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

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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
>>
>>
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>>
>>
>
>
>
> --
> 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