[seek-taxon] TCS help: Placeholder question
Matt Jones
jones at nceas.ucsb.edu
Wed Nov 30 09:18:38 PST 2005
Just an aside -- the EML citation module is also based on EndNote and
pretty much models the fields that can be stored in EndNote. We did a
little field renaming for readability or clarity.
Matt
Kennedy, Jessie wrote:
> Hi Guys
>
> I agree with both of you. I'm not clear either about how TDWG are going
> to deal with modularisation of schemas - and hope they look at it soon -
> but have fears about this - I'll email them and see what they say they
> are doing as it's important - and will let you know.
> I checked with Robert here about where our Publication structure came
> from before we started using placeholders and it is based on EndNote as
> modelled in Rich Pyle's Taxonomer DB. Basically an XML representation of
> what Rich had. Not what is in EML.
>
> As it's not part of the TCS standard as such I don't mind which XML
> structure we use to represent publications and as Robert says TOS will
> store it - but I guess at some point Bob or other users will like to be
> able to do useful things with it - even if it's just displaying them
> nicely.
>
> I guess at some point we'll need to decide on that....
>
> Speak soon,
>
> Jessie
>
>
>>-----Original Message-----
>>From: Robert Gales [mailto:rgales at ku.edu]
>>Sent: 30 November 2005 14:56
>>To: Robert K. Peet
>>Cc: Kennedy, Jessie; seek-taxon at ecoinformatics.org; Robert Liu
>>Subject: Re: [seek-taxon] TCS help: Placeholder question
>>
>>Hi Bob,
>>
>>Thanks for the response, I was just making sure that we are on the
>
> same
>
>>page for the current round of implementation of the TOS.
>>
>>Currently we are doing pretty much what you suggest, storing the
>
> entire
>
>>XML fragment in the database so it can be displayed to users or
>>applications that pull data from TOS and understand what the structure
>>and semantics of the data contained within the Placeholder can do
>>something meaningful with it.
>>
>>It definitely would be an interesting topic of discussion for a
>>conference call and falls into the broader discussion of GUIDs and
>>schema modularization by TDWG. Its not clear, at least to me, what
>
> the
>
>>current plan from TDWG is for handling schema modularization (xsd:any,
>>substitution groups have been proposed, exploring semantic modeling
>
> with
>
>>RDF/OWL, etc.). At the least something like a "best practices"
>
> document
>
>>for the schemas would be useful as the community moves towards
>>modularization.
>>
>>- Rob
>>
>>Robert K. Peet wrote:
>>
>>>Hi Robert,
>>>
>>>I would like to hear Jessie's view on this. We should avoid getting
>>>sidetracked by these relatively unimportant yet big topics.
>>>
>>>I don't imagine that specimens matter for TOS as we currently
>
> imagine
>
>>it.
>>
>>>Publications obviously do matter, so we should discuss this in our
>
> next
>
>>>phone call if not before.
>>>
>>>Perhaps TOC can simply cashe EML publication records in the
>>>PublicationDetailed field and thereby avoid the issue for present.
>
> I do
>
>>>imagine that software that interfaces with TOS will need to display
>>>publication details of the complexity supported by EML.
>>>
>>>Would this sort of solution work?
>>>
>>>Bob
>>>
>>>
>>>
>>>On Tue, 29 Nov 2005, Robert Gales wrote:
>>>
>>>
>>>>Good Morning Jessie, Bob,
>>>>
>>>>Actually we are using the standard 1.01 version of the schema in
>
> this
>
>>>>latest version, so the PublicationDetailed is a Placeholder in the
>>>>current work.
>>>>
>>>>Out of curiousity, what is the intention of the additional data,
>
> other
>
>>>>than just more detailed information? Is TOS expected to handle and
>
> do
>
>>>>something meaningful with this extra data?
>>>>
>>>>- Rob
>>>>
>>>>Kennedy, Jessie wrote:
>>>>
>>>>
>>>>>Hi Bob
>>>>>
>>>>>I think Robert has an older version of the schema which uses an
>
> EML
>
>>like
>>
>>>>>publication - I'm happy if you use either that or directly the one
>>
>>from
>>
>>>>>EML - I think we based it on EML anyway.
>>>>>
>>>>>For specimens feel free to use ABCD but it's very big - not sure
>
> how
>
>>>>>much of it you'll need. I think it would be safe to use a valid
>
> subset
>
>>>>>of it if necessary. This is something I hope will get sorted out
>
> via
>
>>>>>TDWG when we look at modularising the schemas.
>>>>>
>>>>>Jessie
>>>>>
>>>>>
>>>>>
>>>>>>-----Original Message-----
>>>>>>From: seek-taxon-bounces at ecoinformatics.org [mailto:seek-taxon-
>>>>>>bounces at ecoinformatics.org] On Behalf Of Robert K. Peet
>>>>>>Sent: 28 November 2005 20:19
>>>>>>To: Robert Gales
>>>>>>Cc: seek-taxon at ecoinformatics.org; Robert Liu
>>>>>>Subject: Re: [seek-taxon] TCS help: Placeholder question
>>>>>>
>>>>>>
>>>>>>Robert,
>>>>>>
>>>>>>What do you recommend that we use for specimen and and for
>
> reference?
