treebase-devel — TreeBASE developer mailing list

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Hi Rutger,

Thanks for spending all this time working through this!

When I've used the url https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java for checkout, rather than https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ I don't have the Examples folder that the hyperlink.xml file is in, so I can't read that.

But about using the first url, I now have the problem that when I try to export in Nexml I no longer get the default hyperlink.xml that treated hyperlink as a predicate; instead it crashes, with the log file reproduced below. What's odd is that for Mesquite to even load nexml now, predicateHandlerMapping.properties must be commented out. 

So, two log files. The fist is where the .properties file is commented out in my classpaths.xml file and thus Mesquite loads the nexml module, provides exporting as NeXml as an option, but crashes when I try to export. The second is when the .properties file isn't commented out in my classpaths.xml file, but not you don't see that Mesquite loads nexml in the log.

Error message when I try to export with nexml. Log:


Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/dom4j-1.6.1.jar
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/JSci.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/pal.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/Jama-1.0.1.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/iText.jar
Mesquite version 2.6+ (build 499)
Copyright (c) 1997-2009 W. Maddison and D. Maddison
The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License.   Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and lack of warranty see the GNU Lesser General Public License by selecting "Display License" from the Window menu or at www.gnu.org

Principal Authors: Wayne Maddison & David Maddison
Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver
Development Team Alumnus: Danny Mandel

 
Wed Jun 10 16:25:01 EDT 2009
Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on Linux 2.6.28-13-generic (architecture: i386)
User: kasia
 
Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/  dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar


Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/
Log file located in: /home/kasia/Mesquite_Support_Files
Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs
 
Modules loading from directory /home/kasia/workspace/Mesquite Project/Mesquite_Folder/mesquite/

 ancstates basic categ charMatrices charts cont genesis io lists minimal parsimony stochchar trees align assoc batchArch coalesce consensus correl distance diverse dmanager mb meristic molec ornamental pairwise rhetenor search tol treefarm iText jama jsci pal trunk

Additional modules loaded from /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder


Additional modules loaded from /home/kasia/workspace/nexmltest/java/bin
 nexml
 
687 modules installed.
1 prerelease substantive modules installed.
 
Mesquite makes use of BrowserLauncher by Eric Albert,  corejava.Format by Horstmann & Cornell, and iText by Lowagie & Soares

------------------------------


 

THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this version without permission of authors.

Loading manual for searching..... manual ready.
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:25:13 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Location: http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

Reading NEXUS file hyperlink.nex
Reading block: TAXA
Reading block: TREES
Reading block: NOTES
Reading block: MESQUITE
File reading complete (file hyperlink.nex)
Basic File Coordinator > export
Dialog box shown.  Title: Export format

For console choice use component numbers
      Export part or all of the information as a file of the following format
     --------------
     1 List 
       1 *Export NEXUS Tree File
       2  Export NEXUS Tree File from Tree Source
       3  Phylip (trees)
       4  Export Taxa Distance Matrix
       5  NeXML (taxa, matrices, trees and annotations)
     --------------
      Exports NEXUS file with a tree block, and optionally a taxa block.
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a list or choice menu, enter
 both number of component and number of item within it to choose
 (e.g. if a list is component 1, and you want to select its item 2, enter "1 2"


(Export format) # 
(Mesquite) # Dialog closed
(Following stack trace from object of class: class mesquite.lib.PendingCommand)
java.lang.NullPointerException
	at java.util.Properties$LineReader.readLine(Properties.java:418)
	at java.util.Properties.load0(Properties.java:337)
	at java.util.Properties.load(Properties.java:325)
	at mesquite.nexml.InterpretNEXML.InterpretNEXML.exportFile(Unknown Source)
	at mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.export(BasicFileCoordinator.java:1003)
	at mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.doCommand(BasicFileCoordinator.java:1488)
	at mesquite.lib.PendingCommand.go(PendingCommand.java:205)
	at mesquite.lib.MainThread.run(MainThread.java:116)

Dialog box shown.  Title: Crash

For console choice use component numbers
      A command could not be completed because an exception occurred (i.e. a crash; class java.lang.NullPointerException ). WARNING: there is a chance this crash could have corrupted your data.  Please check your data carefully.  If you save any files, you might best use Save As... in case file saving doesn't work properly.

Please send a report of this crash to the Mesquite server, to help us debug it and improve Mesquite.  None of your data will be sent, but your log file up to this point will be sent.
     1 (Close without sending)
     2 (OK, Send and Force Quit)
     3 (OK, Send Report and Continue)
Enter number of component to select.

(Crash) # 
(Mesquite) # Dialog closed




- Curiously, when I change my classpaths.xml file so that predicateHandlerMapping isn't commented out, the nexml module doesn't even load and exporting as NeXml isn't an option. classpaths.xml:

<?xml version="1.0"?>
<mesquite>
	<classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
	<classpath>predicateHandlerMapping.properties</classpath>
	<!-- classpath>../../nexml/java</classpath-->
	<!--classpath>../..nexml/java/src</classpath-->

	<!--classpath>../../teest/java/bin</classpath> < The test that worked to bring up nexml option again, but crashed. Only needed this classpath. -->
	<!--classpath>../../nexmltest3/nexml/java/bin</classpath-->
	<classpath>../../nexmltest/java/bin</classpath>

</mesquite>


Log:

Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/dom4j-1.6.1.jar
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/JSci.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/pal.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/Jama-1.0.1.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/iText.jar
Mesquite version 2.6+ (build 499)
Copyright (c) 1997-2009 W. Maddison and D. Maddison
The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License.   Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and lack of warranty see the GNU Lesser General Public License by selecting "Display License" from the Window menu or at www.gnu.org

Principal Authors: Wayne Maddison & David Maddison
Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver
Development Team Alumnus: Danny Mandel

 
Wed Jun 10 16:30:03 EDT 2009
Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on Linux 2.6.28-13-generic (architecture: i386)
User: kasia
 
Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/  dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar


Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/
Log file located in: /home/kasia/Mesquite_Support_Files
Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs
 
Modules loading from directory /home/kasia/workspace/Mesquite Project/Mesquite_Folder/mesquite/

 ancstates basic categ charMatrices charts cont genesis io lists minimal parsimony stochchar trees align assoc batchArch coalesce consensus correl distance diverse dmanager mb meristic molec ornamental pairwise rhetenor search tol treefarm iText jama jsci pal trunk

Additional modules loaded from /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder


Additional modules loaded from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/predicateHandlerMapping.properties

 
686 modules installed.
1 prerelease substantive modules installed.
 
Mesquite makes use of BrowserLauncher by Eric Albert,  corejava.Format by Horstmann & Cornell, and iText by Lowagie & Soares

---------------------


THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this version without permission of authors.

Loading manual for searching..... manual ready.
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:31:08 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:31:25 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Location: http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

Reading NEXUS file hyperlink.nex
Reading block: TAXA
Reading block: TREES
Reading block: NOTES
Reading block: MESQUITE
File reading complete (file hyperlink.nex)
Basic File Coordinator > export
Dialog box shown.  Title: Export format

For console choice use component numbers
      Export part or all of the information as a file of the following format
     --------------
     1 List 
       1 *Export NEXUS Tree File
       2  Export NEXUS Tree File from Tree Source
       3  Phylip (trees)
       4  Export Taxa Distance Matrix
     --------------
      Exports NEXUS file with a tree block, and optionally a taxa block.
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a list or choice menu, enter
 both number of component and number of item within it to choose
 (e.g. if a list is component 1, and you want to select its item 2, enter "1 2"


(Export format) # 
(Mesquite) # Dialog closed


Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: Rutger Vos [mailto:rut...@gm...]
Sent: Wed 6/10/2009 3:52 PM
To: Hayden, Katherine M.
Cc: Wayne Maddison; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Ok, so now that you have nexml as an export option, could you send the
log for when you're reading the hyperlink.xml file?

On Wed, Jun 10, 2009 at 8:41 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I couldn't get NeXml as an export option with these new instructions, but
> when I made a test directory and used the old checkout url
> (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the
> option to export as NeXml was back. Still trying to figure out the
> difference.
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rut...@gm...]
> Sent: Wed 6/10/2009 7:07 AM
> To: Wayne Maddison
> Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli;
> ju...@ig...; nex...@li...;
> ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Wayne, thanks for chiming in - I changed the way the properties file
> is loaded a little bit (sorry I left the absolute paths in
> previously!). Kasia, could you try the following,
>
> - assuming $NEXMLTRUNK is your local equivalent for
> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
> - assuming $MESQUITE_FOLDER is your local equivalent for
> http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/
>
> * cd $NEXMLTRUNK/java
> * export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
> * ant mesquite
> * pico "$MESQUITE_FOLDER/classpaths.xml"
> * add an entry in classpaths.xml:
> <classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
> be substituted for the real path (either relative or absolute) to the
> bin folder in which ant placed the compiled classes. Attached is how I
> have it, which works when you check the mesquite trunk and the full
> nexml code (trunk and branches) in the same folder (for me that's
> ~/Documents/workspace but it shouldn't matter)
>
> Now, when Mesquite starts up, could you copy and paste what happens in
> the log window when you read the local version of this file:
> $NEXMLTRUNK/examples/translations/hyperlink.xml
>
> Hope this helps!
>
> Rutger

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rut...@gm...>]

Ok, so now that you have nexml as an export option, could you send the
log for when you're reading the hyperlink.xml file?

