[seek-taxon] TCS help: Placeholder question
Richard Pyle
deepreef at bishopmuseum.org
Wed Nov 30 10:03:53 PST 2005
Hi All,
Sorry for the intrusion, but I just thought I'd comment quickly on EndNote.
I modelled Taxonomer after EndNote v7. I selected it in (large) part
because a lot of folks here at the Museum use it for their reference data
management, and I wanted to make the import/export process as painless as
possible. Unfortunately, the EndNote solution is somewhat of a moving
target (v8 already had some substantial changes from v7, and I think they're
up to v10 now). Most of our users haven't upgraded EndNote versions yet,
but I'm sure they will at some point. I think the current model is "mostly"
backwards compatible with earlier versions, but the general trend is to add
more dedicated fields, and more finely split reference types. Also, I'm not
sure about the latest versions, but v7 did incorporate some (not always
intuitive) overlap of fields across different types, which is why I found a
need to create a matrix table to track which field is used for what purpose
in what reference type.
Sometime in the next few months, I'm going to completely re-design the
Taxonomer Publication/Reference structure -- moving to something that is
more hierarchical [Series, with child Volumes, with child Sections
(=articles), with child Subsections (="microreference")], and with fewer
dedicated fields (e.g., a generic "CodeNumber" approach to the various ISBN,
ISSN, Call Numbers, etc.). I will try to maintain general compatibility
with EndNote, but will no longer use it as the foundation of the data
structure.
So...my suggestion for SEEK would be to adopt something a little more stable
than EndNote/Taxonomer (like EML) -- at least until TDWG develops a standard
(I believe Anna Weitzman is spearheading that effort).
Aloha,
Rich
Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
and Associate Zoologist in Ichthyology
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html
> -----Original Message-----
> From: seek-taxon-bounces at ecoinformatics.org
> [mailto:seek-taxon-bounces at ecoinformatics.org]On Behalf Of Kennedy,
> Jessie
> Sent: Wednesday, November 30, 2005 5:16 AM
> To: rgales at ku.edu; Robert K. Peet
> Cc: seek-taxon at ecoinformatics.org
> Subject: Re: [seek-taxon] TCS help: Placeholder question
>
>
> 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*
> > >>>>>> Single? There's someone we'd like you to meet.
> > >>>>>> Lot's of someone's, actually. Yahoo! Personals
> > >>>>>> <http://us.rd.yahoo.com/evt=36108/*http://personals.yahoo.com >
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>
> ----------------------------------------------------------------------
> > -
> > >>>
> > >>>> -
> > >>>>
> > >>>>>> _______________________________________________
> > >>>>>> 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
> > >>> This message is intended for the addressee(s) only and should not
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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/
> > >
> ====================================================================
>
> This message is intended for the addressee(s) only and should not
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> University without the permission of the sender.
> It is your responsibility to ensure that this message and any
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> University does not accept liability for any loss
> or damage which may result from this email or any attachment, or
> for errors or omissions arising after it was sent. Email is not a
> secure medium. Email entering the
> University's system is subject to routine monitoring and
> filtering by the University.
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