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Re: [Treebase-devel] search by DOI
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From: Rutger V. <rut...@gm...> - 2012-02-21 16:40:34
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> There's nothing wrong with computed metadata. It's just not something that > TreeBASE does right now. It isn't? We let people search on ntax and nchar... > On Feb 21, 2012, at 11:30 AM, Carl Boettiger wrote: > > Hi Hilmar, list, > > Good point, I see the importance of not departing from the standards. > > I wouldn't phrase this as an "absence of data", but rather as fundemental > metadata describing the kind of data provided -- i.e. is the data just a > topology, is it a phylogram where branch lengths describe mutational steps, > or is it a chronogram/ultrametric tree where branch lengths are calibrated > into units of time? (notably, knowing whether a tree was ultrametric/time > calibrated or if branch lengths were in units of mutational steps would be > very useful thing to know through the API). I'm not quite sure why this is > any less metadata while things like tb:kind.tree (i.e. Species Tree / gene > tree), or tb.quality, etc. > > > > -Carl > > On Mon, Feb 20, 2012 at 8:33 PM, Hilmar Lapp <hl...@ne...> wrote: >> >> I agree this would be quite useful. At present all PhyloWS query >> attributes map directly to attributes of the data. Querying presence of >> absence of would be a departure from that. >> >> I think ideally I'd like to see this supported through CDAO terms. Whether >> a tree has branch lengths or not is a piece of semantic metadata about the >> tree. A tree with branch lengths could be declared as an Instance of the >> subclass of trees that also have branch lengths. >> >> -hilmar >> >> On Feb 20, 2012, at 8:41 PM, Carl Boettiger wrote: >> >> Hi Treebase developers, >> >> How difficult would it be to include the ability to restrict phylows API >> queries to only trees having branch length data? Can this be done already? >> If not, is it a straight forward modification? I would find this very >> useful (and would reduce my load on the server, since otherwise I have to do >> pull down each tree and check if it has this data...) >> >> Many thanks, >> >> Carl >> >> On Fri, Feb 17, 2012 at 10:32 AM, Rutger Vos <rut...@gm...> wrote: >>> >>> Hi all, >>> >>> I've made some recent enhancements to the search facilities: >>> >>> - there was a bug in searching by tree quality, this has now been >>> corrected >>> >>> - we can now search by doi, it is an option in the pull down menu on the >>> study search page, and has also been added to the PhyloWS API: >>> >>> >>> http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi="10.1016/j.ympev.2009.03.021" >>> >>> - I also added buttons to the twitter account and the mendeley group. >>> >>> Maybe we can push these things to production? >>> >>> Rutger >>> >>> -- >>> Dr. Rutger A. Vos >>> Bioinformaticist >>> NCB Naturalis >>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the >>> Netherlands >>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands >>> http://rutgervos.blogspot.com >>> >>> >>> ------------------------------------------------------------------------------ >>> Virtualization & Cloud Management Using Capacity Planning >>> Cloud computing makes use of virtualization - but cloud computing >>> also focuses on allowing computing to be delivered as a service. >>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >> >> >> >> -- >> Carl Boettiger >> UC Davis >> http://www.carlboettiger.info/ >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> >> http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ >> >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