On Wed, Jun 10, 2009 at 8:41 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I couldn't get NeXml as an export option with these new instructions, but
> when I made a test directory and used the old checkout url
> (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the
> option to export as NeXml was back. Still trying to figure out the
> difference.
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rut...@gm...]
> Sent: Wed 6/10/2009 7:07 AM
> To: Wayne Maddison
> Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli;
> ju...@ig...; nex...@li...;
> ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Wayne, thanks for chiming in - I changed the way the properties file
> is loaded a little bit (sorry I left the absolute paths in
> previously!). Kasia, could you try the following,
>
> - assuming $NEXMLTRUNK is your local equivalent for
> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
> - assuming $MESQUITE_FOLDER is your local equivalent for
> http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/
>
> * cd $NEXMLTRUNK/java
> * export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
> * ant mesquite
> * pico "$MESQUITE_FOLDER/classpaths.xml"
> * add an entry in classpaths.xml:
> <classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
> be substituted for the real path (either relative or absolute) to the
> bin folder in which ant placed the compiled classes. Attached is how I
> have it, which works when you check the mesquite trunk and the full
> nexml code (trunk and branches) in the same folder (for me that's
> ~/Documents/workspace but it shouldn't matter)
>
> Now, when Mesquite starts up, could you copy and paste what happens in
> the log window when you read the local version of this file:
> $NEXMLTRUNK/examples/translations/hyperlink.xml
>
> Hope this helps!
>
> Rutger
>
> On Tue, Jun 9, 2009 at 8:36 PM, Wayne
> Maddison<wma...@in...> wrote:
>> Sorry, I haven't been following this, but, classpaths.xml should be
>> in the Mesquite_Folder that initiates Mesquite starting up.  To see
>> if it's being read, include a line like:
>>
>>  <classpath>../../MySideProject/Mesquite_Folder</classpath>
>>
>>
>> in which case the log should say something like this:
>>
>> =====
>> Modules loading from directory
>> /Users/wmaddisn/Mesquite_Workspace/Mesquite
>> Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/
>>
>>  ancstates basic categ charMatrices charts cont genesis io lists
>> minimal parsimony stochchar trees align assoc batchArch coalesce
>> consensus correl distance diverse dmanager mb meristic molec
>> ornamental pairwise rhetenor search tol treefarm iText jama jsci pal
>> trunk
>>
>> Additional modules loaded from
>> /Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
>> =====
>>
>> However, this puts the paths in Java's classpath.  I suspect this may
>> not help with the .properties file; this may use a different sense of
>> application's path.  With pPod communication I seem to recall that
>> some of the auxiliary files had to live in your initiating
>> Mesquite_Folder.
>>
>> Wayne
>>
>>
>> At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>>>Content-type: multipart/alternative;
>>>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>>>Content-class: urn:content-classes:message
>>>
>>>Sorry, I'm a little confused. If my classpaths.xml is in
>>>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't
>>>it already in the root of my the Mesquite_Folder?
>>>
>>>Or are you saying to instead put it in
>>>/home/kasia/workspace/Mesquite Project, which is one directory
>>>above? (When I do this I no longer have the option to export as
>>>NEXML, even when I remember that I have to change the relative paths
>>>after bumping up the classpaths.xml file one directory :)
>>>
>>>
>>>Kasia
>>>
>>>
>>>
>>>Katherine "Kasia" Hayden
>>>Bennington College, Class of 2011
>>>312.576.8175
>>>kh...@be...
>>>
>>>
>>>
>>>-----Original Message-----
>>>From: rut...@gm... on behalf of Rutger Vos
>>>Sent: Tue 6/9/2009 4:52 PM
>>>To: Hayden, Katherine M.
>>>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>>ju...@ig...; nex...@li...;
>>>ph...@go...
>>>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>Hi Kasia,
>>>
>>>I don't think classpaths.xml modifies the system classpath variable,
>>>so adding the properties file here won't do anything - as far as I
>>>understand the xml file is read by Mesquite's module loading system.
>>>Maybe try placing the file in the root of the Mesquite_Folder?
>>>
>>>Rutger
>>>
>>>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>>>M.<KH...@be...> wrote:
>>>>  Rutger,
>>>>
>>>>  I changed what you suggested and still get the same output.
>>>>
>>>>  This is what my classpaths.xml file looks like:
>>>>
>>>>  <?xml version="1.0"?>
>>>>  <mesquite>
>>>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>>>          <!--
>>>>
>>>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>>>  -->
>>>>          <classpath>../../RutgersNexml/java/src</classpath>
>>>>  </mesquite>
>>>>
>>>>
>>>>  I wasn't sure if the .properties file needed to be pointed to directly
>>>> or if
>>>>  its directory needed to be specified, so I tried both. No luck with
>>>> either.
>>>>
>>>>  My classpaths.xml file is in ~/workspace/Mesquite
>>>> Project/Mesquite_Folder.
>>>>
>>>>
>>>>  Can't think of what else might be accounting for the difference.. Do
>>>> you
>>>>  have any other suggestions?
>>>>
>>>>
>>>>  Kasia
>>>>
>>>>
>>>>
>>>>  Katherine "Kasia" Hayden
>>>>  Bennington College, Class of 2011
>>>>  312.576.8175
>>>>  kh...@be...
>>>>
>>>>
>>>>
>>>>  -----Original Message-----
>>>>  From: rut...@gm... on behalf of Rutger Vos
>>>>  Sent: Fri 6/5/2009 5:23 PM
>>>>  To: Hayden, Katherine M.
>>>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>>> ju...@ig...;
>>>  > nex...@li...; ph...@go...
>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>
>>>>  Hi Katherine,
>>>>
>>>>  is it possible that the predicateHandlerMapping.properties file isn't
>>>>  in your classpath? The output you produced is the default output which
>>>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>>>  instead of the href/rel construct. The properties file defines which
>>>>  class is used for which internal name, and it should make Mesquite
>>>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>>>  attachment (but clearly it's not working in your output).
>>>>
>>>>  Rutger
>>>>
>>>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>>>  M.<KH...@be...> wrote:
>>>>>  Hi Rutger,
>>>>>
>>>>>  I just built this and got different results for my hyperlink.xml
>>>>> output
>>>>>  that
>>>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java
>>>>> version
>>>>>  1.6.0_13.
>>>>>
>>>>>  Specifically, here's the annotation attached to otu elements:
>>>>>
>>>>>  <meta
>>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>>
>>>>>
>>>>>  And here's the whole thing:
>>>>>
>>>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>>>  <nex:nexml
>>>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>>
>>>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>>>>
>>>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>>    <otus
>>>>> xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>>>        <meta content="http" datatype="xsd:string"
>>>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>        <meta content="0" datatype="xsd:integer"
>>>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>      </otu>
>>>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>>>        <meta
>>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>>        <meta content="1" datatype="xsd:integer"
>>>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>      </otu>
>>>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>>>        <meta
>>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>>        <meta content="2" datatype="xsd:integer"
>>>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>      </otu>
>>>>>    </otus>
>>>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>>>  Trees"
>>>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>>      <tree
>>>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated
>>>>> by
>>>>>  Uniform speciation (Yule)"
>>>>>
>>>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>>>  >> xsi:type="nex:FloatTree">
>>>>>        <meta content="1" datatype="xsd:long"
>>>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>>>  xsi:type="nex:LiteralMeta"/>
>>>>>        <meta content="2" datatype="xsd:integer"
>>>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>>>  length="3.1643765725844055"
>>>>> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>>>  length="6.835623427415595"
>>>>> source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>>>  length="6.835623427415595"
>>>>> source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>>>      </tree>
>>>>>    </trees>
>>>>>  </nex:nexml>
>>>>>
>>>>>
>>>>>  Kasia
>>>>>
>>>>>
>>>>>
>>>>>  Katherine "Kasia" Hayden
>>>>>  Bennington College, Class of 2011
>>>>>  312.576.8175
>>>>>  kh...@be...
>>>>>
>>>>>
>>>>>
>>>>>  -----Original Message-----
>>>>>  From: Rutger Vos
>>>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>>>  Sent: Fri 6/5/2009 3:53 AM
>>>>>  To: Arlin Stoltzfus
>>>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>>>  nex...@li...; ph...@go...
>>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>>
>>>>>  Hi,
>>>>>
>>>>>  Can we work along a use case? I've just committed some code to import
>>>>>  and export nexml (with annotations) into mesquite using the
>>>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>>>  play along - you don't *have* to build this):
>>>>>
>>>>>  * svn co
>>>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>>>  * cd java
>>>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>>>  * ant mesquite
>>>>>
>>>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>>>  classpaths.xml file, which should contain an entry that points to the
>>>>>  bin folder that the ant task created:
>>>>>
>>>>>  <?xml version="1.0"?>
>>>>>  <mesquite>
>>>>>              <!-- perhaps other classpath entries here -->
>>>>>          <classpath>/path/to/java/bin</classpath>
>>>>>  </mesquite>
>>>>>
>>>>>  Now, start mesquite and open this url from within mesquite (File >
>>>>>  Open other... > URL...):
>>>>>
>>>>>
>>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>>>
>>>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>>>  look in the nexus "source" you can see these URLs are written in the
>>>>>  notes block. If you now choose file > export, NeXML should be one of
>>>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>>>  output should look like this:
>>>>>
>>>>>
>>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>>>
>>>>>  The salient point of the output is the annotation attached to otu
>>>>>  elements:
>>>>>
>>>>>  <meta
>>>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>>>  irrelevant for now...] />
>>>>>
>>>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>>>  store a url, and the "rel" attribute will describe the relationship
>>>  >> between the subject (the earliest enclosing element that has an
>>>>>  "about" attribute) and the resource on the other end. I *think* we
>>>>>  agreed that such a simple relationship could be described as
>>>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>>>  CDAO owl file.
>>>>>
>>>>>  So what about other annotations? You can see in the produced nexml
>>>>>  that mesquite is also storing internal object IDs to various
>>>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>>>  service queries which we would like to implement, and we want the
>>>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>>>
>>>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>>>  able to put it in a queue somewhere, but I would be very interested to
>>>>>  see what Brandon comes up with for term suggestion interface -
>>>>>  obviously it will be better for all involved if the term suggestion
>>>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>>>  hierarchy (as opposed to a rambling email like this one).
>>>>>
>>>>>  Rutger
>>>>>
>>>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>>>  wrote:
>>>>>>  We're listening.  Brandon has developed a term-request server to
>>>>>> process
>>>>>>  requests for concepts and relations, but its still in an early stage.
>>>>>>  In
>>>>>>  a
>>>>>>  few weeks we will be in a better position to have this discussion.
>>>>>>
>>>>>>  Arlin
>>>>>>
>>>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>>>
>>>>>>>  Hi,
>>>>>>>
>>>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>>>  extractors can turn <meta/> elements - the new dictionaries - into
>>>>>>> RDF
>>>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I
>>>>>>> hope
>>>>>>>  that the examples I've mailed out give you enough of a template to
>>>>>>> do
>>>>>>>  this in python too, but please let me know of I can help - I know
>>>>>>> that
>>>>>>>  the wiki needs updating, for starters).
>>>>>>>
>>>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>>>  discussions it's been decided that CDAO will be the principal
>>>>>>> artifact
>>>>>>>  for their mediation - so what's the community process for inclusion
>>>>>>> of
>>>>>>>  new predicates?
>>>>>>>
>>>>>>>  Val and I have sketched out a couple of TreeBASE services whose
>>>>>>> search
>>>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>>>  tree.label, etc.), and this is just one use case of a project having
>>>>>>> a
>>>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>>>
>>>>>>>  It would be great if team CDAO could tell us where to send our list
>>>>>>> of
>>>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>>>  that includes them :-)
>>>>>>>
>>>>>>>  I note that there is a wiki page about this
>>>>>>>
>>>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request),
>>>>>>>but ideally
>>>>>>>  there would be some sort of issue tracker with structured input
>>>>>>> fields
>>>>>>>  (e.g. subject/predicate/object name="XXX", suggested
>>>>>>> superclass="YYY",
>>>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>>>  would be a team of curators that will promptly pick up a posted
>>>>>>> issue
>>>>>>>  and work towards a solution.
>>>>>>>
>>>>>>>  I realize that this involves a support commitment from team CDAO,
>>>>>>> but
>>>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>>>
>>>>>>>  Any comments?
>>>>>>>
>>>>>>>  Rutger
>>>>>>>
>>>>>>>  --
>>>>>>>  Dr. Rutger A. Vos
>>>>>>>  Department of zoology
>>>>>>>  University of British Columbia
>>>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  --
>>>>>  Dr. Rutger A. Vos
>>>>>  Department of zoology
>>>  >> University of British Columbia
>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>
>>>>>
>>>>>
>>>>>------------------------------------------------------------------------------
>>>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>>>  looking to deploy the next generation of Solaris that includes the
>>>>> latest
>>>>>  innovations from Sun and the OpenSource community. Download a copy and
>>>>>  enjoy capabilities such as Networking, Storage and Virtualization.
>>>>>  Go to:
>>>>><http://p.sf.net/sfu/opensolaris-get>http://p.sf.net/sfu/opensolaris-get
>>>>>  _______________________________________________
>>>>>  Nexml-discuss mailing list
>>>>>  Nex...@li...
>>>>>
>>>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>>  Dr. Rutger A. Vos
>>>>  Department of zoology
>>>>  University of British Columbia
>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>
>>>
>>>
>>>--
>>>Dr. Rutger A. Vos
>>>Department of zoology
>>>University of British Columbia
>>><http://www.nexml.org>http://www.nexml.org
>>><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>>
>>>------------------------------------------------------------------------------
>>>Crystal Reports - New Free Runtime and 30 Day Trial
>>>Check out the new simplified licensing option that enables unlimited
>>>royalty-free distribution of the report engine for externally facing
>>>server and web deployment.
>>>http://p.sf.net/sfu/businessobjects
>>>
>>>_______________________________________________
>>>Nexml-discuss mailing list
>>>Nex...@li...
>>>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>
>>
>> --
>> --------------------------------------------------------
>> Wayne Maddison
>>  Professor and Canada Research Chair
>>          Depts. of Zoology and Botany and
>>          Biodiversity Research Centre
>>  & Director
>>          Beaty Biodiversity Museum
>>  6270 University Boulevard
>>  University of British Columbia
>>  Vancouver, BC  V6T 1Z4   Canada
>>
>> email: wma...@in...   FAX: +1 604 822-2416
>>
>> Mesquite: http://mesquiteproject.org
>> MacClade: http://macclade.org
>> Salticidae:  http://salticidae.org
>> Tree of Life: http://tolweb.org
>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
>> Home page: http://salticidae.org/wpm/home.html
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> Nexml-discuss mailing list
>> Nex...@li...
>> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Sample output from our table dumper

[Hilmar L. <hl...@du...>]

This looks great, except that each INSERT needs to be terminated by a  
semicolon.

Good news also on the file sizes, I'm pretty optimistic that we can  
work it this way.

Thanks for the update. Are you (or anyone else on this list, e.g.  
Rutger, Bill, or Val?) going to the Evolution Meetings this week?

	-hilmar

On Jun 10, 2009, at 3:30 PM, Mark Dominus wrote:

> Hilmar:
>
> The program we are writing that dumps out data from our DB2 database  
> is not complete, but Val suggested that we send you some sample  
> output so that you can see if it is what you wanted.
>
> Unless you say otherwise, the output will all look substantially  
> like the attached file.
>
> As you may recall, there is one gigantic table, MATRIXELEMENT, with  
> around 3e8 records and about 25.8 gb of data.  I have not tried  
> dumping this yet.
>
> But the next-largest table is MATRIXCOLUMN, with 5.6 million records  
> and 310 MB of data.  The dumper takes 7 minutes to write the  
> compressed dump file, which takes up 32 MB.
>
> If the MATRIXELEMENT table behaves similarly, it will take around  
> 5.5 hours to write and will take up a mere 2.6 GB, so transferring  
> it will not be as big a job as we feared.
>
> < 
> matrix 
> .gz 
> > 
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
===========================================================

[Treebase-devel] Sample output from our table dumper

[Mark D. <mjd...@ge...>]

Hilmar:

The program we are writing that dumps out data from our DB2 database is 
not complete, but Val suggested that we send you some sample output so 
that you can see if it is what you wanted.

Unless you say otherwise, the output will all look substantially like 
the attached file.

As you may recall, there is one gigantic table, MATRIXELEMENT, with 
around 3e8 records and about 25.8 gb of data.  I have not tried dumping 
this yet.

But the next-largest table is MATRIXCOLUMN, with 5.6 million records and 
310 MB of data.  The dumper takes 7 minutes to write the compressed dump 
file, which takes up 32 MB.

If the MATRIXELEMENT table behaves similarly, it will take around 5.5 
hours to write and will take up a mere 2.6 GB, so transferring it will 
not be as big a job as we feared.

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Hi Rutger,

I couldn't get NeXml as an export option with these new instructions, but when I made a test directory and used the old checkout url (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the option to export as NeXml was back. Still trying to figure out the difference.

Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: Rutger Vos [mailto:rut...@gm...]
Sent: Wed 6/10/2009 7:07 AM
To: Wayne Maddison
Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi,

Wayne, thanks for chiming in - I changed the way the properties file
is loaded a little bit (sorry I left the absolute paths in
previously!). Kasia, could you try the following,

- assuming $NEXMLTRUNK is your local equivalent for
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
- assuming $MESQUITE_FOLDER is your local equivalent for
http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/

* cd $NEXMLTRUNK/java
* export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
* ant mesquite
* pico "$MESQUITE_FOLDER/classpaths.xml"
* add an entry in classpaths.xml:
<classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
be substituted for the real path (either relative or absolute) to the
bin folder in which ant placed the compiled classes. Attached is how I
have it, which works when you check the mesquite trunk and the full
nexml code (trunk and branches) in the same folder (for me that's
~/Documents/workspace but it shouldn't matter)

Now, when Mesquite starts up, could you copy and paste what happens in
the log window when you read the local version of this file:
$NEXMLTRUNK/examples/translations/hyperlink.xml

Hope this helps!

Rutger

On Tue, Jun 9, 2009 at 8:36 PM, Wayne
Maddison<wma...@in...> wrote:
> Sorry, I haven't been following this, but, classpaths.xml should be
> in the Mesquite_Folder that initiates Mesquite starting up.  To see
> if it's being read, include a line like:
>
>  <classpath>../../MySideProject/Mesquite_Folder</classpath>
>
>
> in which case the log should say something like this:
>
> =====
> Modules loading from directory
> /Users/wmaddisn/Mesquite_Workspace/Mesquite
> Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/
>
>  ancstates basic categ charMatrices charts cont genesis io lists
> minimal parsimony stochchar trees align assoc batchArch coalesce
> consensus correl distance diverse dmanager mb meristic molec
> ornamental pairwise rhetenor search tol treefarm iText jama jsci pal
> trunk
>
> Additional modules loaded from
> /Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
> =====
>
> However, this puts the paths in Java's classpath.  I suspect this may
> not help with the .properties file; this may use a different sense of
> application's path.  With pPod communication I seem to recall that
> some of the auxiliary files had to live in your initiating
> Mesquite_Folder.
>
> Wayne
>
>
> At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>>Content-type: multipart/alternative;
>>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>>Content-class: urn:content-classes:message
>>
>>Sorry, I'm a little confused. If my classpaths.xml is in
>>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't
>>it already in the root of my the Mesquite_Folder?
>>
>>Or are you saying to instead put it in
>>/home/kasia/workspace/Mesquite Project, which is one directory
>>above? (When I do this I no longer have the option to export as
>>NEXML, even when I remember that I have to change the relative paths
>>after bumping up the classpaths.xml file one directory :)
>>
>>
>>Kasia
>>
>>
>>
>>Katherine "Kasia" Hayden
>>Bennington College, Class of 2011
>>312.576.8175
>>kh...@be...
>>
>>
>>
>>-----Original Message-----
>>From: rut...@gm... on behalf of Rutger Vos
>>Sent: Tue 6/9/2009 4:52 PM
>>To: Hayden, Katherine M.
>>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>ju...@ig...; nex...@li...;
>>ph...@go...
>>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>>Hi Kasia,
>>
>>I don't think classpaths.xml modifies the system classpath variable,
>>so adding the properties file here won't do anything - as far as I
>>understand the xml file is read by Mesquite's module loading system.
>>Maybe try placing the file in the root of the Mesquite_Folder?
>>
>>Rutger
>>
>>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>>M.<KH...@be...> wrote:
>>>  Rutger,
>>>
>>>  I changed what you suggested and still get the same output.
>>>
>>>  This is what my classpaths.xml file looks like:
>>>
>>>  <?xml version="1.0"?>
>>>  <mesquite>
>>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>>          <!--
>>>
>>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>>  -->
>>>          <classpath>../../RutgersNexml/java/src</classpath>
>>>  </mesquite>
>>>
>>>
>>>  I wasn't sure if the .properties file needed to be pointed to directly or if
>>>  its directory needed to be specified, so I tried both. No luck with either.
>>>
>>>  My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>>>
>>>
>>>  Can't think of what else might be accounting for the difference.. Do you
>>>  have any other suggestions?
>>>
>>>
>>>  Kasia
>>>
>>>
>>>
>>>  Katherine "Kasia" Hayden
>>>  Bennington College, Class of 2011
>>>  312.576.8175
>>>  kh...@be...
>>>
>>>
>>>
>>>  -----Original Message-----
>>>  From: rut...@gm... on behalf of Rutger Vos
>>>  Sent: Fri 6/5/2009 5:23 PM
>>>  To: Hayden, Katherine M.
>>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>  > nex...@li...; ph...@go...
>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>  Hi Katherine,
>>>
>>>  is it possible that the predicateHandlerMapping.properties file isn't
>>>  in your classpath? The output you produced is the default output which
>>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>>  instead of the href/rel construct. The properties file defines which
>>>  class is used for which internal name, and it should make Mesquite
>>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>>  attachment (but clearly it's not working in your output).
>>>
>>>  Rutger
>>>
>>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>>  M.<KH...@be...> wrote:
>>>>  Hi Rutger,
>>>>
>>>>  I just built this and got different results for my hyperlink.xml output
>>>>  that
>>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>>>>  1.6.0_13.
>>>>
>>>>  Specifically, here's the annotation attached to otu elements:
>>>>
>>>>  <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>
>>>>
>>>>  And here's the whole thing:
>>>>
>>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>>  <nex:nexml
>>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>
>>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>    <otus xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>>        <meta content="http" datatype="xsd:string"
>>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="0" datatype="xsd:integer"
>>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="1" datatype="xsd:integer"
>>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>    </otus>
>>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>>  Trees"
>>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <tree
>>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>>>>  Uniform speciation (Yule)"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>>  >> xsi:type="nex:FloatTree">
>>>>        <meta content="1" datatype="xsd:long"
>>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>>  length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>>      </tree>
>>>>    </trees>
>>>>  </nex:nexml>
>>>>
>>>>
>>>>  Kasia
>>>>
>>>>
>>>>
>>>>  Katherine "Kasia" Hayden
>>>>  Bennington College, Class of 2011
>>>>  312.576.8175
>>>>  kh...@be...
>>>>
>>>>
>>>>
>>>>  -----Original Message-----
>>>>  From: Rutger Vos
>>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>>  Sent: Fri 6/5/2009 3:53 AM
>>>>  To: Arlin Stoltzfus
>>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>>  nex...@li...; ph...@go...
>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>
>>>>  Hi,
>>>>
>>>>  Can we work along a use case? I've just committed some code to import
>>>>  and export nexml (with annotations) into mesquite using the
>>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>>  play along - you don't *have* to build this):
>>>>
>>>>  * svn co
>>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>>  * cd java
>>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>>  * ant mesquite
>>>>
>>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>>  classpaths.xml file, which should contain an entry that points to the
>>>>  bin folder that the ant task created:
>>>>
>>>>  <?xml version="1.0"?>
>>>>  <mesquite>
>>>>              <!-- perhaps other classpath entries here -->
>>>>          <classpath>/path/to/java/bin</classpath>
>>>>  </mesquite>
>>>>
>>>>  Now, start mesquite and open this url from within mesquite (File >
>>>>  Open other... > URL...):
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>>
>>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>>  look in the nexus "source" you can see these URLs are written in the
>>>>  notes block. If you now choose file > export, NeXML should be one of
>>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>>  output should look like this:
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>>
>>>>  The salient point of the output is the annotation attached to otu
>>>>  elements:
>>>>
>>>>  <meta
>>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>>  irrelevant for now...] />
>>>>
>>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>>  store a url, and the "rel" attribute will describe the relationship
>>  >> between the subject (the earliest enclosing element that has an
>>>>  "about" attribute) and the resource on the other end. I *think* we
>>>>  agreed that such a simple relationship could be described as
>>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>>  CDAO owl file.
>>>>
>>>>  So what about other annotations? You can see in the produced nexml
>>>>  that mesquite is also storing internal object IDs to various
>>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>>  service queries which we would like to implement, and we want the
>>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>>
>>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>>  able to put it in a queue somewhere, but I would be very interested to
>>>>  see what Brandon comes up with for term suggestion interface -
>>>>  obviously it will be better for all involved if the term suggestion
>>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>>  hierarchy (as opposed to a rambling email like this one).
>>>>
>>>>  Rutger
>>>>
>>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>>  wrote:
>>>>>  We're listening.  Brandon has developed a term-request server to process
>>>>>  requests for concepts and relations, but its still in an early stage.  In
>>>>>  a
>>>>>  few weeks we will be in a better position to have this discussion.
>>>>>
>>>>>  Arlin
>>>>>
>>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>>
>>>>>>  Hi,
>>>>>>
>>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>>  extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>>>>  that the examples I've mailed out give you enough of a template to do
>>>>>>  this in python too, but please let me know of I can help - I know that
>>>>>>  the wiki needs updating, for starters).
>>>>>>
>>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>>  discussions it's been decided that CDAO will be the principal artifact
>>>>>>  for their mediation - so what's the community process for inclusion of
>>>>>>  new predicates?
>>>>>>
>>>>>>  Val and I have sketched out a couple of TreeBASE services whose search
>>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>>  tree.label, etc.), and this is just one use case of a project having a
>>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>>
>>>>>>  It would be great if team CDAO could tell us where to send our list of
>>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>>  that includes them :-)
>>>>>>
>>>>>>  I note that there is a wiki page about this
>>>>>>
>>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request),
>>>>>>but ideally
>>>>>>  there would be some sort of issue tracker with structured input fields
>>>>>>  (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>>  would be a team of curators that will promptly pick up a posted issue
>>>>>>  and work towards a solution.
>>>>>>
>>>>>>  I realize that this involves a support commitment from team CDAO, but
>>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>>
>>>>>>  Any comments?
>>>>>>
>>>>>>  Rutger
>>>>>>
>>>>>>  --
>>>>>>  Dr. Rutger A. Vos
>>>>>>  Department of zoology
>>>>>>  University of British Columbia
>>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>>  Dr. Rutger A. Vos
>>>>  Department of zoology
>>  >> University of British Columbia
>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>>
>>>>------------------------------------------------------------------------------
>>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>>  looking to deploy the next generation of Solaris that includes the latest
>>>>  innovations from Sun and the OpenSource community. Download a copy and
>>>>  enjoy capabilities such as Networking, Storage and Virtualization.
>>>>  Go to:
>>>><http://p.sf.net/sfu/opensolaris-get>http://p.sf.net/sfu/opensolaris-get
>>>>  _______________________________________________
>>>>  Nexml-discuss mailing list
>>>>  Nex...@li...
>>>>
>>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>  --
>>>  Dr. Rutger A. Vos
>>>  Department of zoology
>>>  University of British Columbia
>>>  <http://www.nexml.org>http://www.nexml.org
>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>>--
>>Dr. Rutger A. Vos
>>Department of zoology
>>University of British Columbia
>><http://www.nexml.org>http://www.nexml.org
>><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>
>>
>>
>>------------------------------------------------------------------------------
>>Crystal Reports - New Free Runtime and 30 Day Trial
>>Check out the new simplified licensing option that enables unlimited
>>royalty-free distribution of the report engine for externally facing
>>server and web deployment.
>>http://p.sf.net/sfu/businessobjects
>>
>>_______________________________________________
>>Nexml-discuss mailing list
>>Nex...@li...
>>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
> --
> --------------------------------------------------------
> Wayne Maddison
>  Professor and Canada Research Chair
>          Depts. of Zoology and Botany and
>          Biodiversity Research Centre
>  & Director
>          Beaty Biodiversity Museum
>  6270 University Boulevard
>  University of British Columbia
>  Vancouver, BC  V6T 1Z4   Canada
>
> email: wma...@in...   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Hey Rutger,

