[seek-taxon] TCS help: Placeholder question
Kennedy, Jessie
J.Kennedy at napier.ac.uk
Wed Nov 30 07:16:04 PST 2005
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
> >>>>>>
> >>>>>>
> >>>
> >>>
----------------------------------------------------------------------
> -
> >>>
> >>>> -
> >>>>
> >>>>>> *Yahoo! Personals*
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> >>>>>> Lot's of someone's, actually. Yahoo! Personals
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> >>>>>>
> >>>>>>
> >>>>>>
> >>>
----------------------------------------------------------------------
> -
> >>>
> >>>> -
> >>>>
> >>>>>> _______________________________________________
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> >>>>>>
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/
> >>>>
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> >>>>
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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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