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OBO-Edit 1.000-beta4 now available

John Day-Richter john.richter at aya.yale.edu
Mon May 2 02:07:32 PDT 2005


OBO-Edit 1.000-beta4 is now available from

	http://sourceforge.net/projects/geneontology

This version fixes bugs (of course), but the major enhancement is in the 
totally retooled data adapter system. The data adapter interface has been 
*greatly* simplified (until you hit the "advanced" button), error messages 
are much better, and any data adapter operation can be cancelled while in 
progress.

The OBOFileAdapter now allows you to select which version of the OBO file 
format you'd like to write. The OBOFileAdapter also uses some new 
experimental code that saves all files into a temporary directory before 
moving the files to their final destination. This should prevent you from 
losing your files if OBO-Edit crashes during a save.

Finally, you can now load files from the OBO-Edit command line. To load OBO 
Format files, just specify a list of files on the command line, like so:

	./oboedit ~/downloads/gene_ontology.obo

To load non-OBO files, you need to specify a data adapter switch. A list of 
data adapter switches can be printed with the command

	./oboedit --listadapters

Once you know what data adapter switch you want to use, you can load files by 
specifying an adapter switch and then a list of files, like so:

./oboedit -OBOEDIT:GOFlatFileAdapter \ 		
	http://www.geneontology.org/ontology/function.ontology 

Note that some features have been disabled, as I'm in the midst of changing 
all the code over to the new data adapter system. The "save" menu item has 
been disabled, and most of the history loading and saving code has been taken 
offline in this version.

	-John


P.S. To load a definition file in the new GO Flat File Adapter interface, just 
specify the definition file name in the "Load files" box along with the other 
ontology files you are loading. OBO-Edit will figure out which file is the 
definitions file.

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