Here's what I got:

...
Loading manual for searching..... manual ready.
Mesquite > openFile
Opening file
     at Wed Jun 10 10:35:17 EDT 2009
Open File Dialog box shown.  Message: Open file as independent project:

Directory : /home/kasia/workspace/Mesquite Project/Mesquite_Folder/examples/Basic_Examples/tree_manipulation/
  1 - 12-treeSources.nex
  2 - 06-branchSelection.nex
  3 - 05-branchColorNames.nex
  4 - 09-treeBlocks.nex
  5 - 11-treeSources.nex
  6 - 10-externalTrees.nex
  7 - 03-editingTrees.nex
  8 - 04-branchLengths.nex
  9 - 07-storedTrees.nex
  10 - 02-editingTrees.nex
  11 - 10-treeFile.nex
  12 - 08-listOfTrees.nex
  13 - 13-instability.nex
  14 - 01-editingTrees.nex
Enter number to select file

(File Dialog: Open file as independent project: (/home/kasia/workspace/Mesquite Project/Mesquite_Folder/examples/Basic_Examples/tree_manipulation/)) # Location: /home/kasia/workspace/nexml/examples/translations/hyperlink.xml

Dialog box shown.  Title: Import File

For console choice use component numbers
     --------------
     1 List 
       1 *Clustal (DNA/RNA)
       2  Clustal (protein)
       3  FASTA (DNA/RNA)
       4  FASTA (protein)
       5  GenBank (DNA/RNA)
       6  GenPept (Protein)
       7  NBRF/PIR (DNA/RNA)
       8  NBRF/PIR (protein)
       9  NONA, Hennig86, PiWe, WinClada
       10  Phylip (categorical data)
       11  Phylip (DNA/RNA)
       12  Phylip (protein)
       13  Phylip (trees)
       14  Simple (categorical data)
       15  Simple (continuous data)
       16  Simple (Geographic data)
       17  TNT
       18  Tab-delimited categorical data file
       19  Tab-delimited continuous data file
       20  Pagel format (ppy) file for Discrete
       21  Pagel format (ppy) file for Multistate
     --------------
      Imports Clustal files that consist of DNA or RNA sequence data.
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a list or choice menu, enter
 both number of component and number of item within it to choose
 (e.g. if a list is component 1, and you want to select its item 2, enter "1 2"


(Import File) # 


Your instructions were slightly different from last time where you're having us checkout for the nexml trunk https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ rather than https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java. You're probably aware of that, but since you didn't explicitly point it out I just wanted to do that, to make sure that you weren't leaving off the java at the end accidentally.

Also, I'm not having nexml as an export option anymore, but I'm still working through all the possibilities on my end, so more on that later.


Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: Rutger Vos [mailto:rut...@gm...]
Sent: Wed 6/10/2009 7:07 AM
To: Wayne Maddison
Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi,

Wayne, thanks for chiming in - I changed the way the properties file
is loaded a little bit (sorry I left the absolute paths in
previously!). Kasia, could you try the following,

- assuming $NEXMLTRUNK is your local equivalent for
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
- assuming $MESQUITE_FOLDER is your local equivalent for
http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/

* cd $NEXMLTRUNK/java
* export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
* ant mesquite
* pico "$MESQUITE_FOLDER/classpaths.xml"
* add an entry in classpaths.xml:
<classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
be substituted for the real path (either relative or absolute) to the
bin folder in which ant placed the compiled classes. Attached is how I
have it, which works when you check the mesquite trunk and the full
nexml code (trunk and branches) in the same folder (for me that's
~/Documents/workspace but it shouldn't matter)

Now, when Mesquite starts up, could you copy and paste what happens in
the log window when you read the local version of this file:
$NEXMLTRUNK/examples/translations/hyperlink.xml

Hope this helps!

Rutger

On Tue, Jun 9, 2009 at 8:36 PM, Wayne
Maddison<wma...@in...> wrote:
> Sorry, I haven't been following this, but, classpaths.xml should be
> in the Mesquite_Folder that initiates Mesquite starting up.  To see
> if it's being read, include a line like:
>
>  <classpath>../../MySideProject/Mesquite_Folder</classpath>
>
>
> in which case the log should say something like this:
>
> =====
> Modules loading from directory
> /Users/wmaddisn/Mesquite_Workspace/Mesquite
> Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/
>
>  ancstates basic categ charMatrices charts cont genesis io lists
> minimal parsimony stochchar trees align assoc batchArch coalesce
> consensus correl distance diverse dmanager mb meristic molec
> ornamental pairwise rhetenor search tol treefarm iText jama jsci pal
> trunk
>
> Additional modules loaded from
> /Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
> =====
>
> However, this puts the paths in Java's classpath.  I suspect this may
> not help with the .properties file; this may use a different sense of
> application's path.  With pPod communication I seem to recall that
> some of the auxiliary files had to live in your initiating
> Mesquite_Folder.
>
> Wayne
>
>
> At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>>Content-type: multipart/alternative;
>>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>>Content-class: urn:content-classes:message
>>
>>Sorry, I'm a little confused. If my classpaths.xml is in
>>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't
>>it already in the root of my the Mesquite_Folder?
>>
>>Or are you saying to instead put it in
>>/home/kasia/workspace/Mesquite Project, which is one directory
>>above? (When I do this I no longer have the option to export as
>>NEXML, even when I remember that I have to change the relative paths
>>after bumping up the classpaths.xml file one directory :)
>>
>>
>>Kasia
>>
>>
>>
>>Katherine "Kasia" Hayden
>>Bennington College, Class of 2011
>>312.576.8175
>>kh...@be...
>>
>>
>>
>>-----Original Message-----
>>From: rut...@gm... on behalf of Rutger Vos
>>Sent: Tue 6/9/2009 4:52 PM
>>To: Hayden, Katherine M.
>>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>ju...@ig...; nex...@li...;
>>ph...@go...
>>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>>Hi Kasia,
>>
>>I don't think classpaths.xml modifies the system classpath variable,
>>so adding the properties file here won't do anything - as far as I
>>understand the xml file is read by Mesquite's module loading system.
>>Maybe try placing the file in the root of the Mesquite_Folder?
>>
>>Rutger
>>
>>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>>M.<KH...@be...> wrote:
>>>  Rutger,
>>>
>>>  I changed what you suggested and still get the same output.
>>>
>>>  This is what my classpaths.xml file looks like:
>>>
>>>  <?xml version="1.0"?>
>>>  <mesquite>
>>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>>          <!--
>>>
>>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>>  -->
>>>          <classpath>../../RutgersNexml/java/src</classpath>
>>>  </mesquite>
>>>
>>>
>>>  I wasn't sure if the .properties file needed to be pointed to directly or if
>>>  its directory needed to be specified, so I tried both. No luck with either.
>>>
>>>  My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>>>
>>>
>>>  Can't think of what else might be accounting for the difference.. Do you
>>>  have any other suggestions?
>>>
>>>
>>>  Kasia
>>>
>>>
>>>
>>>  Katherine "Kasia" Hayden
>>>  Bennington College, Class of 2011
>>>  312.576.8175
>>>  kh...@be...
>>>
>>>
>>>
>>>  -----Original Message-----
>>>  From: rut...@gm... on behalf of Rutger Vos
>>>  Sent: Fri 6/5/2009 5:23 PM
>>>  To: Hayden, Katherine M.
>>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>  > nex...@li...; ph...@go...
>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>  Hi Katherine,
>>>
>>>  is it possible that the predicateHandlerMapping.properties file isn't
>>>  in your classpath? The output you produced is the default output which
>>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>>  instead of the href/rel construct. The properties file defines which
>>>  class is used for which internal name, and it should make Mesquite
>>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>>  attachment (but clearly it's not working in your output).
>>>
>>>  Rutger
>>>
>>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>>  M.<KH...@be...> wrote:
>>>>  Hi Rutger,
>>>>
>>>>  I just built this and got different results for my hyperlink.xml output
>>>>  that
>>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>>>>  1.6.0_13.
>>>>
>>>>  Specifically, here's the annotation attached to otu elements:
>>>>
>>>>  <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>
>>>>
>>>>  And here's the whole thing:
>>>>
>>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>>  <nex:nexml
>>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>
>>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>    <otus xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>>        <meta content="http" datatype="xsd:string"
>>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="0" datatype="xsd:integer"
>>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="1" datatype="xsd:integer"
>>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>    </otus>
>>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>>  Trees"
>>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <tree
>>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>>>>  Uniform speciation (Yule)"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>>  >> xsi:type="nex:FloatTree">
>>>>        <meta content="1" datatype="xsd:long"
>>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>>  length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>>      </tree>
>>>>    </trees>
>>>>  </nex:nexml>
>>>>
>>>>
>>>>  Kasia
>>>>
>>>>
>>>>
>>>>  Katherine "Kasia" Hayden
>>>>  Bennington College, Class of 2011
>>>>  312.576.8175
>>>>  kh...@be...
>>>>
>>>>
>>>>
>>>>  -----Original Message-----
>>>>  From: Rutger Vos
>>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>>  Sent: Fri 6/5/2009 3:53 AM
>>>>  To: Arlin Stoltzfus
>>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>>  nex...@li...; ph...@go...
>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>
>>>>  Hi,
>>>>
>>>>  Can we work along a use case? I've just committed some code to import
>>>>  and export nexml (with annotations) into mesquite using the
>>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>>  play along - you don't *have* to build this):
>>>>
>>>>  * svn co
>>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>>  * cd java
>>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>>  * ant mesquite
>>>>
>>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>>  classpaths.xml file, which should contain an entry that points to the
>>>>  bin folder that the ant task created:
>>>>
>>>>  <?xml version="1.0"?>
>>>>  <mesquite>
>>>>              <!-- perhaps other classpath entries here -->
>>>>          <classpath>/path/to/java/bin</classpath>
>>>>  </mesquite>
>>>>
>>>>  Now, start mesquite and open this url from within mesquite (File >
>>>>  Open other... > URL...):
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>>
>>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>>  look in the nexus "source" you can see these URLs are written in the
>>>>  notes block. If you now choose file > export, NeXML should be one of
>>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>>  output should look like this:
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>>
>>>>  The salient point of the output is the annotation attached to otu
>>>>  elements:
>>>>
>>>>  <meta
>>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>>  irrelevant for now...] />
>>>>
>>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>>  store a url, and the "rel" attribute will describe the relationship
>>  >> between the subject (the earliest enclosing element that has an
>>>>  "about" attribute) and the resource on the other end. I *think* we
>>>>  agreed that such a simple relationship could be described as
>>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>>  CDAO owl file.
>>>>
>>>>  So what about other annotations? You can see in the produced nexml
>>>>  that mesquite is also storing internal object IDs to various
>>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>>  service queries which we would like to implement, and we want the
>>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>>
>>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>>  able to put it in a queue somewhere, but I would be very interested to
>>>>  see what Brandon comes up with for term suggestion interface -
>>>>  obviously it will be better for all involved if the term suggestion
>>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>>  hierarchy (as opposed to a rambling email like this one).
>>>>
>>>>  Rutger
>>>>
>>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>>  wrote:
>>>>>  We're listening.  Brandon has developed a term-request server to process
>>>>>  requests for concepts and relations, but its still in an early stage.  In
>>>>>  a
>>>>>  few weeks we will be in a better position to have this discussion.
>>>>>
>>>>>  Arlin
>>>>>
>>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>>
>>>>>>  Hi,
>>>>>>
>>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>>  extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>>>>  that the examples I've mailed out give you enough of a template to do
>>>>>>  this in python too, but please let me know of I can help - I know that
>>>>>>  the wiki needs updating, for starters).
>>>>>>
>>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>>  discussions it's been decided that CDAO will be the principal artifact
>>>>>>  for their mediation - so what's the community process for inclusion of
>>>>>>  new predicates?
>>>>>>
>>>>>>  Val and I have sketched out a couple of TreeBASE services whose search
>>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>>  tree.label, etc.), and this is just one use case of a project having a
>>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>>
>>>>>>  It would be great if team CDAO could tell us where to send our list of
>>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>>  that includes them :-)
>>>>>>
>>>>>>  I note that there is a wiki page about this
>>>>>>
>>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request),
>>>>>>but ideally
>>>>>>  there would be some sort of issue tracker with structured input fields
>>>>>>  (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>>  would be a team of curators that will promptly pick up a posted issue
>>>>>>  and work towards a solution.
>>>>>>
>>>>>>  I realize that this involves a support commitment from team CDAO, but
>>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>>
>>>>>>  Any comments?
>>>>>>
>>>>>>  Rutger
>>>>>>
>>>>>>  --
>>>>>>  Dr. Rutger A. Vos
>>>>>>  Department of zoology
>>>>>>  University of British Columbia
>>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>>  Dr. Rutger A. Vos
>>>>  Department of zoology
>>  >> University of British Columbia
>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>>
>>>>------------------------------------------------------------------------------
>>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>>  looking to deploy the next generation of Solaris that includes the latest
>>>>  innovations from Sun and the OpenSource community. Download a copy and
>>>>  enjoy capabilities such as Networking, Storage and Virtualization.
>>>>  Go to:
>>>><http://p.sf.net/sfu/opensolaris-get>http://p.sf.net/sfu/opensolaris-get
>>>>  _______________________________________________
>>>>  Nexml-discuss mailing list
>>>>  Nex...@li...
>>>>
>>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>  --
>>>  Dr. Rutger A. Vos
>>>  Department of zoology
>>>  University of British Columbia
>>>  <http://www.nexml.org>http://www.nexml.org
>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>>--
>>Dr. Rutger A. Vos
>>Department of zoology
>>University of British Columbia
>><http://www.nexml.org>http://www.nexml.org
>><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>
>>
>>
>>------------------------------------------------------------------------------
>>Crystal Reports - New Free Runtime and 30 Day Trial
>>Check out the new simplified licensing option that enables unlimited
>>royalty-free distribution of the report engine for externally facing
>>server and web deployment.
>>http://p.sf.net/sfu/businessobjects
>>
>>_______________________________________________
>>Nexml-discuss mailing list
>>Nex...@li...
>>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
> --
> --------------------------------------------------------
> Wayne Maddison
>  Professor and Canada Research Chair
>          Depts. of Zoology and Botany and
>          Biodiversity Research Centre
>  & Director
>          Beaty Biodiversity Museum
>  6270 University Boulevard
>  University of British Columbia
>  Vancouver, BC  V6T 1Z4   Canada
>
> email: wma...@in...   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
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> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rut...@gm...>]

