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

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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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