Wikimania 2011 abstract
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- Title of the submission
- Type of submission (workshop, tutorial, panel, presentation)
Presentation
- Author of the submission
Juha Villman, Einari Happonen, Teemu Rintala
- Abstract (please use no less than 300 words to describe your proposal)
Something about Opasnet, Opasnet Base, R, table2base and Base UI.
Opasnet is a website (running on Mediawiki) and workspace for a mass collaboration project that aims to improve societal decision-making. Opasnet is hosted by THL (National Institute for Health and Welfare, Finland), The Department of Environmental Health. The original motivation was to improve environmental health assessments and thus decisions related to environment and health. However, as the methods have developed and the project has grown, the scope has been widened to policy-making in any field. One of the major topics in Opasnet is climate change, which is clearly a multi-disciplinary field. Opasnet is based on open participation by anyone interested, free distribution of information, and strict application of the scientific method.
Opasnet is based on the idea that assessments should no longer be done in closed expert groups that produce some static reports that may or may not answer the questions a decision-maker actually has, and that are only as credible as the expert group is. Instead, two improvements are needed. First, an assessment should be built on an explicit information need that is defined by an open deliberation between experts, decision-makers, and stakeholders. Second, everything in the assessment - including premises, data sources, modelling, and conclusions - is open to scientific criticism.
Mediawiki is designed mainly for encyclopedia use so it is good for displaying text and images. Assessments in Opasnet requires also text and images but often we need massive amounts of numerical data. Instead of saving all the numerical data into Mediawiki's own database we use separate database. For this purpose we have developed Opasnet Base. Opasnet Base is MySQL database which is used as a storage and retrieval system for results of variables and data from studies. It is designed to be flexible enough to store information in almost any format: probability distributions or deterministic point estimates; spatially or temporally distributed data; or data with multiple dimensions. It can be used as a direct source of model input data, thus making it possible to use shared input information sources such as population data, climate scenarios, or dose-responses of pollutants. Opasnet Base is integrated into Mediawiki as an extension which has its own special page for browsing the data.
Currently there is 2 methods to upload data into Opasnet Base. For smaller datasets (rows < 100) we have developed Table2Base -extension. It enables data upload directly from tables in wikipages. Syntax of these tables is quite similar to standard wikitables. Instead of headers you need to define indices, cells are separated by a single |-sign and line break starts a new row of data. Every time table is updated a new set of data is stored into Opasnet Base. Old data is also kept in the database meaning that full history is accessible just like page history in Wikipedia.
Second method for data upload is to use some statistical software which has ODBC capabilities. So far we have built functionalities for this purpose for R and Analytica. Using R or Analytica it is easy to download data from Opasnet Base, use it on your analyses and then upload new data directly into Base. Using external statistical software is recommended if you have large dataset to upload. Especially we recommend use of R which is a free software available for multiple platforms.
Something about R extension
- Track (People and Community/Knowledge and Collaboration/Infrastructure)
Infrastructure
- Slides or further information (optional)