Open Flow Biological Network Initiative

2009 April 13

by abhishektiwari

One of the my favorite talks at CellML et al workshop 2009 by Hiroaki Kitano, and the real mantra behind the talk is Web 2.0 and its impact on community curation and collaborated biological modelling. Community-annotation efforts such as Wikiprofessional, WikiGene, WikiPathways and many more other projects rely on the crowd sourcing and benefits from the curation of knowledge through collective intelligence. Community biocurators populate the specific databases with information gathered from literature, apart from submitting structured data these curators also create structured metadata which is an important part of the curation process. The main theme of the talk was PAYAO tool which is a community tagging system for systems biology pathway and models. PAYAO aims to provide a framework to facilitate tracking and update mechanism for the collaborated model building and pathway curation.

“Payao” system aims to enable a community to work on the same models concurrently, insert tags to the specific parts of the model, exchange comments, search for the relevant publication using text mining technology (PathText), record the discussions so that we can update the models accurately.

PAYAO community system is built on Web 2.0 technologies coupled with a powerful text mining system-PathText which serves as bridge between biological pathways and text mining. Idea is to supplement the structured metadata with informal annotations, tags and comments to add more value and enhance discovery potential. Kitano also adumbrated the evolution of system biology data models and databases in 5 generations-

1st Generation- Isolated databases, domain specific models (KEGG, Panther Pathway DB, Reactome, etc).
2nd Generation- Model repositories (Biomodels, CellML), development of systems biology standards and guidelines (CellML, SBML, SBGN, BioPAX, MIRIAM etc)
3rd Generation- Stress on database integration, community curation, model sharing, open flow
4th Generation– Integration simulation, Plug-in Scalable System
5th Generation– Integrate with original resource banks

Talk emphasized on open flow of the information at the community level system biology activities in 3rd generation. In a personal discussion Kitano mentioned about a new kind of scoring metric based on contributions or entries user have made in database as annotation or curation, these scores can be further used for hiring new biocurators or as scholarly factor.

Hiroaki Kitano, The Systems Biology Institute and OIST

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Abhishek Tiwari permalink

April 14, 2009

Open Flow Biological Network Initiative: One of the my favorite talks at CellML et al workshop 2009 by Hiroaki K.. http://tinyurl.com/cje5kv

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