Hi,

Wayne, thanks for chiming in - I changed the way the properties file
is loaded a little bit (sorry I left the absolute paths in
previously!). Kasia, could you try the following,

- assuming $NEXMLTRUNK is your local equivalent for
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
- assuming $MESQUITE_FOLDER is your local equivalent for
http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/

* cd $NEXMLTRUNK/java
* export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
* ant mesquite
* pico "$MESQUITE_FOLDER/classpaths.xml"
* add an entry in classpaths.xml:
<classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
be substituted for the real path (either relative or absolute) to the
bin folder in which ant placed the compiled classes. Attached is how I
have it, which works when you check the mesquite trunk and the full
nexml code (trunk and branches) in the same folder (for me that's
~/Documents/workspace but it shouldn't matter)

Now, when Mesquite starts up, could you copy and paste what happens in
the log window when you read the local version of this file:
$NEXMLTRUNK/examples/translations/hyperlink.xml

Hope this helps!

Rutger

On Tue, Jun 9, 2009 at 8:36 PM, Wayne
Maddison<wma...@in...> wrote:
> Sorry, I haven't been following this, but, classpaths.xml should be
> in the Mesquite_Folder that initiates Mesquite starting up.  To see
> if it's being read, include a line like:
>
>  <classpath>../../MySideProject/Mesquite_Folder</classpath>
>
>
> in which case the log should say something like this:
>
> =====
> Modules loading from directory
> /Users/wmaddisn/Mesquite_Workspace/Mesquite
> Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/
>
>  ancstates basic categ charMatrices charts cont genesis io lists
> minimal parsimony stochchar trees align assoc batchArch coalesce
> consensus correl distance diverse dmanager mb meristic molec
> ornamental pairwise rhetenor search tol treefarm iText jama jsci pal
> trunk
>
> Additional modules loaded from
> /Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
> =====
>
> However, this puts the paths in Java's classpath.  I suspect this may
> not help with the .properties file; this may use a different sense of
> application's path.  With pPod communication I seem to recall that
> some of the auxiliary files had to live in your initiating
> Mesquite_Folder.
>
> Wayne
>
>
> At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>>Content-type: multipart/alternative;
>>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>>Content-class: urn:content-classes:message
>>
>>Sorry, I'm a little confused. If my classpaths.xml is in
>>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't
>>it already in the root of my the Mesquite_Folder?
>>
>>Or are you saying to instead put it in
>>/home/kasia/workspace/Mesquite Project, which is one directory
>>above? (When I do this I no longer have the option to export as
>>NEXML, even when I remember that I have to change the relative paths
>>after bumping up the classpaths.xml file one directory :)
>>
>>
>>Kasia
>>
>>
>>
>>Katherine "Kasia" Hayden
>>Bennington College, Class of 2011
>>312.576.8175
>>kh...@be...
>>
>>
>>
>>-----Original Message-----
>>From: rut...@gm... on behalf of Rutger Vos
>>Sent: Tue 6/9/2009 4:52 PM
>>To: Hayden, Katherine M.
>>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>ju...@ig...; nex...@li...;
>>ph...@go...
>>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>>Hi Kasia,
>>
>>I don't think classpaths.xml modifies the system classpath variable,
>>so adding the properties file here won't do anything - as far as I
>>understand the xml file is read by Mesquite's module loading system.
>>Maybe try placing the file in the root of the Mesquite_Folder?
>>
>>Rutger
>>
>>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>>M.<KH...@be...> wrote:
>>>  Rutger,
>>>
>>>  I changed what you suggested and still get the same output.
>>>
>>>  This is what my classpaths.xml file looks like:
>>>
>>>  <?xml version="1.0"?>
>>>  <mesquite>
>>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>>          <!--
>>>
>>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>>  -->
>>>          <classpath>../../RutgersNexml/java/src</classpath>
>>>  </mesquite>
>>>
>>>
>>>  I wasn't sure if the .properties file needed to be pointed to directly or if
>>>  its directory needed to be specified, so I tried both. No luck with either.
>>>
>>>  My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>>>
>>>
>>>  Can't think of what else might be accounting for the difference.. Do you
>>>  have any other suggestions?
>>>
>>>
>>>  Kasia
>>>
>>>
>>>
>>>  Katherine "Kasia" Hayden
>>>  Bennington College, Class of 2011
>>>  312.576.8175
>>>  kh...@be...
>>>
>>>
>>>
>>>  -----Original Message-----
>>>  From: rut...@gm... on behalf of Rutger Vos
>>>  Sent: Fri 6/5/2009 5:23 PM
>>>  To: Hayden, Katherine M.
>>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>  > nex...@li...; ph...@go...
>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>  Hi Katherine,
>>>
>>>  is it possible that the predicateHandlerMapping.properties file isn't
>>>  in your classpath? The output you produced is the default output which
>>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>>  instead of the href/rel construct. The properties file defines which
>>>  class is used for which internal name, and it should make Mesquite
>>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>>  attachment (but clearly it's not working in your output).
>>>
>>>  Rutger
>>>
>>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>>  M.<KH...@be...> wrote:
>>>>  Hi Rutger,
>>>>
>>>>  I just built this and got different results for my hyperlink.xml output
>>>>  that
>>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>>>>  1.6.0_13.
>>>>
>>>>  Specifically, here's the annotation attached to otu elements:
>>>>
>>>>  <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>
>>>>
>>>>  And here's the whole thing:
>>>>
>>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>>  <nex:nexml
>>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>
>>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>    <otus xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>>        <meta content="http" datatype="xsd:string"
>>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="0" datatype="xsd:integer"
>>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="1" datatype="xsd:integer"
>>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>    </otus>
>>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>>  Trees"
>>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <tree
>>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>>>>  Uniform speciation (Yule)"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>>  >> xsi:type="nex:FloatTree">
>>>>        <meta content="1" datatype="xsd:long"
>>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>>  length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>>      </tree>
>>>>    </trees>
>>>>  </nex:nexml>
>>>>
>>>>
>>>>  Kasia
>>>>
>>>>
>>>>
>>>>  Katherine "Kasia" Hayden
>>>>  Bennington College, Class of 2011
>>>>  312.576.8175
>>>>  kh...@be...
>>>>
>>>>
>>>>
>>>>  -----Original Message-----
>>>>  From: Rutger Vos
>>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>>  Sent: Fri 6/5/2009 3:53 AM
>>>>  To: Arlin Stoltzfus
>>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>>  nex...@li...; ph...@go...
>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>
>>>>  Hi,
>>>>
>>>>  Can we work along a use case? I've just committed some code to import
>>>>  and export nexml (with annotations) into mesquite using the
>>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>>  play along - you don't *have* to build this):
>>>>
>>>>  * svn co
>>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>>  * cd java
>>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>>  * ant mesquite
>>>>
>>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>>  classpaths.xml file, which should contain an entry that points to the
>>>>  bin folder that the ant task created:
>>>>
>>>>  <?xml version="1.0"?>
>>>>  <mesquite>
>>>>              <!-- perhaps other classpath entries here -->
>>>>          <classpath>/path/to/java/bin</classpath>
>>>>  </mesquite>
>>>>
>>>>  Now, start mesquite and open this url from within mesquite (File >
>>>>  Open other... > URL...):
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>>
>>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>>  look in the nexus "source" you can see these URLs are written in the
>>>>  notes block. If you now choose file > export, NeXML should be one of
>>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>>  output should look like this:
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>>
>>>>  The salient point of the output is the annotation attached to otu
>>>>  elements:
>>>>
>>>>  <meta
>>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>>  irrelevant for now...] />
>>>>
>>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>>  store a url, and the "rel" attribute will describe the relationship
>>  >> between the subject (the earliest enclosing element that has an
>>>>  "about" attribute) and the resource on the other end. I *think* we
>>>>  agreed that such a simple relationship could be described as
>>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>>  CDAO owl file.
>>>>
>>>>  So what about other annotations? You can see in the produced nexml
>>>>  that mesquite is also storing internal object IDs to various
>>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>>  service queries which we would like to implement, and we want the
>>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>>
>>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>>  able to put it in a queue somewhere, but I would be very interested to
>>>>  see what Brandon comes up with for term suggestion interface -
>>>>  obviously it will be better for all involved if the term suggestion
>>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>>  hierarchy (as opposed to a rambling email like this one).
>>>>
>>>>  Rutger
>>>>
>>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>>  wrote:
>>>>>  We're listening.  Brandon has developed a term-request server to process
>>>>>  requests for concepts and relations, but its still in an early stage.  In
>>>>>  a
>>>>>  few weeks we will be in a better position to have this discussion.
>>>>>
>>>>>  Arlin
>>>>>
>>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>>
>>>>>>  Hi,
>>>>>>
>>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>>  extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>>>>  that the examples I've mailed out give you enough of a template to do
>>>>>>  this in python too, but please let me know of I can help - I know that
>>>>>>  the wiki needs updating, for starters).
>>>>>>
>>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>>  discussions it's been decided that CDAO will be the principal artifact
>>>>>>  for their mediation - so what's the community process for inclusion of
>>>>>>  new predicates?
>>>>>>
>>>>>>  Val and I have sketched out a couple of TreeBASE services whose search
>>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>>  tree.label, etc.), and this is just one use case of a project having a
>>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>>
>>>>>>  It would be great if team CDAO could tell us where to send our list of
>>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>>  that includes them :-)
>>>>>>
>>>>>>  I note that there is a wiki page about this
>>>>>>
>>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request),
>>>>>>but ideally
>>>>>>  there would be some sort of issue tracker with structured input fields
>>>>>>  (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>>  would be a team of curators that will promptly pick up a posted issue
>>>>>>  and work towards a solution.
>>>>>>
>>>>>>  I realize that this involves a support commitment from team CDAO, but
>>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>>
>>>>>>  Any comments?
>>>>>>
>>>>>>  Rutger
>>>>>>
>>>>>>  --
>>>>>>  Dr. Rutger A. Vos
>>>>>>  Department of zoology
>>>>>>  University of British Columbia
>>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>>  Dr. Rutger A. Vos
>>>>  Department of zoology
>>  >> University of British Columbia
>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>>
>>>>------------------------------------------------------------------------------
>>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>>  looking to deploy the next generation of Solaris that includes the latest
>>>>  innovations from Sun and the OpenSource community. Download a copy and
>>>>  enjoy capabilities such as Networking, Storage and Virtualization.
>>>>  Go to:
>>>><http://p.sf.net/sfu/opensolaris-get>http://p.sf.net/sfu/opensolaris-get
>>>>  _______________________________________________
>>>>  Nexml-discuss mailing list
>>>>  Nex...@li...
>>>>
>>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>  --
>>>  Dr. Rutger A. Vos
>>>  Department of zoology
>>>  University of British Columbia
>>>  <http://www.nexml.org>http://www.nexml.org
>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>>--
>>Dr. Rutger A. Vos
>>Department of zoology
>>University of British Columbia
>><http://www.nexml.org>http://www.nexml.org
>><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>
>>
>>
>>------------------------------------------------------------------------------
>>Crystal Reports - New Free Runtime and 30 Day Trial
>>Check out the new simplified licensing option that enables unlimited
>>royalty-free distribution of the report engine for externally facing
>>server and web deployment.
>>http://p.sf.net/sfu/businessobjects
>>
>>_______________________________________________
>>Nexml-discuss mailing list
>>Nex...@li...
>>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
> --
> --------------------------------------------------------
> Wayne Maddison
>  Professor and Canada Research Chair
>          Depts. of Zoology and Botany and
>          Biodiversity Research Centre
>  & Director
>          Beaty Biodiversity Museum
>  6270 University Boulevard
>  University of British Columbia
>  Vancouver, BC  V6T 1Z4   Canada
>
> email: wma...@in...   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Wayne M. <wma...@in...>]

Sorry, I haven't been following this, but, classpaths.xml should be 
in the Mesquite_Folder that initiates Mesquite starting up.  To see 
if it's being read, include a line like:

  <classpath>../../MySideProject/Mesquite_Folder</classpath>


in which case the log should say something like this:

=====
Modules loading from directory 
/Users/wmaddisn/Mesquite_Workspace/Mesquite 
Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/

  ancstates basic categ charMatrices charts cont genesis io lists 
minimal parsimony stochchar trees align assoc batchArch coalesce 
consensus correl distance diverse dmanager mb meristic molec 
ornamental pairwise rhetenor search tol treefarm iText jama jsci pal 
trunk

Additional modules loaded from 
/Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
=====

However, this puts the paths in Java's classpath.  I suspect this may 
not help with the .properties file; this may use a different sense of 
application's path.  With pPod communication I seem to recall that 
some of the auxiliary files had to live in your initiating 
Mesquite_Folder.

