </Node> </Model> Web Service A user then logs in to the Payao community tagging system and selects a pathway model. When a model is selected, a request is sent to the PathText Web Service for publications matching any node in the selected model. The Pathtext Web Service then returns an xml result containing the matching publications.

13 Payao then displays document icons on the matching nodes. Note: This process will begin either automatically and/or when the Automatic Search-Search button is clicked. The document icons are hyperlinks that when selected, open a PathText Results Page in a new tab of the user s browser.

14 The PathText Results Page displays the results matching the selected node in Payao from both the PathText Annotation Tool and text mining queries.

15 In Manual Search Mode, a search for Co-Occurrences will take place. (Note: This is essentially the same as the current prototype and will use the current web service) A user selects one or more nodes and/or reactions and clicks the Search button.

16 The results are displayed in Facta, allowing the user to then continue on with other searches using the Facta system.

17 PubMed ID Link

18 Pathway Curation Suite: Open Flow Model Workflow System Resources / tools Check Existing Data Convert to standard format External Pathway Database Adaptor for BioPAX and SBML BioModels.net Reactome PathwayCommons etc To develop Edit/Layout Pathways curator CellDesigner To enhance Compliant graphical notation Genome annotation General annotation Store Data Community annotation Share Data curator users Annotation Plugins Central Database Pathway models Community base tagging system PAYAO db Annotation data Publish / Public View To develop MIRIAM / MIASE compliant annotation To develop To enhance To enhance CellDesigner Applet

19 Open Flow Trials Public DB Integration Panther, Reactome, Pathway Commons, etc. Open Yeast Extensive Mapping and Annotation for Budding Yeast

20 Digital Yeast High-precision comprehensive budding yeast Molecular-based computational model that can predict physiological responses of budding yeast against genetic mutations and drugs perturbations at more than 90% of accuracy. Medical implications as well Histon regulation system is highly homologous to human Sir2 discovered in yeast, now important in human aging

21 Open Yeast Initiative Open collaboration initiative to uncover molecular interactions Evolving DB and models Hot Plug-in and Play simulation platform (in future)

22 Budding Yeast Cell Cycle and Signaling

23 Genome-wide in vivo robustness profile

24 Multi-scale heterogeneous models " ( u(x,y ( h(x,y ( f(x,y ( g(x,y Integration Communication " ( u(x,y ( f(x,y ( h(x,y ( g(i,j ( a(i,j ( g(x,y ( b(i,j Encapsulation We need: 1-Standards of representation ( ontologies ) 2-Interfaces 3-Trusted data resources

25 Proof-of-Concept Project Digital Yeast Project Open Yeast Initiative

26 Open Biology Project Software-related Research and Development Digital Yeast / Open Yeast Project Location: Okinawa Institute for Science and Technology Launch of the project conditional on agreement of contract details.

27 Acknowledgement PAYAO SBI Haruka Sugimura Hayama Yukiko Matsuoka MKI Norihiko Kikuchi OIST Hiroaki Kitano PathTEXT Univ. of Tokyo Rune Saetrea Brian Kemper Yoshimasa Tsuruoka Kanae Oda Naoaki Okazakia National Centre for Text Mining (NaCTeM) Sophia Ananiadoue Junichi Tsujii

28 THANK YOU