>
>>>>>
>>>>>I
>>>>>
>>>>>
>>>>>>am inclined to think that we should default to abcd for
>
> specimens,
>
>>and
>>
>>>>>
>>>>>to
>>>>>
>>>>>
>>>>>>EML for references.
>>>>>>
>>>>>>Bob
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Mon, 28 Nov 2005, Robert Gales wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Hi Xianhua,
>>>>>>>
>>>>>>>The Placeholder class is xsd:any/xsd:anyAttribute with ##any
>>>>>
>>>>>
>>>>>namespace.
>>>>>
>>>>>
>>>>>>This
>>>>>>
>>>>>>
>>>>>>>means that you can plug in elements from any namespace or even
>
> no
>
>>>>>>
>>>>>>namespace.
>>>>>>
>>>>>>
>>>>>>>For example with SpecimenItem:
>>>>>>>
>>>>>>><SpecimenItem identifier="cn55">
>>>>>>><DataSets xmlns="http://www.tdwg.org/schemas/abcd/2.06">
>>>>>>> ...
>>>>>>> <Unit>
>>>>>>> <UnitId>cn55</abcd:UnitID>
>>>>>>> ...
>>>>>>> </Unit>
>>>>>>></DataSets>
>>>>>>></SpecimenItem>
>>>>>>>
>>>>>>>or...
>>>>>>>
>>>>>>><SpecimenItem identifier="cn55">
>>>>>>><CatalogNumber>55</CatalogNumber>
>>>>>>><Locality>5 mi west of Lawrence</Locality>
>>>>>>><State>Kansas</State>
>>>>>>><County>Douglas</County>
>>>>>>><Country>United States</Country>
>>>>>>></SpecimenItem>
>>>>>>>
>>>>>>>- Rob
>>>>>>>
>>>>>>>Robert Liu wrote:
>>>>>>>
>>>>>>>
>>>>>>>>Jessie & Robert:
>>>>>>>>I am trying to convert data into TCS 1.01 and am not sure how
>
> to
>
>>>>>>
>>>>>>handle
>>>>>>
>>>>>>
>>>>>>>>the Class Placeholder. Several elements in TCS are defined as
>
> class
>
>>>>>>>>Placeholder, such as CharacterCircumscription,
>
> Specimen-Collection.
>
>>>>>
>>>>>I
>>>>>
>>>>>
>>>>>>>>wonder how to extend Placeholder to incorperate detail
>
> information
>
>>>>>
>>>>>for
>>>>>
>>>>>
>>>>>>each
>>>>>>
>>>>>>
>>>>>>>>specific element. Thanks.
>>>>>>>>Xianhua
>>>>>>>>
>>>>>>>>
>>>>>
>>>>>
> ----------------------------------------------------------------------
>
>>-
>>
>>>>>>-
>>>>>>
>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>>
> ----------------------------------------------------------------------
>
>>-
>>
>>>>>>-
>>>>>>
>>>>>>
>>>>>>>>_______________________________________________
>>>>>>>>Seek-taxon mailing list
>>>>>>>>Seek-taxon at ecoinformatics.org
>>>>>>>>
>
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-
>
>>>>>>
>>>>>>taxon
>>>>>>
>>>>>>
> ====================================================================
>
>>>>>> Robert K. Peet, Professor Phone: 919-962-6942
>>>>>> Department of Biology, CB#3280 Fax: 919-962-6930
>>>>>> University of North Carolina Cell: 919-368-4971
>>>>>> Chapel Hill, NC 27599-3280 USA Email: peet at unc.edu
>>>>>>
>>>>>> http://www.bio.unc.edu/faculty/peet/
>>>>>>
>
> ====================================================================
>
>>>>>>_______________________________________________
>>>>>>Seek-taxon mailing list
>>>>>>Seek-taxon at ecoinformatics.org
>>>>>>
>>>>>
>>>>>
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-
>
>>taxon
>>
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>>>>
>>>>
>>>>
>>>
> ====================================================================
>
>>> Robert K. Peet, Professor Phone: 919-962-6942
>>> Department of Biology, CB#3280 Fax: 919-962-6930
>>> University of North Carolina Cell: 919-368-4971
>>> Chapel Hill, NC 27599-3280 USA Email: peet at unc.edu
>>>
>>> http://www.bio.unc.edu/faculty/peet/
>>>
>
> ====================================================================
>
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--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matt Jones Ph: 907-789-0496
jones at nceas.ucsb.edu SIP #: 1-747-626-7082
National Center for Ecological Analysis and Synthesis (NCEAS)
UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics
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