Wayne


At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>Content-type: multipart/alternative;
>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>Content-class: urn:content-classes:message
>
>Sorry, I'm a little confused. If my classpaths.xml is in 
>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't 
>it already in the root of my the Mesquite_Folder?
>
>Or are you saying to instead put it in 
>/home/kasia/workspace/Mesquite Project, which is one directory 
>above? (When I do this I no longer have the option to export as 
>NEXML, even when I remember that I have to change the relative paths 
>after bumping up the classpaths.xml file one directory :)
>
>
>Kasia
>
>
>
>Katherine "Kasia" Hayden
>Bennington College, Class of 2011
>312.576.8175
>kh...@be...
>
>
>
>-----Original Message-----
>From: rut...@gm... on behalf of Rutger Vos
>Sent: Tue 6/9/2009 4:52 PM
>To: Hayden, Katherine M.
>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; 
>ju...@ig...; nex...@li...; 
>ph...@go...
>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
>Hi Kasia,
>
>I don't think classpaths.xml modifies the system classpath variable,
>so adding the properties file here won't do anything - as far as I
>understand the xml file is read by Mesquite's module loading system.
>Maybe try placing the file in the root of the Mesquite_Folder?
>
>Rutger
>
>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>M.<KH...@be...> wrote:
>>  Rutger,
>>
>>  I changed what you suggested and still get the same output.
>>
>>  This is what my classpaths.xml file looks like:
>>
>>  <?xml version="1.0"?>
>>  <mesquite>
>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>          <!--
>> 
>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>  -->
>>          <classpath>../../RutgersNexml/java/src</classpath>
>>  </mesquite>
>>
>>
>>  I wasn't sure if the .properties file needed to be pointed to directly or if
>>  its directory needed to be specified, so I tried both. No luck with either.
>>
>>  My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>>
>>
>>  Can't think of what else might be accounting for the difference.. Do you
>>  have any other suggestions?
>>
>>
>>  Kasia
>>
>>
>>
>>  Katherine "Kasia" Hayden
>>  Bennington College, Class of 2011
>>  312.576.8175
>>  kh...@be...
>>
>>
>>
>>  -----Original Message-----
>>  From: rut...@gm... on behalf of Rutger Vos
>>  Sent: Fri 6/5/2009 5:23 PM
>>  To: Hayden, Katherine M.
>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>  > nex...@li...; ph...@go...
>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>>  Hi Katherine,
>>
>>  is it possible that the predicateHandlerMapping.properties file isn't
>>  in your classpath? The output you produced is the default output which
>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>  instead of the href/rel construct. The properties file defines which
>>  class is used for which internal name, and it should make Mesquite
>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>  attachment (but clearly it's not working in your output).
>>
>>  Rutger
>>
>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>  M.<KH...@be...> wrote:
>>>  Hi Rutger,
>>>
>>>  I just built this and got different results for my hyperlink.xml output
>>>  that
>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>>>  1.6.0_13.
>>>
>>>  Specifically, here's the annotation attached to otu elements:
>>>
>>>  <meta 
>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>
>>>
>>>  And here's the whole thing:
>>>
>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>  <nex:nexml 
>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>> 
>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>> 
>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>    <otus xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>  xsi:type="nex:LiteralMeta"/>
>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>        <meta content="http" datatype="xsd:string"
>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>  xsi:type="nex:LiteralMeta"/>
>>>        <meta content="0" datatype="xsd:integer"
>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>  xsi:type="nex:LiteralMeta"/>
>>>      </otu>
>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>        <meta 
>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>        <meta content="1" datatype="xsd:integer"
>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>  xsi:type="nex:LiteralMeta"/>
>>>      </otu>
>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>        <meta 
>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>        <meta content="2" datatype="xsd:integer"
>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>  xsi:type="nex:LiteralMeta"/>
>>>      </otu>
>>>    </otus>
>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>  Trees"
>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>      <tree 
>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>>>  Uniform speciation (Yule)"
>>> 
>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>  >> xsi:type="nex:FloatTree">
>>>        <meta content="1" datatype="xsd:long"
>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>  xsi:type="nex:LiteralMeta"/>
>>>        <meta content="2" datatype="xsd:integer"
>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>  length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>      </tree>
>>>    </trees>
>>>  </nex:nexml>
>>>
>>>
>>>  Kasia
>>>
>>>
>>>
>>>  Katherine "Kasia" Hayden
>>>  Bennington College, Class of 2011
>>>  312.576.8175
>>>  kh...@be...
>>>
>>>
>>>
>>>  -----Original Message-----
>>>  From: Rutger Vos 
>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>  Sent: Fri 6/5/2009 3:53 AM
>>>  To: Arlin Stoltzfus
>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>  nex...@li...; ph...@go...
>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>  Hi,
>>>
>>>  Can we work along a use case? I've just committed some code to import
>>>  and export nexml (with annotations) into mesquite using the
>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>  play along - you don't *have* to build this):
>>>
>>>  * svn co 
>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>  * cd java
>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>  * ant mesquite
>>>
>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>  classpaths.xml file, which should contain an entry that points to the
>>>  bin folder that the ant task created:
>>>
>>>  <?xml version="1.0"?>
>>>  <mesquite>
>>>              <!-- perhaps other classpath entries here -->
>>>          <classpath>/path/to/java/bin</classpath>
>>>  </mesquite>
>>>
>>>  Now, start mesquite and open this url from within mesquite (File >
>>>  Open other... > URL...):
>>>
>>> 
>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>
>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>  look in the nexus "source" you can see these URLs are written in the
>>>  notes block. If you now choose file > export, NeXML should be one of
>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>  output should look like this:
>>>
>>> 
>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>
>>>  The salient point of the output is the annotation attached to otu
>>>  elements:
>>>
>>>  <meta 
>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>  irrelevant for now...] />
>>>
>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>  store a url, and the "rel" attribute will describe the relationship
>  >> between the subject (the earliest enclosing element that has an
>>>  "about" attribute) and the resource on the other end. I *think* we
>>>  agreed that such a simple relationship could be described as
>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>  CDAO owl file.
>>>
>>>  So what about other annotations? You can see in the produced nexml
>>>  that mesquite is also storing internal object IDs to various
>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>  service queries which we would like to implement, and we want the
>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>
>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>  able to put it in a queue somewhere, but I would be very interested to
>>>  see what Brandon comes up with for term suggestion interface -
>>>  obviously it will be better for all involved if the term suggestion
>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>  hierarchy (as opposed to a rambling email like this one).
>>>
>>>  Rutger
>>>
>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>  wrote:
>>>>  We're listening.  Brandon has developed a term-request server to process
>>>>  requests for concepts and relations, but its still in an early stage.  In
>>>>  a
>>>>  few weeks we will be in a better position to have this discussion.
>>>>
>>>>  Arlin
>>>>
>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>
>>>>>  Hi,
>>>>>
>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>  extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>>>  that the examples I've mailed out give you enough of a template to do
>>>>>  this in python too, but please let me know of I can help - I know that
>>>>>  the wiki needs updating, for starters).
>>>>>
>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>  discussions it's been decided that CDAO will be the principal artifact
>>>>>  for their mediation - so what's the community process for inclusion of
>>>>>  new predicates?
>>>>>
>>>>>  Val and I have sketched out a couple of TreeBASE services whose search
>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>  tree.label, etc.), and this is just one use case of a project having a
>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>
>>>>>  It would be great if team CDAO could tell us where to send our list of
>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>  that includes them :-)
>>>>>
>>>>>  I note that there is a wiki page about this
>>>>> 
>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request), 
>>>>>but ideally
>>>>>  there would be some sort of issue tracker with structured input fields
>>>>>  (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>  would be a team of curators that will promptly pick up a posted issue
>>>>>  and work towards a solution.
>>>>>
>>>>>  I realize that this involves a support commitment from team CDAO, but
>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>
>>>>>  Any comments?
>>>>>
>>>>>  Rutger
>>>>>
>>>>>  --
>>>>>  Dr. Rutger A. Vos
>>>>>  Department of zoology
>>>>>  University of British Columbia
>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>
>>>
>>>
>>>  --
>>>  Dr. Rutger A. Vos
>>>  Department of zoology
>  >> University of British Columbia
>>>  <http://www.nexml.org>http://www.nexml.org
>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>> 
>>>------------------------------------------------------------------------------
>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>  looking to deploy the next generation of Solaris that includes the latest
>>>  innovations from Sun and the OpenSource community. Download a copy and
>>>  enjoy capabilities such as Networking, Storage and Virtualization.
>>>  Go to: 
>>><http://p.sf.net/sfu/opensolaris-get>http://p.sf.net/sfu/opensolaris-get
>>>  _______________________________________________
>>>  Nexml-discuss mailing list
>>>  Nex...@li...
>>> 
>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>
>>>
>>>
>>
>>
>>
>>  --
>>  Dr. Rutger A. Vos
>>  Department of zoology
>>  University of British Columbia
>>  <http://www.nexml.org>http://www.nexml.org
>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>
>>
>
>
>
>--
>Dr. Rutger A. Vos
>Department of zoology
>University of British Columbia
><http://www.nexml.org>http://www.nexml.org
><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>
>
>
>------------------------------------------------------------------------------
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-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wma...@in...   FAX: +1 604 822-2416

Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae:  http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Sorry, I'm a little confused. If my classpaths.xml is in /home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't it already in the root of my the Mesquite_Folder? 

Or are you saying to instead put it in /home/kasia/workspace/Mesquite Project, which is one directory above? (When I do this I no longer have the option to export as NEXML, even when I remember that I have to change the relative paths after bumping up the classpaths.xml file one directory :)


Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: rut...@gm... on behalf of Rutger Vos
Sent: Tue 6/9/2009 4:52 PM
To: Hayden, Katherine M.
Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi Kasia,

I don't think classpaths.xml modifies the system classpath variable,
so adding the properties file here won't do anything - as far as I
understand the xml file is read by Mesquite's module loading system.
Maybe try placing the file in the root of the Mesquite_Folder?

Rutger

On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Rutger,
>
> I changed what you suggested and still get the same output.
>
> This is what my classpaths.xml file looks like:
>
> <?xml version="1.0"?>
> <mesquite>
>         <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>         <classpath>../../RutgersNexml/java/bin</classpath>
>         <!--
> <classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
> -->
>         <classpath>../../RutgersNexml/java/src</classpath>
> </mesquite>
>
>
> I wasn't sure if the .properties file needed to be pointed to directly or if
> its directory needed to be specified, so I tried both. No luck with either.
>
> My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>
>
> Can't think of what else might be accounting for the difference.. Do you
> have any other suggestions?
>
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: rut...@gm... on behalf of Rutger Vos
> Sent: Fri 6/5/2009 5:23 PM
> To: Hayden, Katherine M.
> Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
> nex...@li...; ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi Katherine,
>
> is it possible that the predicateHandlerMapping.properties file isn't
> in your classpath? The output you produced is the default output which
> uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
> instead of the href/rel construct. The properties file defines which
> class is used for which internal name, and it should make Mesquite
> load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
> attachment (but clearly it's not working in your output).
>
> Rutger
>
> On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
> M.<KH...@be...> wrote:
>> Hi Rutger,
>>
>> I just built this and got different results for my hyperlink.xml output
>> that
>> I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>> 1.6.0_13.
>>
>> Specifically, here's the annotation attached to otu elements:
>>
>> <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>
>>
>> And here's the whole thing:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>> xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance"
>> generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>> xmlns:nex="http://www.nexml.org/1.0">
>>   <otus xmlns:msq="http://mesquiteproject.org#"
>> about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>> id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>> xmlns="http://www.nexml.org/1.0">
>>     <meta content="0121b10b3afc1" datatype="xsd:string"
>> id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>> xsi:type="nex:LiteralMeta"/>
>>     <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>> id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>       <meta content="http" datatype="xsd:string"
>> id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>> xsi:type="nex:LiteralMeta"/>
>>       <meta content="0" datatype="xsd:integer"
>> id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>     <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>> id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>       <meta content="1" datatype="xsd:integer"
>> id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>     <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>> id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>       <meta content="2" datatype="xsd:integer"
>> id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>   </otus>
>>   <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>> Trees"
>> otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>> xmlns="http://www.nexml.org/1.0">
>>     <tree xmlns:msq="http://mesquiteproject.org#"
>> about="#a72f25756-9b46-465a-9865-24960220a821"
>> id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>> Uniform speciation (Yule)"
>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>> xsi:type="nex:FloatTree">
>>       <meta content="1" datatype="xsd:long"
>> id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>> xsi:type="nex:LiteralMeta"/>
>>       <meta content="2" datatype="xsd:integer"
>> id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>> property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>       <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>       <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>> otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>       <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>       <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>> otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>       <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>> otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>       <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>> target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>       <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>> length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>> target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>       <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>> target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>       <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>> target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>     </tree>
>>   </trees>
>> </nex:nexml>
>>
>>
>> Kasia
>>
>>
>>
>> Katherine "Kasia" Hayden
>> Bennington College, Class of 2011
>> 312.576.8175
>> kh...@be...
>>
>>
>>
>> -----Original Message-----
>> From: Rutger Vos [mailto:rv...@in...]
>> Sent: Fri 6/5/2009 3:53 AM
>> To: Arlin Stoltzfus
>> Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>> nex...@li...; ph...@go...
>> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>> Hi,
>>
>> Can we work along a use case? I've just committed some code to import
>> and export nexml (with annotations) into mesquite using the
>> hackathon's nexml/java API. To run it, here's what you do (ok, just
>> play along - you don't *have* to build this):
>>
>> * svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>> * cd java
>> * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>> * ant mesquite
>>
>> Then, inside your Mesquite_Folder, either create or edit your
>> classpaths.xml file, which should contain an entry that points to the
>> bin folder that the ant task created:
>>
>> <?xml version="1.0"?>
>> <mesquite>
>>             <!-- perhaps other classpath entries here -->
>>         <classpath>/path/to/java/bin</classpath>
>> </mesquite>
>>
>> Now, start mesquite and open this url from within mesquite (File >
>> Open other... > URL...):
>>
>> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>
>> You'll see a tree with some dummy URLs on the terminal nodes. If you
>> look in the nexus "source" you can see these URLs are written in the
>> notes block. If you now choose file > export, NeXML should be one of
>> the options so you can write hyperlink.xml out to a file. The produced
>> output should look like this:
>>
>> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>
>> The salient point of the output is the annotation attached to otu
>> elements:
>>
>> <meta href="http://8ball.sdsc.edu:6666/treebase-web"
>>    rel="cdao:has_External_Reference" [...other attributes are
>> irrelevant for now...] />
>>
>> According to the RDFa rules, we can just use the "href" attribute to
>> store a url, and the "rel" attribute will describe the relationship
>> between the subject (the earliest enclosing element that has an
>> "about" attribute) and the resource on the other end. I *think* we
>> agreed that such a simple relationship could be described as
>> has_External_Reference, we use it on the wiki and I've found it in the
>> CDAO owl file.
>>
>> So what about other annotations? You can see in the produced nexml
>> that mesquite is also storing internal object IDs to various
>> predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>> msq:taxonUID and msq:treeUID). Can we have something like these as
>> properties in CDAO? The TreeBASE2 team has been sketching out some
>> service queries which we would like to implement, and we want the
>> search fields we expose be mediated by CDAO. One of the obvious search
>> fields would be something like cdao.treeUID, where perhaps the value
>> would be a namespaced id string (TreeBASE:Tr3242, for example).
>>
>> Can we have something like that? I like Hilmar's suggestion of being
>> able to put it in a queue somewhere, but I would be very interested to
>> see what Brandon comes up with for term suggestion interface -
>> obviously it will be better for all involved if the term suggestion
>> was as specific as possible, perhaps already fitted into CDAO's class
>> hierarchy (as opposed to a rambling email like this one).
>>
>> Rutger
>>
>> On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>> wrote:
>>> We're listening.  Brandon has developed a term-request server to process
>>> requests for concepts and relations, but its still in an early stage.  In
>>> a
>>> few weeks we will be in a better position to have this discussion.
>>>
>>> Arlin
>>>
>>> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>
>>>> Hi,
>>>>
>>>> I've done enough experimentation to establish the correct syntax for
>>>> attaching valid RDFa attachments to nexml so that standard RDFa
>>>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>> that the examples I've mailed out give you enough of a template to do
>>>> this in python too, but please let me know of I can help - I know that
>>>> the wiki needs updating, for starters).
>>>>
>>>> The key issue now is the definition of predicates, i.e. the value of
>>>> the @property and @rel attributes. Over the course of many EvoInfo
>>>> discussions it's been decided that CDAO will be the principal artifact
>>>> for their mediation - so what's the community process for inclusion of
>>>> new predicates?
>>>>
>>>> Val and I have sketched out a couple of TreeBASE services whose search
>>>> keys should be part of a controlled vocabulary (things like tree.id,
>>>> tree.label, etc.), and this is just one use case of a project having a
>>>> potentially large number of predicates (other example: Mesquite).
>>>>
>>>> It would be great if team CDAO could tell us where to send our list of
>>>> proposed terms and where we can download an amended version of CDAO
>>>> that includes them :-)
>>>>
>>>> I note that there is a wiki page about this
>>>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>>>> there would be some sort of issue tracker with structured input fields
>>>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>> would be a team of curators that will promptly pick up a posted issue
>>>> and work towards a solution.
>>>>
>>>> I realize that this involves a support commitment from team CDAO, but
>>>> I think that's what we agreed to over free-form key/value pairs,
>>>> homegrown vocabularies or a BioMoby-like free-for-all.
>>>>
>>>> Any comments?
>>>>
>>>> Rutger
>>>>
>>>> --
>>>> Dr. Rutger A. Vos
>>>> Department of zoology
>>>> University of British Columbia
>>>> http://www.nexml.org
>>>> http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>> ------------------------------------------------------------------------------
>> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>> looking to deploy the next generation of Solaris that includes the latest
>> innovations from Sun and the OpenSource community. Download a copy and
>> enjoy capabilities such as Networking, Storage and Virtualization.
>> Go to: http://p.sf.net/sfu/opensolaris-get
>> _______________________________________________
>> Nexml-discuss mailing list
>> Nex...@li...
>> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rv...@in...>]

Hi Kasia,

I don't think classpaths.xml modifies the system classpath variable,
so adding the properties file here won't do anything - as far as I
understand the xml file is read by Mesquite's module loading system.
Maybe try placing the file in the root of the Mesquite_Folder?

