Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-25

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All times shown according to UTC.

Time Nick Message
05:54 Gpox joined #bioclipse
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07:13 olas joined #bioclipse
07:13 olas hi
07:21 masak joined #bioclipse
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08:10 jonalv joined #bioclipse
08:42 egonw joined #bioclipse
09:01 malick joined #bioclipse
09:03 egonw masak: the tiny url's are broken
09:03 egonw just fyi
09:03 masak egonw: :/
09:04 egonw might just be tinyurl.com or whatever
09:04 egonw not zarah itself
09:04 olas egonw: question
09:04 masak ah, that kind of broken
09:04 olas how do I parse OWL in java?
09:04 olas in particular, the BO descriptor ontology
09:05 olas egonw: btw, di you get my mail about the descr ontol?
09:07 egonw CDK has code that create a Java data model for OWL
09:07 egonw yes, but too busy to reply at this moment
09:07 egonw JOELib used it too
09:07 egonw but that's about it
09:07 egonw unfortunately
09:07 egonw yes, would be good if we would link Dragon descriptors to the ontology too...
09:07 egonw been on my mind since I started that ontology...
09:08 olas ok, good
09:08 olas is there no framework for OWL parsing in java?
09:08 olas what does CDK use?
09:09 egonw custom code
09:09 egonw should be in cdk.dict I think
09:09 egonw alternatively, you'd use sesame/openrdf
09:09 egonw that's where we really should be heading instead
09:10 olas which one?
09:10 olas sesame or openrdf?
09:10 egonw but, I'd be fine with postponing that to october :)
09:10 egonw that's the same :)
09:10 egonw openrdf.org
09:10 olas sure
09:10 olas hmm
09:10 olas will try it out
09:11 * masak too
09:16 olas egonw: sesame seems rather large
09:17 olas is there no leightweight framework to just parse/serialize owl into java? like xom for xml?
09:17 egonw that's why CDK currently has some custom code too...
09:17 olas aha
09:17 egonw BC1 has an OpenRDF plugin
09:18 olas which does?
09:18 egonw provide the openrdf library
09:18 egonw nothing more
09:18 olas jopw about jena?
09:18 olas how about jena?
09:18 egonw that's the competitor
09:18 olas good?
09:18 egonw no idea
09:19 olas ok
09:19 thomas_ku joined #bioclipse
09:19 egonw I like openrdf as it is Java
09:19 egonw and said to be better than Jena
09:19 egonw KDE even uses openrdf
09:19 egonw C code, using a Java library :)
09:19 olas jena is java too
09:21 egonw ah, ok
09:21 egonw well, that indicates how much I know about jena :)
09:21 olas it seems nice
09:22 olas egonw: what is the relation between RDF and OWL?
09:24 olas egonw: I guess all relevant info is in the descriptor-algorithms.owl file, and that I need to parse it
09:24 olas right?
09:25 CIA-51 bioclipse: jonalv * r6729 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): [structuredb] changed name of setLabel to setAnnotation in internal structuredb manager
09:26 masak olas: RDF describes relations between entities, OWL describes properties of classes of things
09:27 masak example: RDF: "ball number 3 has the colour red", OWL: "all balls in storage room 7 are small, red and made of rubber"
09:31 olas egonw: when you have put the descriptor OWL back online, isthere a URL for it?
09:32 egonw olas: yes
09:32 egonw olas: OWL is an application in RDF
09:33 egonw masak: actually... the latter sounds more like reasoning...
09:33 masak egonw: it is.
09:33 egonw but OWL indeed has classes, but RDF has types too...
09:35 masak egonw: not sure what you mean by "OWL is an application in RDF". I'd say they are two different applications, but OWL makes use of RDF for some things.
09:35 * olas just read his first OWL using EODM: http://www.eclipse.org/modeling/mdt/?project=eodm
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09:35 olas looks _very_ nice
09:36 egonw masak: as in: any OWL document is an RDF document
09:36 masak hm, I guess. never thought of it that way before.
09:38 egonw olas: looks very promosing indeed!
09:38 egonw what OWL does on top of RDF, is define new RDF types, e.g. the owl:Class
09:38 egonw and new predictes, like owl:whatIsItAgain...
09:39 egonw dataProperty and objectProperty
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12:18 olas egonw: is the descr owl using an old owl version?
12:18 olas it can't be read by EODM
12:18 olas can I send you the two files and you can look at them?
12:21 masak OWL version?
12:33 egonw olas: how urgent is this?
12:33 egonw really don't have much time this week...
12:33 egonw need to finish the paper drafts...
12:40 olas ok
12:40 olas using jena with some progress
12:41 zarah joined #bioclipse
