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Re: [SO-devel] Re: Vol 1 #279 Add Genome
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From: Karen E. <ei...@fr...> - 2006-02-17 18:28:32
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Hi Bob, Thank you for not throwing genome into the chaos at the meeting. The whole point of making an ontology is to have the terms defined and computable. Having a concept with a 'define as you like' does not achieve that. Also placing the concept in the ontology adds to the definition, as it constrains the term by telling us what kind of thing it is, and what it is composed of and related to. So we need to have some idea of what it is before we can place it in the ontology. My point is that genome is not a region as it is not continuous sequence. I think chromosome should be the biggest continuous sequence in SO. The MODs should be responsible for defining what they mean by genome, and annotate their genomes content using SO, but keep the actual 'genome' concept external from the ontology. Thanks for your thoughts, I appreciate your input, Karen On Feb 17, 2006, at 7:12 AM, Bob Sinclair wrote: > I _almost_ brought this up at that fun meeting we had, but bit my > tongue. > > Adding genome makes sense for "completeness," which I like. But it > adds some significant questions: if "genome" is all encompassing I > really don't think it adds anything of substance to the SO (i.e. if > everything is part of the genome), but if (as makes more biological > sense) some things are not part of the genome (some of the mobile > elements for example) then it could be a useful addition. The reason I > didn't bring it up is that it opens the same can of works we were > dealing with for "gene" -- is the genome the sum total of all DNA > (RNA) that's inside a given organism's boundary at a given time, or is > it the chromosomes and known (stable) extrachromosomal stuff? If you > look at the google defs provided you'll immediately see that problem > (def1 "complete set of genetic info including DNA and RNA" vs def 4 > "all the genes") It also leads us into more territory where our > definitions will break down under close scrutiny (complete genetic > content of an organism vs. genetic endowment of a species, for > example). > > Left with a "define as you see fit" you could probably include it > without causing too much trouble. > > One other place where I think Genome might be useful as a term is for > the environmental sequencers (but of course then genome would not be > the top-level term, itself being part of a pooled DNA sample). > > Bob > > > > son...@li... wrote: > >> Send SOng-devel mailing list submissions to >> son...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/song-devel >> or, via email, send a message with subject or body 'help' to >> son...@li... >> >> You can reach the person managing the list at >> son...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of SOng-devel digest..." >> >> >> Today's Topics: >> >> 1. New SO things (Karen Eilbeck) >> 2. New term suggestion (Karen Eilbeck) >> >> --__--__-- >> >> Message: 1 >> To: son...@li... >> From: Karen Eilbeck <ei...@fr...> >> Date: Thu, 16 Feb 2006 16:24:46 -0700 >> Subject: [SO-devel] New SO things >> Reply-To: son...@li... >> >> Hi all, >> >> Some new things about SO. >> >> SO release >> I have made a file release of SO. You can find it here: >> http://sourceforge.net/project/showfiles.php? >> group_id=72703&package_id=179383 >> I am going to start saving my edits in the CVS using obo format 1_2: >> http://www.godatabase.org/dev/doc/obo_format_spec.html >> >> This is because I need the added expressiveness to capture the >> cross-product terms being incorporated in to SO. If you don't want to >> use the bleeding edge CVS files, please use the release system. >> >> Term Tracker >> I have made a term tracker for people to use to make suggestions >> about terms. Someone found it before I announced it and has already >> requested a new term. More about that later. >> http://sourceforge.net/tracker/?group_id=72703&atid=810408 >> >> SO Browser >> I have created a prototype browser called miSO to view SO terms >> online. >> This is very new (a day old) so its not very mature, but maybe useful >> to people who do not use OBO-edit. >> http://song.sourceforge.net/SO_view/index.html >> >> Cheers, >> Karen >> >> >> >> --__--__-- >> >> Message: 2 >> To: son...@li... >> From: Karen Eilbeck <ei...@fr...> >> Date: Thu, 16 Feb 2006 16:25:03 -0700 >> Subject: [SO-devel] New term suggestion >> Reply-To: son...@li... >> >> genome has been suggested as a new term. >> I am wary of this because a genome is for the most part >> discontinuous, and stitching it up to make a region of continuous >> sequence would be somewhat arbitrary. >> >> Anyone else have an opinion? >> --Karen >> >> Initial Comment: >> Suggestion: How about a term "genome" ? >> >> It itself is used within other term names, their definitions, and >> even a >> relationship (genome_of). Primarily, I was simply hoping to reason >> that a >> chromosome was part_of a genome, but presumably this term would be >> wide-reaching (many possible "parts")... >> >> Possible defs: >> http://www.google.com/search?oi=defmore&defl=en&q=define:Genome >> >> >> >> >> --__--__-- >> >> _______________________________________________ >> SOng-devel mailing list >> SOn...@li... >> https://lists.sourceforge.net/lists/listinfo/song-devel >> >> >> End of SOng-devel Digest >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > SOng-devel mailing list > SOn...@li... > https://lists.sourceforge.net/lists/listinfo/song-devel > Karen Eilbeck Research Assistant Professor Department of Human Genetics University of Utah 15 No. 2030 E. SLC UT 84112 |