Rutger

On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Rutger,
>
> I changed what you suggested and still get the same output.
>
> This is what my classpaths.xml file looks like:
>
> <?xml version="1.0"?>
> <mesquite>
>         <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>         <classpath>../../RutgersNexml/java/bin</classpath>
>         <!--
> <classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
> -->
>         <classpath>../../RutgersNexml/java/src</classpath>
> </mesquite>
>
>
> I wasn't sure if the .properties file needed to be pointed to directly or if
> its directory needed to be specified, so I tried both. No luck with either.
>
> My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>
>
> Can't think of what else might be accounting for the difference.. Do you
> have any other suggestions?
>
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: rut...@gm... on behalf of Rutger Vos
> Sent: Fri 6/5/2009 5:23 PM
> To: Hayden, Katherine M.
> Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
> nex...@li...; ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi Katherine,
>
> is it possible that the predicateHandlerMapping.properties file isn't
> in your classpath? The output you produced is the default output which
> uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
> instead of the href/rel construct. The properties file defines which
> class is used for which internal name, and it should make Mesquite
> load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
> attachment (but clearly it's not working in your output).
>
> Rutger
>
> On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
> M.<KH...@be...> wrote:
>> Hi Rutger,
>>
>> I just built this and got different results for my hyperlink.xml output
>> that
>> I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>> 1.6.0_13.
>>
>> Specifically, here's the annotation attached to otu elements:
>>
>> <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>
>>
>> And here's the whole thing:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>> xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance"
>> generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>> xmlns:nex="http://www.nexml.org/1.0">
>>   <otus xmlns:msq="http://mesquiteproject.org#"
>> about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>> id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>> xmlns="http://www.nexml.org/1.0">
>>     <meta content="0121b10b3afc1" datatype="xsd:string"
>> id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>> xsi:type="nex:LiteralMeta"/>
>>     <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>> id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>       <meta content="http" datatype="xsd:string"
>> id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>> xsi:type="nex:LiteralMeta"/>
>>       <meta content="0" datatype="xsd:integer"
>> id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>     <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>> id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>       <meta content="1" datatype="xsd:integer"
>> id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>     <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>> id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
>> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>       <meta content="2" datatype="xsd:integer"
>> id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>> xsi:type="nex:LiteralMeta"/>
>>     </otu>
>>   </otus>
>>   <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>> Trees"
>> otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>> xmlns="http://www.nexml.org/1.0">
>>     <tree xmlns:msq="http://mesquiteproject.org#"
>> about="#a72f25756-9b46-465a-9865-24960220a821"
>> id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>> Uniform speciation (Yule)"
>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>> xsi:type="nex:FloatTree">
>>       <meta content="1" datatype="xsd:long"
>> id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>> xsi:type="nex:LiteralMeta"/>
>>       <meta content="2" datatype="xsd:integer"
>> id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>> property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>       <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>       <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>> otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>       <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>       <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>> otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>       <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>> otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>       <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>> target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>       <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>> length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>> target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>       <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>> target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>       <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>> target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>     </tree>
>>   </trees>
>> </nex:nexml>
>>
>>
>> Kasia
>>
>>
>>
>> Katherine "Kasia" Hayden
>> Bennington College, Class of 2011
>> 312.576.8175
>> kh...@be...
>>
>>
>>
>> -----Original Message-----
>> From: Rutger Vos [mailto:rv...@in...]
>> Sent: Fri 6/5/2009 3:53 AM
>> To: Arlin Stoltzfus
>> Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>> nex...@li...; ph...@go...
>> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>> Hi,
>>
>> Can we work along a use case? I've just committed some code to import
>> and export nexml (with annotations) into mesquite using the
>> hackathon's nexml/java API. To run it, here's what you do (ok, just
>> play along - you don't *have* to build this):
>>
>> * svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>> * cd java
>> * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>> * ant mesquite
>>
>> Then, inside your Mesquite_Folder, either create or edit your
>> classpaths.xml file, which should contain an entry that points to the
>> bin folder that the ant task created:
>>
>> <?xml version="1.0"?>
>> <mesquite>
>>             <!-- perhaps other classpath entries here -->
>>         <classpath>/path/to/java/bin</classpath>
>> </mesquite>
>>
>> Now, start mesquite and open this url from within mesquite (File >
>> Open other... > URL...):
>>
>> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>
>> You'll see a tree with some dummy URLs on the terminal nodes. If you
>> look in the nexus "source" you can see these URLs are written in the
>> notes block. If you now choose file > export, NeXML should be one of
>> the options so you can write hyperlink.xml out to a file. The produced
>> output should look like this:
>>
>> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>
>> The salient point of the output is the annotation attached to otu
>> elements:
>>
>> <meta href="http://8ball.sdsc.edu:6666/treebase-web"
>>    rel="cdao:has_External_Reference" [...other attributes are
>> irrelevant for now...] />
>>
>> According to the RDFa rules, we can just use the "href" attribute to
>> store a url, and the "rel" attribute will describe the relationship
>> between the subject (the earliest enclosing element that has an
>> "about" attribute) and the resource on the other end. I *think* we
>> agreed that such a simple relationship could be described as
>> has_External_Reference, we use it on the wiki and I've found it in the
>> CDAO owl file.
>>
>> So what about other annotations? You can see in the produced nexml
>> that mesquite is also storing internal object IDs to various
>> predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>> msq:taxonUID and msq:treeUID). Can we have something like these as
>> properties in CDAO? The TreeBASE2 team has been sketching out some
>> service queries which we would like to implement, and we want the
>> search fields we expose be mediated by CDAO. One of the obvious search
>> fields would be something like cdao.treeUID, where perhaps the value
>> would be a namespaced id string (TreeBASE:Tr3242, for example).
>>
>> Can we have something like that? I like Hilmar's suggestion of being
>> able to put it in a queue somewhere, but I would be very interested to
>> see what Brandon comes up with for term suggestion interface -
>> obviously it will be better for all involved if the term suggestion
>> was as specific as possible, perhaps already fitted into CDAO's class
>> hierarchy (as opposed to a rambling email like this one).
>>
>> Rutger
>>
>> On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>> wrote:
>>> We're listening.  Brandon has developed a term-request server to process
>>> requests for concepts and relations, but its still in an early stage.  In
>>> a
>>> few weeks we will be in a better position to have this discussion.
>>>
>>> Arlin
>>>
>>> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>
>>>> Hi,
>>>>
>>>> I've done enough experimentation to establish the correct syntax for
>>>> attaching valid RDFa attachments to nexml so that standard RDFa
>>>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>> that the examples I've mailed out give you enough of a template to do
>>>> this in python too, but please let me know of I can help - I know that
>>>> the wiki needs updating, for starters).
>>>>
>>>> The key issue now is the definition of predicates, i.e. the value of
>>>> the @property and @rel attributes. Over the course of many EvoInfo
>>>> discussions it's been decided that CDAO will be the principal artifact
>>>> for their mediation - so what's the community process for inclusion of
>>>> new predicates?
>>>>
>>>> Val and I have sketched out a couple of TreeBASE services whose search
>>>> keys should be part of a controlled vocabulary (things like tree.id,
>>>> tree.label, etc.), and this is just one use case of a project having a
>>>> potentially large number of predicates (other example: Mesquite).
>>>>
>>>> It would be great if team CDAO could tell us where to send our list of
>>>> proposed terms and where we can download an amended version of CDAO
>>>> that includes them :-)
>>>>
>>>> I note that there is a wiki page about this
>>>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>>>> there would be some sort of issue tracker with structured input fields
>>>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>> would be a team of curators that will promptly pick up a posted issue
>>>> and work towards a solution.
>>>>
>>>> I realize that this involves a support commitment from team CDAO, but
>>>> I think that's what we agreed to over free-form key/value pairs,
>>>> homegrown vocabularies or a BioMoby-like free-for-all.
>>>>
>>>> Any comments?
>>>>
>>>> Rutger
>>>>
>>>> --
>>>> Dr. Rutger A. Vos
>>>> Department of zoology
>>>> University of British Columbia
>>>> http://www.nexml.org
>>>> http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>> ------------------------------------------------------------------------------
>> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>> looking to deploy the next generation of Solaris that includes the latest
>> innovations from Sun and the OpenSource community. Download a copy and
>> enjoy capabilities such as Networking, Storage and Virtualization.
>> Go to: http://p.sf.net/sfu/opensolaris-get
>> _______________________________________________
>> Nexml-discuss mailing list
>> Nex...@li...
>> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Hey Rutger,

One step in the right direction (I think) is that in the InterpretNEXML.java file there were complete paths to the predicateHandlerMapping.properties file on _your_ machine, so I switched those up to reflect mine.

Ex:
...
	    try {
		properties.load(new FileInputStream("/home/kasia/workspace/nexml/java/src/predicateHandlerMapping.properties"));
	        //properties.load(new FileInputStream("/Users/rvosa/Documents/workspace/nexml/trunk/nexml/java/src/predicateHandlerMapping.properties"));
...

I only found this in two places, and only in InterpretNEXML.java but perhaps there are others that you know of that I missed?


Even after changing that I still don't get my output to resemble yours, still unsolved.



Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: rut...@gm... on behalf of Rutger Vos
Sent: Fri 6/5/2009 5:23 PM
To: Hayden, Katherine M.
Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi Katherine,

is it possible that the predicateHandlerMapping.properties file isn't
in your classpath? The output you produced is the default output which
uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
instead of the href/rel construct. The properties file defines which
class is used for which internal name, and it should make Mesquite
load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
attachment (but clearly it's not working in your output).

Rutger

On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I just built this and got different results for my hyperlink.xml output that
> I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
> 1.6.0_13.
>
> Specifically, here's the annotation attached to otu elements:
>
> <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>
>
> And here's the whole thing:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
> xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance"
> generator="org.nexml.model.impl.DocumentImpl" version="0.8"
> xmlns:nex="http://www.nexml.org/1.0">
>   <otus xmlns:msq="http://mesquiteproject.org#"
> about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
> xmlns="http://www.nexml.org/1.0">
>     <meta content="0121b10b3afc1" datatype="xsd:string"
> id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
> xsi:type="nex:LiteralMeta"/>
>     <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
> id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>       <meta content="http" datatype="xsd:string"
> id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="0" datatype="xsd:integer"
> id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
> id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="1" datatype="xsd:integer"
> id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
> id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>   </otus>
>   <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated Trees"
> otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> xmlns="http://www.nexml.org/1.0">
>     <tree xmlns:msq="http://mesquiteproject.org#"
> about="#a72f25756-9b46-465a-9865-24960220a821"
> id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
> Uniform speciation (Yule)"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xsi:type="nex:FloatTree">
>       <meta content="1" datatype="xsd:long"
> id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="a93297efc-f077-43fd-88b1-e5a0866c0303"
> property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>       <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>       <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
> otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>       <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>       <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
> otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>       <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
> otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>       <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>       <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
> length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>       <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>       <edge id="a116f17be-c512-4680-a850-c4d467451f68"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>     </tree>
>   </trees>
> </nex:nexml>
>
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rv...@in...]
> Sent: Fri 6/5/2009 3:53 AM
> To: Arlin Stoltzfus
> Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
> nex...@li...; ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Can we work along a use case? I've just committed some code to import
> and export nexml (with annotations) into mesquite using the
> hackathon's nexml/java API. To run it, here's what you do (ok, just
> play along - you don't *have* to build this):
>
> * svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
> * cd java
> * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
> * ant mesquite
>
> Then, inside your Mesquite_Folder, either create or edit your
> classpaths.xml file, which should contain an entry that points to the
> bin folder that the ant task created:
>
> <?xml version="1.0"?>
> <mesquite>
>             <!-- perhaps other classpath entries here -->
>         <classpath>/path/to/java/bin</classpath>
> </mesquite>
>
> Now, start mesquite and open this url from within mesquite (File >
> Open other... > URL...):
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>
> You'll see a tree with some dummy URLs on the terminal nodes. If you
> look in the nexus "source" you can see these URLs are written in the
> notes block. If you now choose file > export, NeXML should be one of
> the options so you can write hyperlink.xml out to a file. The produced
> output should look like this:
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>
> The salient point of the output is the annotation attached to otu elements:
>
> <meta href="http://8ball.sdsc.edu:6666/treebase-web"
>    rel="cdao:has_External_Reference" [...other attributes are
> irrelevant for now...] />
>
> According to the RDFa rules, we can just use the "href" attribute to
> store a url, and the "rel" attribute will describe the relationship
> between the subject (the earliest enclosing element that has an
> "about" attribute) and the resource on the other end. I *think* we
> agreed that such a simple relationship could be described as
> has_External_Reference, we use it on the wiki and I've found it in the
> CDAO owl file.
>
> So what about other annotations? You can see in the produced nexml
> that mesquite is also storing internal object IDs to various
> predicates under the msq: namespace prefix (i.e. msq:taxaUID,
> msq:taxonUID and msq:treeUID). Can we have something like these as
> properties in CDAO? The TreeBASE2 team has been sketching out some
> service queries which we would like to implement, and we want the
> search fields we expose be mediated by CDAO. One of the obvious search
> fields would be something like cdao.treeUID, where perhaps the value
> would be a namespaced id string (TreeBASE:Tr3242, for example).
>
> Can we have something like that? I like Hilmar's suggestion of being
> able to put it in a queue somewhere, but I would be very interested to
> see what Brandon comes up with for term suggestion interface -
> obviously it will be better for all involved if the term suggestion
> was as specific as possible, perhaps already fitted into CDAO's class
> hierarchy (as opposed to a rambling email like this one).
>
> Rutger
>
> On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
> wrote:
>> We're listening.  Brandon has developed a term-request server to process
>> requests for concepts and relations, but its still in an early stage.  In
>> a
>> few weeks we will be in a better position to have this discussion.
>>
>> Arlin
>>
>> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>
>>> Hi,
>>>
>>> I've done enough experimentation to establish the correct syntax for
>>> attaching valid RDFa attachments to nexml so that standard RDFa
>>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>> that the examples I've mailed out give you enough of a template to do
>>> this in python too, but please let me know of I can help - I know that
>>> the wiki needs updating, for starters).
>>>
>>> The key issue now is the definition of predicates, i.e. the value of
>>> the @property and @rel attributes. Over the course of many EvoInfo
>>> discussions it's been decided that CDAO will be the principal artifact
>>> for their mediation - so what's the community process for inclusion of
>>> new predicates?
>>>
>>> Val and I have sketched out a couple of TreeBASE services whose search
>>> keys should be part of a controlled vocabulary (things like tree.id,
>>> tree.label, etc.), and this is just one use case of a project having a
>>> potentially large number of predicates (other example: Mesquite).
>>>
>>> It would be great if team CDAO could tell us where to send our list of
>>> proposed terms and where we can download an amended version of CDAO
>>> that includes them :-)
>>>
>>> I note that there is a wiki page about this
>>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>>> there would be some sort of issue tracker with structured input fields
>>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>> would be a team of curators that will promptly pick up a posted issue
>>> and work towards a solution.
>>>
>>> I realize that this involves a support commitment from team CDAO, but
>>> I think that's what we agreed to over free-form key/value pairs,
>>> homegrown vocabularies or a BioMoby-like free-for-all.
>>>
>>> Any comments?
>>>
>>> Rutger
>>>
>>> --
>>> Dr. Rutger A. Vos
>>> Department of zoology
>>> University of British Columbia
>>> http://www.nexml.org
>>> http://rutgervos.blogspot.com
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [PhyloWS] Re: CDAO term inclusion community process

[Hilmar L. <hl...@du...>]

So it seems I'm not disciplined enough yet for putting the URLs in  
citations ... here goes.