12:53 CIA-51 bioclipse: carl_masak * r6730 /bot/trunk/zarah.pl: [zarah] now keeps quiet if tinyurls do not work
12:53 masak CIA-51: you're slow.
13:02 steinbeck joined #bioclipse
13:09 edrin joined #bioclipse
13:09 edrin hi
13:09 zarah hi edrin
13:10 olas hi edin
13:11 masak hi edrin
13:15 * olas successfully parsed the BO descr ontology with jena
13:15 olas :-)
13:16 olas now: coffee
13:16 masak olas++
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13:44 CIA-51 bioclipse: carl_masak * r6731 /bot/trunk/zarah.pl: [zarah] now tells every user whose nick starts with jonalv to use swedish layout
13:44 edrin anyone has experiences with any XML Data binding libraries, for example Castor or JAXB or JiBX ??
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13:46 CIA-51 bioclipse: carl_masak * r6732 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] selections now survive zooming
13:49 olas edrin: I use EMF
13:49 olas and I really like it
13:49 olas other than that I'm not experienced
13:50 olas (actually I'm not that experienced with EMF either)
13:50 olas :-)
13:50 olas egonw: is probably the right man to ask
13:50 edrin olas: can it dynamically spawn objects via schemata at runtime?
13:53 egonw edrin: I used Castor in the past
13:53 egonw liked it more than JAXB
13:53 egonw but really don't like either
13:54 edrin heh :)
13:54 egonw the are not flexible, large...
13:54 egonw often easier to hack something together yourself...
13:54 edrin and do you know JiBX ?
13:54 egonw the post IO process really determines what you can do with the input, so full support of an XSD is often not needed anyway
13:55 egonw no, that one is new to me
13:55 edrin egonw: i would need some lib that can directly spawn a class+its object at runtime from a schema...
13:55 edrin http://jibx.sourceforge.net/
13:55 egonw xom?
13:55 olas edrin: is your schemata in XSD?
13:56 edrin egonw: this way it would be possible to do xws stuff at runtime from js console...
13:56 egonw things like castor pregenerate a data model based on the XSD, not on the fly, AFAIK
13:56 edrin olas: I think so, why not?
13:57 edrin egonw: i c. but i think there are libs that can do it on the fly...
13:57 olas edrin: EMF can do that
13:57 olas http://www.devx.com/Java/A​rticle/29093/1954?pf=true
13:57 olas see " Generating Dynamic Ecore from XML Schema"
13:58 olas it uses an XSDEcoreBuilder
13:59 edrin olas: looks good
13:59 olas more info: http://www.theserverside.com/tt/art​icles/article.tss?l=BindingXMLJava
13:59 edrin egonw: how do you like xom?
13:59 olas my last link has sample code
14:00 egonw I like XOM a lot
14:00 edrin good :)
14:02 olas can XOM generate model from schema?
14:02 * olas thinks edrin should go with EMF
14:03 olas :-)
14:03 edrin yeh, lets more carefully compare them ;)
14:03 olas no really, choose what you like most
14:03 olas my last link is a comparison
14:03 olas I read it a while ago and liked it
14:05 egonw I do not know the context, and do note endorse any toolkit
14:05 egonw the speak with Shagge... It Wasn't Me
14:05 egonw s/e/y/
14:26 edrin olas: does EMF eat/work with w3c DOM?
14:34 olas edrin: no idea
14:35 olas EMF newsgroup is extremely good
14:35 olas ask there
14:35 olas they answer practically everything :-)
14:35 edrin k
14:35 edrin XWS library gets really large
14:35 edrin i think it's around 100 .java files now
14:39 edrin the idea is that someone could finally generate a client stub with just the function name and service JID. and this should work both, at runtime generating dynamic objects in memory and for java source code: to generate a .java to use the service...
14:39 CIA-51 bioclipse: carl_masak * r6733 /bioclipse2/trunk/plugins/net.bioclip​se.cdk10.ui/src/net/bioclipse/cdk10/u​i/content/MoleculeLabelProvider.java: [MoleculeLabelProvider.java] changed file ending from .gif to .png
14:40 edrin olas: is the server now configured for internet access ?
14:45 CIA-51 bioclipse: carl_masak * r6734 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): [MoleculeLabelProvider.java] changed file ending from .gif to .png
15:05 malic1 left #bioclipse
15:07 edrin egonw: available?
15:10 egonw sort of
15:10 egonw doing major hacking on metware
15:12 edrin egonw: I have a chemical question regarding diffusion
15:32 olas edrin: yes, server now configured
15:32 edrin ok
15:33 edrin olas: what are your plans with development of the server side service? what do you need for the client side?
16:06 olas no finalized plans yet
16:06 olas need to think about it
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22:55 CIA-51 bioclipse: edrin_t * r6735 /xws/trunk/xws4j/src/net/bioclipse/xws/client/ (19 files in 6 dirs):

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