User:Jmuhlich/ICSB 2008 SBWiki presentation: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
Line 38: Line 38:
|}
|}


Ontologies like SBO and BioPax are sound Computer Science theory, but to biologists this is just mapping one hairball onto another!
* MI (Minimum Information) efforts such as MIAME and MIRIAM are good for published data, but too rigid for daily use
* Ontologies like SBO and BioPax are sound computer science theory, but to biologists this is just mapping one hairball onto another
</div>
</div>


Revision as of 01:25, 23 August 2008


<html> <script> function addStylesheet(url) { 

   // presentation mode
   if (document.createStyleSheet) {
       document.createStyleSheet(url);
   }
   else {
       var styles = "@import url('" + url +  "');";
       var newSS=document.createElement('link');
       newSS.rel='stylesheet';
       newSS.href='data:text/css,'+escape(styles);
       document.getElementsByTagName("head")[0].appendChild(newSS);
   }

} if (location.href.indexOf('action=render') > 0) { 

   document.write("<head><title>Presentation</title></head>"); // need this for some browsers for addStylesheet to work
   addStylesheet('http://www.w3.org/Talks/Tools/Slidy/slidy.css');
   addStylesheet("/skins/monobook/main.css");
   addStylesheet("/index.php?title=MediaWiki:Common.css&usemsgcache=yes&action=raw&ctype=text/css&smaxage=18000");
   addStylesheet("/index.php?title=MediaWiki:Monobook.css&usemsgcache=yes&action=raw&ctype=text/css&smaxage=18000");
   addStylesheet("/index.php?title=-&action=raw&gen=css&maxage=18000&smaxage=0&ts=20070606210926");
   document.write('<script src="http://www.w3.org/Talks/Tools/Slidy/slidy.js" type="text/javascript"><' + '/script>');
   document.write('<script type="text/javascript">wgBreakFrames = false;<' + '/script>'); // for wikibits.js
   document.write('<script src="/skins/common/wikibits.js" type="text/javascript"><' + '/script>');
   document.write('<script src="/index.php?title=-&action=raw&smaxage=0&gen=js" type="text/javascript"><' + '/script>');

} else { 

   // wiki mode
   if (wgServer)
       document.write('<a href="' + wgServer + '/index.php?title=' + wgPageName + '&action=render"><b><em>=> Start web presentation</em></b></a>');

} </script> </html>




SBWiki

A semantic structured wiki for systems biology research

Jeremy Muhlich


Current Practice

raw spreadsheets & SBML hairballs


New Standards Help...

BioPax
  • MI (Minimum Information) efforts such as MIAME and MIRIAM are good for published data, but too rigid for daily use
  • Ontologies like SBO and BioPax are sound computer science theory, but to biologists this is just mapping one hairball onto another


SB-Wiki: Practical Documentation

  • Annotate early, during research not after
  • Use concepts from existing standards
  • Rigorously apply "80/20" rule


Benefits

  • Group consensus documentation, collaboration
  • Easy sharing
  • Change tracking / history preservation


Design

MIBBI SB-Wiki

Overall structure based on MIBBI (Minimum Information for Biological and Biomedical Investigations)


==


==


Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Jmuhlich/ICSB_2008_SBWiki_presentation&oldid=234422"