[1] http://apps.sourceforge.net/mediawiki/treebase/index.php?title=Main_Page

On Jun 8, 2009, at 7:18 AM, Hilmar Lapp wrote:

>
>
> On Jun 6, 2009, at 6:59 PM, Hilmar Lapp wrote:
>
>>> Would it make sense to just have a google excel
>>> sheet or something to put them in?
>>
>> Sure, that's a good idea - go ahead, and we can add columns for
>> comments, etc.
>
>
> BTW we could also create a page under the group. I've now also enabled
> a wiki for TreeBASE development (see [1], also linked under "Hosted
> Apps"), where such things could be built more collaboratively.
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> ===========================================================
>
>
>
>
>
> --~--~---------~--~----~------------~-------~--~----~
> You received this message because you are subscribed to the Google  
> Groups "PhyloWS" group.
> To post to this group, send email to ph...@go...
> To unsubscribe from this group, send email to phy...@go...
> For more options, visit this group at http://groups.google.com/group/phylows?hl=en
> -~----------~----~----~----~------~----~------~--~---
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
===========================================================

Re: [Treebase-devel] CDAO term inclusion community process

[Hilmar L. <hl...@du...>]

On Jun 6, 2009, at 6:59 PM, Hilmar Lapp wrote:

>> Would it make sense to just have a google excel
>> sheet or something to put them in?
>
> Sure, that's a good idea - go ahead, and we can add columns for
> comments, etc.


BTW we could also create a page under the group. I've now also enabled  
a wiki for TreeBASE development (see [1], also linked under "Hosted  
Apps"), where such things could be built more collaboratively.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
===========================================================

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Rutger,

I changed what you suggested and still get the same output.

This is what my classpaths.xml file looks like:

<?xml version="1.0"?>
<mesquite>
	<classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
	<classpath>../../RutgersNexml/java/bin</classpath>
	<!-- <classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath> -->
	<classpath>../../RutgersNexml/java/src</classpath>
</mesquite>


I wasn't sure if the .properties file needed to be pointed to directly or if its directory needed to be specified, so I tried both. No luck with either.

My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.


Can't think of what else might be accounting for the difference.. Do you have any other suggestions?


Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: rut...@gm... on behalf of Rutger Vos
Sent: Fri 6/5/2009 5:23 PM
To: Hayden, Katherine M.
Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi Katherine,

is it possible that the predicateHandlerMapping.properties file isn't
in your classpath? The output you produced is the default output which
uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
instead of the href/rel construct. The properties file defines which
class is used for which internal name, and it should make Mesquite
load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
attachment (but clearly it's not working in your output).

Rutger

On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I just built this and got different results for my hyperlink.xml output that
> I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
> 1.6.0_13.
>
> Specifically, here's the annotation attached to otu elements:
>
> <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>
>
> And here's the whole thing:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
> xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance"
> generator="org.nexml.model.impl.DocumentImpl" version="0.8"
> xmlns:nex="http://www.nexml.org/1.0">
>   <otus xmlns:msq="http://mesquiteproject.org#"
> about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
> xmlns="http://www.nexml.org/1.0">
>     <meta content="0121b10b3afc1" datatype="xsd:string"
> id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
> xsi:type="nex:LiteralMeta"/>
>     <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
> id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>       <meta content="http" datatype="xsd:string"
> id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="0" datatype="xsd:integer"
> id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
> id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="1" datatype="xsd:integer"
> id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
> id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>   </otus>
>   <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated Trees"
> otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> xmlns="http://www.nexml.org/1.0">
>     <tree xmlns:msq="http://mesquiteproject.org#"
> about="#a72f25756-9b46-465a-9865-24960220a821"
> id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
> Uniform speciation (Yule)"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xsi:type="nex:FloatTree">
>       <meta content="1" datatype="xsd:long"
> id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="a93297efc-f077-43fd-88b1-e5a0866c0303"
> property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>       <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>       <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
> otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>       <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>       <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
> otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>       <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
> otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>       <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>       <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
> length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>       <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>       <edge id="a116f17be-c512-4680-a850-c4d467451f68"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>     </tree>
>   </trees>
> </nex:nexml>
>
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rv...@in...]
> Sent: Fri 6/5/2009 3:53 AM
> To: Arlin Stoltzfus
> Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
> nex...@li...; ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Can we work along a use case? I've just committed some code to import
> and export nexml (with annotations) into mesquite using the
> hackathon's nexml/java API. To run it, here's what you do (ok, just
> play along - you don't *have* to build this):
>
> * svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
> * cd java
> * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
> * ant mesquite
>
> Then, inside your Mesquite_Folder, either create or edit your
> classpaths.xml file, which should contain an entry that points to the
> bin folder that the ant task created:
>
> <?xml version="1.0"?>
> <mesquite>
>             <!-- perhaps other classpath entries here -->
>         <classpath>/path/to/java/bin</classpath>
> </mesquite>
>
> Now, start mesquite and open this url from within mesquite (File >
> Open other... > URL...):
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>
> You'll see a tree with some dummy URLs on the terminal nodes. If you
> look in the nexus "source" you can see these URLs are written in the
> notes block. If you now choose file > export, NeXML should be one of
> the options so you can write hyperlink.xml out to a file. The produced
> output should look like this:
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>
> The salient point of the output is the annotation attached to otu elements:
>
> <meta href="http://8ball.sdsc.edu:6666/treebase-web"
>    rel="cdao:has_External_Reference" [...other attributes are
> irrelevant for now...] />
>
> According to the RDFa rules, we can just use the "href" attribute to
> store a url, and the "rel" attribute will describe the relationship
> between the subject (the earliest enclosing element that has an
> "about" attribute) and the resource on the other end. I *think* we
> agreed that such a simple relationship could be described as
> has_External_Reference, we use it on the wiki and I've found it in the
> CDAO owl file.
>
> So what about other annotations? You can see in the produced nexml
> that mesquite is also storing internal object IDs to various
> predicates under the msq: namespace prefix (i.e. msq:taxaUID,
> msq:taxonUID and msq:treeUID). Can we have something like these as
> properties in CDAO? The TreeBASE2 team has been sketching out some
> service queries which we would like to implement, and we want the
> search fields we expose be mediated by CDAO. One of the obvious search
> fields would be something like cdao.treeUID, where perhaps the value
> would be a namespaced id string (TreeBASE:Tr3242, for example).
>
> Can we have something like that? I like Hilmar's suggestion of being
> able to put it in a queue somewhere, but I would be very interested to
> see what Brandon comes up with for term suggestion interface -
> obviously it will be better for all involved if the term suggestion
> was as specific as possible, perhaps already fitted into CDAO's class
> hierarchy (as opposed to a rambling email like this one).
>
> Rutger
>
> On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
> wrote:
>> We're listening.  Brandon has developed a term-request server to process
>> requests for concepts and relations, but its still in an early stage.  In
>> a
>> few weeks we will be in a better position to have this discussion.
>>
>> Arlin
>>
>> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>
>>> Hi,
>>>
>>> I've done enough experimentation to establish the correct syntax for
>>> attaching valid RDFa attachments to nexml so that standard RDFa
>>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>> that the examples I've mailed out give you enough of a template to do
>>> this in python too, but please let me know of I can help - I know that
>>> the wiki needs updating, for starters).
>>>
>>> The key issue now is the definition of predicates, i.e. the value of
>>> the @property and @rel attributes. Over the course of many EvoInfo
>>> discussions it's been decided that CDAO will be the principal artifact
>>> for their mediation - so what's the community process for inclusion of
>>> new predicates?
>>>
>>> Val and I have sketched out a couple of TreeBASE services whose search
>>> keys should be part of a controlled vocabulary (things like tree.id,
>>> tree.label, etc.), and this is just one use case of a project having a
>>> potentially large number of predicates (other example: Mesquite).
>>>
>>> It would be great if team CDAO could tell us where to send our list of
>>> proposed terms and where we can download an amended version of CDAO
>>> that includes them :-)
>>>
>>> I note that there is a wiki page about this
>>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>>> there would be some sort of issue tracker with structured input fields
>>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>> would be a team of curators that will promptly pick up a posted issue
>>> and work towards a solution.
>>>
>>> I realize that this involves a support commitment from team CDAO, but
>>> I think that's what we agreed to over free-form key/value pairs,
>>> homegrown vocabularies or a BioMoby-like free-for-all.
>>>
>>> Any comments?
>>>
>>> Rutger
>>>
>>> --
>>> Dr. Rutger A. Vos
>>> Department of zoology
>>> University of British Columbia
>>> http://www.nexml.org
>>> http://rutgervos.blogspot.com
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
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> _______________________________________________
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> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [PhyloWS] Re: [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rv...@in...>]

> You mean in NeXML? You could, using CDAO terms will be preferred if
> available, because they will better support inferencing.
>
> I.e., querying with PhyloWS-vocabulary terms does not and should not
> imply that you get back only results that have PhyloWS-vocabulary
> annotations. It is up to the implementing server to determine which
> data and annotation attributes to match a particular PhyloWS-
> vocabulary term with.

I see, so we could do something like (warning, pseudocode coming up):

select * where pws.label='MyTree'

...and the service could decide that a nexml tree with @label='MyTree'
constitutes a match (as could other fields, attributes or annotations,
potentially).

>> Fine by me, but I guess we need to come up with a way to collect
>> those terms, no? Would it make sense to just have a google excel
>> sheet or something to put them in?
>
> Sure, that's a good idea - go ahead, and we can add columns for
> comments, etc.

Alright, Val and I identified some fields, so I'll start with those.



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hilmar L. <hl...@du...>]

On Jun 6, 2009, at 3:57 PM, Rutger Vos wrote:

>> I think that's a good starting point but the way I'm thinking about
>> this at present the "standard" context set (i.e., vocabulary) for
>> PhyloWS finder queries would be informed by (and possibly directly
>> import from) CDAO, but would not be CDAO itself but rather a separate
>> compact vocabulary.
>
> So we're going to have xmlns:pws="http://www.phylows.org#"  
> property="pws:taxonUID"?

You mean in NeXML? You could, using CDAO terms will be preferred if  
available, because they will better support inferencing.

I.e., querying with PhyloWS-vocabulary terms does not and should not  
imply that you get back only results that have PhyloWS-vocabulary  
annotations. It is up to the implementing server to determine which  
data and annotation attributes to match a particular PhyloWS- 
vocabulary term with.

> Fine by me, but I guess we need to come up with a way to collect  
> those terms, no? Would it make sense to just have a google excel  
> sheet or something to put them in?

Sure, that's a good idea - go ahead, and we can add columns for  
comments, etc.

	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
===========================================================

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rv...@in...>]

> I think that's a good starting point but the way I'm thinking about
> this at present the "standard" context set (i.e., vocabulary) for
> PhyloWS finder queries would be informed by (and possibly directly
> import from) CDAO, but would not be CDAO itself but rather a separate
> compact vocabulary.

So we're going to have xmlns:pws="http://www.phylows.org#"
property="pws:taxonUID"? Fine by me, but I guess we need to come up
with a way to collect those terms, no? Would it make sense to just
have a google excel sheet or something to put them in?




-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hilmar L. <hl...@du...>]

On Jun 5, 2009, at 3:53 AM, Rutger Vos wrote:

> You can see in the produced nexml that mesquite is also storing  
> internal object IDs to various predicates under the msq: namespace  
> prefix (i.e. msq:taxaUID,
> msq:taxonUID and msq:treeUID). Can we have something like these as
> properties in CDAO? The TreeBASE2 team has been sketching out some
> service queries which we would like to implement, and we want the
> search fields we expose be mediated by CDAO.

I think that's a good starting point but the way I'm thinking about  
this at present the "standard" context set (i.e., vocabulary) for  
PhyloWS finder queries would be informed by (and possibly directly  
import from) CDAO, but would not be CDAO itself but rather a separate  
compact vocabulary.

That's because CDAO (in my understanding) is an ontology meant to  
formalize our current knowledge about evolutionary substrates,  
processes, phenomena, and data, and how these relate to each other.  
That's different from a compact metadata vocabulary that people browse  
through to quickly identify the suitable term(s) for their query.  
PhyloWS needs the latter, but doesn't in fact need the former. (Though  
the data it returns will be better interpretable if it is  
comprehensively annotated with CDAO.)

Having said that, I don't think that diminishes in any way the need  
for a formal, documented, and agreed upon procedure for requesting  
CDAO term and relationship additions and modifications by the community.

> [...] Can we have something like that? I like Hilmar's suggestion of  
> being
> able to put it in a queue somewhere, but I would be very interested to
> see what Brandon comes up with for term suggestion interface -
> obviously it will be better for all involved if the term suggestion
> was as specific as possible, perhaps already fitted into CDAO's class
> hierarchy (as opposed to a rambling email like this one).


Note that this can be solved by conventions - in the end it is humans  
that need to look at this anyway, not machines. Almost all the OBO  
Foundry ontologies use the tracker system I believe, and there are  
quite a few of them, so there's some evidence that it can work.

Another example is Darwin Core, which uses the Google Code issue  
tracker and pre-defined templates (try to create a new issue and  
choose new term):
http://code.google.com/p/darwincore/wiki/SubmittingIssues

	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
===========================================================

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Rutger V. <rv...@in...>]

Hi Katherine,

is it possible that the predicateHandlerMapping.properties file isn't
in your classpath? The output you produced is the default output which
uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
instead of the href/rel construct. The properties file defines which
class is used for which internal name, and it should make Mesquite
load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
attachment (but clearly it's not working in your output).

