Difference between revisions of "Hackathon wikidb"
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Dongilbert (Talk | contribs) (→Genome wiki from chado notes) |
Dongilbert (Talk | contribs) (→Genome wiki from chado notes) |
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** locate sample chado data (some format) for some genes w/ attributes | ** locate sample chado data (some format) for some genes w/ attributes | ||
** convert to some format suited to wiki loading (as wiki xml?) | ** convert to some format suited to wiki loading (as wiki xml?) | ||
| + | *** dump table via Chado SQL; | ||
| + | see e.g. http://eugenes.org/gmod/genbank2chado/conf/v_genepage3.sql | ||
*** via xml/xslt transforms | *** via xml/xslt transforms | ||
*** via XORT perl parser | *** via XORT perl parser | ||
Revision as of 20:36, 23 August 2007
Genome wiki from chado notes
- From hackathon
- tasks:
- locate sample chado data (some format) for some genes w/ attributes
- convert to some format suited to wiki loading (as wiki xml?)
- dump table via Chado SQL;
see e.g. http://eugenes.org/gmod/genbank2chado/conf/v_genepage3.sql
- via xml/xslt transforms
- via XORT perl parser
- other
- load to wiki
>> this is larger;loading into wikipedia db via wikipedia.xml
- dump wiki table edit (mysql db)
- convert to chado xml (? xml transforms)
** flybase harvard has scripts for general bulk data to chado.xml
- options:
- use chado sql view/procedure to dump tables suited to wikibox_db ?
- easier