Rutger

On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I just built this and got different results for my hyperlink.xml output that
> I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
> 1.6.0_13.
>
> Specifically, here's the annotation attached to otu elements:
>
> <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>
>
> And here's the whole thing:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
> xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance"
> generator="org.nexml.model.impl.DocumentImpl" version="0.8"
> xmlns:nex="http://www.nexml.org/1.0">
>   <otus xmlns:msq="http://mesquiteproject.org#"
> about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
> xmlns="http://www.nexml.org/1.0">
>     <meta content="0121b10b3afc1" datatype="xsd:string"
> id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
> xsi:type="nex:LiteralMeta"/>
>     <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
> id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>       <meta content="http" datatype="xsd:string"
> id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="0" datatype="xsd:integer"
> id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
> id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="1" datatype="xsd:integer"
> id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>     <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
> id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>       <meta content="http://8ball.sdsc.edu:6666/treebase-web"
> datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
> property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
> xsi:type="nex:LiteralMeta"/>
>     </otu>
>   </otus>
>   <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated Trees"
> otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
> xmlns="http://www.nexml.org/1.0">
>     <tree xmlns:msq="http://mesquiteproject.org#"
> about="#a72f25756-9b46-465a-9865-24960220a821"
> id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
> Uniform speciation (Yule)"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xsi:type="nex:FloatTree">
>       <meta content="1" datatype="xsd:long"
> id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
> xsi:type="nex:LiteralMeta"/>
>       <meta content="2" datatype="xsd:integer"
> id="a93297efc-f077-43fd-88b1-e5a0866c0303"
> property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>       <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>       <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
> otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>       <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>       <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
> otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>       <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
> otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>       <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
> source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>       <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
> length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
> target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>       <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>       <edge id="a116f17be-c512-4680-a850-c4d467451f68"
> length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
> target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>     </tree>
>   </trees>
> </nex:nexml>
>
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rv...@in...]
> Sent: Fri 6/5/2009 3:53 AM
> To: Arlin Stoltzfus
> Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
> nex...@li...; ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Can we work along a use case? I've just committed some code to import
> and export nexml (with annotations) into mesquite using the
> hackathon's nexml/java API. To run it, here's what you do (ok, just
> play along - you don't *have* to build this):
>
> * svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
> * cd java
> * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
> * ant mesquite
>
> Then, inside your Mesquite_Folder, either create or edit your
> classpaths.xml file, which should contain an entry that points to the
> bin folder that the ant task created:
>
> <?xml version="1.0"?>
> <mesquite>
>             <!-- perhaps other classpath entries here -->
>         <classpath>/path/to/java/bin</classpath>
> </mesquite>
>
> Now, start mesquite and open this url from within mesquite (File >
> Open other... > URL...):
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>
> You'll see a tree with some dummy URLs on the terminal nodes. If you
> look in the nexus "source" you can see these URLs are written in the
> notes block. If you now choose file > export, NeXML should be one of
> the options so you can write hyperlink.xml out to a file. The produced
> output should look like this:
>
> http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>
> The salient point of the output is the annotation attached to otu elements:
>
> <meta href="http://8ball.sdsc.edu:6666/treebase-web"
>    rel="cdao:has_External_Reference" [...other attributes are
> irrelevant for now...] />
>
> According to the RDFa rules, we can just use the "href" attribute to
> store a url, and the "rel" attribute will describe the relationship
> between the subject (the earliest enclosing element that has an
> "about" attribute) and the resource on the other end. I *think* we
> agreed that such a simple relationship could be described as
> has_External_Reference, we use it on the wiki and I've found it in the
> CDAO owl file.
>
> So what about other annotations? You can see in the produced nexml
> that mesquite is also storing internal object IDs to various
> predicates under the msq: namespace prefix (i.e. msq:taxaUID,
> msq:taxonUID and msq:treeUID). Can we have something like these as
> properties in CDAO? The TreeBASE2 team has been sketching out some
> service queries which we would like to implement, and we want the
> search fields we expose be mediated by CDAO. One of the obvious search
> fields would be something like cdao.treeUID, where perhaps the value
> would be a namespaced id string (TreeBASE:Tr3242, for example).
>
> Can we have something like that? I like Hilmar's suggestion of being
> able to put it in a queue somewhere, but I would be very interested to
> see what Brandon comes up with for term suggestion interface -
> obviously it will be better for all involved if the term suggestion
> was as specific as possible, perhaps already fitted into CDAO's class
> hierarchy (as opposed to a rambling email like this one).
>
> Rutger
>
> On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
> wrote:
>> We're listening.  Brandon has developed a term-request server to process
>> requests for concepts and relations, but its still in an early stage.  In
>> a
>> few weeks we will be in a better position to have this discussion.
>>
>> Arlin
>>
>> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>
>>> Hi,
>>>
>>> I've done enough experimentation to establish the correct syntax for
>>> attaching valid RDFa attachments to nexml so that standard RDFa
>>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>> that the examples I've mailed out give you enough of a template to do
>>> this in python too, but please let me know of I can help - I know that
>>> the wiki needs updating, for starters).
>>>
>>> The key issue now is the definition of predicates, i.e. the value of
>>> the @property and @rel attributes. Over the course of many EvoInfo
>>> discussions it's been decided that CDAO will be the principal artifact
>>> for their mediation - so what's the community process for inclusion of
>>> new predicates?
>>>
>>> Val and I have sketched out a couple of TreeBASE services whose search
>>> keys should be part of a controlled vocabulary (things like tree.id,
>>> tree.label, etc.), and this is just one use case of a project having a
>>> potentially large number of predicates (other example: Mesquite).
>>>
>>> It would be great if team CDAO could tell us where to send our list of
>>> proposed terms and where we can download an amended version of CDAO
>>> that includes them :-)
>>>
>>> I note that there is a wiki page about this
>>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>>> there would be some sort of issue tracker with structured input fields
>>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>> would be a team of curators that will promptly pick up a posted issue
>>> and work towards a solution.
>>>
>>> I realize that this involves a support commitment from team CDAO, but
>>> I think that's what we agreed to over free-form key/value pairs,
>>> homegrown vocabularies or a BioMoby-like free-for-all.
>>>
>>> Any comments?
>>>
>>> Rutger
>>>
>>> --
>>> Dr. Rutger A. Vos
>>> Department of zoology
>>> University of British Columbia
>>> http://www.nexml.org
>>> http://rutgervos.blogspot.com
>>
>>
>
>
>
> --
> Dr. Rutger A. Vos
> Department of zoology
> University of British Columbia
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] taxonomic query telecon

[Val T. <va...@ci...>]

Sorry, I was in a taxi in traffic until a few minutes ago.
I am in my office now.
Val


On Jun 5, 2009, at 2:35 PM, William Piel wrote:

>
> On Jun 4, 2009, at 4:12 PM, Mark Dominus wrote:
>
>> The phone call will be Friday, 5 June at 14:30 EDT, 11:30 PDT.
>>
>> Bill, Rutger, Val and I will attend.  If anyone else wants to be
>> involved, email Val.
>
> I have my iChat switched on -- but I don't see anyone else on-line.  
> Is this really happening? (or is it happening by land-line phone?)
>
> bp
>
>

Re: [Treebase-devel] taxonomic query telecon

[William P. <wil...@ya...>]

On Jun 4, 2009, at 4:12 PM, Mark Dominus wrote:

> The phone call will be Friday, 5 June at 14:30 EDT, 11:30 PDT.
>
> Bill, Rutger, Val and I will attend.  If anyone else wants to be
> involved, email Val.

I have my iChat switched on -- but I don't see anyone else on-line. Is  
this really happening? (or is it happening by land-line phone?)

bp

Re: [Treebase-devel] [eX-purgate bulk]: taxonomic query telecon

[Mark D. <mj...@ge...>]

On Fri, 2009-05-29 at 10:52 -0400, Rutger Vos wrote:
> > I will be in London until the 5th. Conceivably I can Skype from London, but
> > not knowing the conference schedule, I can't commit.
> 
> Obviously you're a key participant so let's just play it by ear; I
> suppose we can start the discussion by email and either call in next
> week or whenever you can make it.

Yes, let's do that.

-- 
Mark Jason Dominus                               mj...@ge...
Penn Genome Frontiers Institute                         +1 215 573 5387

Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

[Hayden, K. M. <KH...@be...>]

Hi Rutger,

I just built this and got different results for my hyperlink.xml output that I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version 1.6.0_13.

Specifically, here's the annotation attached to otu elements:

<meta content="http://8ball.sdsc.edu:6666/treebase-web" datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9" property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>


And here's the whole thing:

<?xml version="1.0" encoding="UTF-8"?>
<nex:nexml xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance" generator="org.nexml.model.impl.DocumentImpl" version="0.8" xmlns:nex="http://www.nexml.org/1.0">
  <otus xmlns:msq="http://mesquiteproject.org#" about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067" id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa" xmlns="http://www.nexml.org/1.0">
    <meta content="0121b10b3afc1" datatype="xsd:string" id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID" xsi:type="nex:LiteralMeta"/>
    <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14" id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
      <meta content="http" datatype="xsd:string" id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
      <meta content="0" datatype="xsd:integer" id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID" xsi:type="nex:LiteralMeta"/>
    </otu>
    <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
      <meta content="http://8ball.sdsc.edu:6666/treebase-web" datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436" property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
      <meta content="1" datatype="xsd:integer" id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID" xsi:type="nex:LiteralMeta"/>
    </otu>
    <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d" id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
      <meta content="http://8ball.sdsc.edu:6666/treebase-web" datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9" property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
      <meta content="2" datatype="xsd:integer" id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID" xsi:type="nex:LiteralMeta"/>
    </otu>
  </otus>
  <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated Trees" otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" xmlns="http://www.nexml.org/1.0">
    <tree xmlns:msq="http://mesquiteproject.org#" about="#a72f25756-9b46-465a-9865-24960220a821" id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by Uniform speciation (Yule)" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="nex:FloatTree">
      <meta content="1" datatype="xsd:long" id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID" xsi:type="nex:LiteralMeta"/>
      <meta content="2" datatype="xsd:integer" id="a93297efc-f077-43fd-88b1-e5a0866c0303" property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
      <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
      <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3" otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
      <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
      <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2" otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
      <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1" otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
      <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0" source="a5ae62a35-5617-46d0-a873-8e37533603e1" target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
      <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd" length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1" target="ae9e03f83-0241-489c-9006-70f606344b48"/>
      <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38" length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48" target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
      <edge id="a116f17be-c512-4680-a850-c4d467451f68" length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48" target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
    </tree>
  </trees>
</nex:nexml>


Kasia



Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...



-----Original Message-----
From: Rutger Vos [mailto:rv...@in...]
Sent: Fri 6/5/2009 3:53 AM
To: Arlin Stoltzfus
Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process
 
Hi,

Can we work along a use case? I've just committed some code to import
and export nexml (with annotations) into mesquite using the
hackathon's nexml/java API. To run it, here's what you do (ok, just
play along - you don't *have* to build this):

* svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
* cd java
* export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
* ant mesquite

Then, inside your Mesquite_Folder, either create or edit your
classpaths.xml file, which should contain an entry that points to the
bin folder that the ant task created:

<?xml version="1.0"?>
<mesquite>
            <!-- perhaps other classpath entries here -->
	<classpath>/path/to/java/bin</classpath>
</mesquite>

Now, start mesquite and open this url from within mesquite (File >
Open other... > URL...):

http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

You'll see a tree with some dummy URLs on the terminal nodes. If you
look in the nexus "source" you can see these URLs are written in the
notes block. If you now choose file > export, NeXML should be one of
the options so you can write hyperlink.xml out to a file. The produced
output should look like this:

http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml

The salient point of the output is the annotation attached to otu elements:

<meta href="http://8ball.sdsc.edu:6666/treebase-web"
   rel="cdao:has_External_Reference" [...other attributes are
irrelevant for now...] />

According to the RDFa rules, we can just use the "href" attribute to
store a url, and the "rel" attribute will describe the relationship
between the subject (the earliest enclosing element that has an
"about" attribute) and the resource on the other end. I *think* we
agreed that such a simple relationship could be described as
has_External_Reference, we use it on the wiki and I've found it in the
CDAO owl file.

So what about other annotations? You can see in the produced nexml
that mesquite is also storing internal object IDs to various
predicates under the msq: namespace prefix (i.e. msq:taxaUID,
msq:taxonUID and msq:treeUID). Can we have something like these as
properties in CDAO? The TreeBASE2 team has been sketching out some
service queries which we would like to implement, and we want the
search fields we expose be mediated by CDAO. One of the obvious search
fields would be something like cdao.treeUID, where perhaps the value
would be a namespaced id string (TreeBASE:Tr3242, for example).

Can we have something like that? I like Hilmar's suggestion of being
able to put it in a queue somewhere, but I would be very interested to
see what Brandon comes up with for term suggestion interface -
obviously it will be better for all involved if the term suggestion
was as specific as possible, perhaps already fitted into CDAO's class
hierarchy (as opposed to a rambling email like this one).

Rutger

On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...> wrote:
> We're listening.  Brandon has developed a term-request server to process
> requests for concepts and relations, but its still in an early stage.  In a
> few weeks we will be in a better position to have this discussion.
>
> Arlin
>
> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>
>> Hi,
>>
>> I've done enough experimentation to establish the correct syntax for
>> attaching valid RDFa attachments to nexml so that standard RDFa
>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>> that the examples I've mailed out give you enough of a template to do
>> this in python too, but please let me know of I can help - I know that
>> the wiki needs updating, for starters).
>>
>> The key issue now is the definition of predicates, i.e. the value of
>> the @property and @rel attributes. Over the course of many EvoInfo
>> discussions it's been decided that CDAO will be the principal artifact
>> for their mediation - so what's the community process for inclusion of
>> new predicates?
>>
>> Val and I have sketched out a couple of TreeBASE services whose search
>> keys should be part of a controlled vocabulary (things like tree.id,
>> tree.label, etc.), and this is just one use case of a project having a
>> potentially large number of predicates (other example: Mesquite).
>>
>> It would be great if team CDAO could tell us where to send our list of
>> proposed terms and where we can download an amended version of CDAO
>> that includes them :-)
>>
>> I note that there is a wiki page about this
>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>> there would be some sort of issue tracker with structured input fields
>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>> would be a team of curators that will promptly pick up a posted issue
>> and work towards a solution.
>>
>> I realize that this involves a support commitment from team CDAO, but
>> I think that's what we agreed to over free-form key/value pairs,
>> homegrown vocabularies or a BioMoby-like free-for-all.
>>
>> Any comments?
>>
>> Rutger
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Nexml-discuss mailing list
Nex...@li...
https://lists.sourceforge.net/lists/listinfo/nexml-discuss

Re: [Treebase-devel] [eX-purgate bulk]: taxonomic query telecon

[Mark D. <mj...@ge...>]

On Thu, 2009-05-28 at 19:56 -0400, William Piel wrote:
> 
> I will be in London until the 5th. Conceivably I can Skype from
> London, but not knowing the conference schedule, I can't commit. 

Okay.  We I picked the call time based on your response to Rutger's
poll.  Maybe we'll just postpone the call until next week.

> It's my understanding that we have not yet imported ncbi's
> classification into TreeBASE2? Is this correct?

Yes.


> 
-- 
Mark Jason Dominus                               mj...@ge...
Penn Genome Frontiers Institute                         +1 215 573 5387

Re: [Treebase-devel] CDAO term inclusion community process

[Rutger V. <rv...@in...>]

Hi,

Can we work along a use case? I've just committed some code to import
and export nexml (with annotations) into mesquite using the
hackathon's nexml/java API. To run it, here's what you do (ok, just
play along - you don't *have* to build this):

* svn co https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
* cd java
* export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
* ant mesquite

Then, inside your Mesquite_Folder, either create or edit your
classpaths.xml file, which should contain an entry that points to the
bin folder that the ant task created:

<?xml version="1.0"?>
<mesquite>
            <!-- perhaps other classpath entries here -->
	<classpath>/path/to/java/bin</classpath>
</mesquite>

Now, start mesquite and open this url from within mesquite (File >
Open other... > URL...):

http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

You'll see a tree with some dummy URLs on the terminal nodes. If you
look in the nexus "source" you can see these URLs are written in the
notes block. If you now choose file > export, NeXML should be one of
the options so you can write hyperlink.xml out to a file. The produced
output should look like this:

http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml

The salient point of the output is the annotation attached to otu elements:

<meta href="http://8ball.sdsc.edu:6666/treebase-web"
   rel="cdao:has_External_Reference" [...other attributes are
irrelevant for now...] />

According to the RDFa rules, we can just use the "href" attribute to
store a url, and the "rel" attribute will describe the relationship
between the subject (the earliest enclosing element that has an
"about" attribute) and the resource on the other end. I *think* we
agreed that such a simple relationship could be described as
has_External_Reference, we use it on the wiki and I've found it in the
CDAO owl file.

So what about other annotations? You can see in the produced nexml
that mesquite is also storing internal object IDs to various
predicates under the msq: namespace prefix (i.e. msq:taxaUID,
msq:taxonUID and msq:treeUID). Can we have something like these as
properties in CDAO? The TreeBASE2 team has been sketching out some
service queries which we would like to implement, and we want the
search fields we expose be mediated by CDAO. One of the obvious search
fields would be something like cdao.treeUID, where perhaps the value
would be a namespaced id string (TreeBASE:Tr3242, for example).

Can we have something like that? I like Hilmar's suggestion of being
able to put it in a queue somewhere, but I would be very interested to
see what Brandon comes up with for term suggestion interface -
obviously it will be better for all involved if the term suggestion
was as specific as possible, perhaps already fitted into CDAO's class
hierarchy (as opposed to a rambling email like this one).

Rutger

On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...> wrote:
> We're listening.  Brandon has developed a term-request server to process
> requests for concepts and relations, but its still in an early stage.  In a
> few weeks we will be in a better position to have this discussion.
>
> Arlin
>
> On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>
>> Hi,
>>
>> I've done enough experimentation to establish the correct syntax for
>> attaching valid RDFa attachments to nexml so that standard RDFa
>> extractors can turn <meta/> elements - the new dictionaries - into RDF
>> triples. I've implemented this in the java and perl APIs (Jeet: I hope
>> that the examples I've mailed out give you enough of a template to do
>> this in python too, but please let me know of I can help - I know that
>> the wiki needs updating, for starters).
>>
>> The key issue now is the definition of predicates, i.e. the value of
>> the @property and @rel attributes. Over the course of many EvoInfo
>> discussions it's been decided that CDAO will be the principal artifact
>> for their mediation - so what's the community process for inclusion of
>> new predicates?
>>
>> Val and I have sketched out a couple of TreeBASE services whose search
>> keys should be part of a controlled vocabulary (things like tree.id,
>> tree.label, etc.), and this is just one use case of a project having a
>> potentially large number of predicates (other example: Mesquite).
>>
>> It would be great if team CDAO could tell us where to send our list of
>> proposed terms and where we can download an amended version of CDAO
>> that includes them :-)
>>
>> I note that there is a wiki page about this
>> (https://www.nescent.org/wg_evoinfo/CDAO_term_request), but ideally
>> there would be some sort of issue tracker with structured input fields
>> (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>> suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>> would be a team of curators that will promptly pick up a posted issue
>> and work towards a solution.
>>
>> I realize that this involves a support commitment from team CDAO, but
>> I think that's what we agreed to over free-form key/value pairs,
>> homegrown vocabularies or a BioMoby-like free-for-all.
>>
>> Any comments?
>>
>> Rutger
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com