[seek-taxon] TCS help: Placeholder question (tentative version for ConceptMapper)
Kennedy, Jessie
J.Kennedy at napier.ac.uk
Tue Dec 6 03:24:56 PST 2005
Hi Guys
In case I'm missing something. If you're using TCS there is a
publication simple element that is used for holding the full text for
the reference it can be used with or without the publication detailed.
So you might be duplicating this. We had been talking about the
publication detailed element of TCS in earlier discussion.
Jessie
> -----Original Message-----
> From: Michael Lee [mailto:mikelee at email.unc.edu]
> Sent: 04 December 2005 00:30
> To: Robert K. Peet
> Cc: Robert Liu; Kennedy, Jessie; seek-taxon at ecoinformatics.org
> Subject: Re: [seek-taxon] TCS help: Placeholder question (tentative
> version for ConceptMapper)
>
> Xianhua,
>
> The key difference VegBank made was in adding a somewhat redundant
field
> called fullText.
>
>
http://vegbank.org/vegdocs/dbdictionary/dd~table~reference~field~fulltex
t~
> type~tableview.html
>
> This was to allow capturing of the full reference text, which EML did
not
> explicitly allow (putting it together from the various fields should
work,
> though). We exchange data with others who store data in this
aggregated
> format, and this field seemed necessary to avoid requiring a person to
> parse each reference into the component fields.
>
> So we prefer that our references be parsed, but allow for them to
arrive
> unparsed if that's all we can get. This gets into the murky waters of
> ideal data and storage format versus trying to store what really is
and
> has been collected. Some standards should include only the former,
> like guidelines for collecting new data, while others may strive to
> include both.
>
> cheers,
> michael
> ----------------------------
> Michael Lee
> VegBank Project Manager
> http://www.vegbank.org
> mikelee at unc.edu
> ----------------------------
>
> On Sat, 3 Dec 2005, Robert K. Peet wrote:
>
> >
> > Hey Xianhua,
> >
> > For VegBank we adopted a slight improvement on EML:
> >
> >
>
http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereference%7Etype%7E
ta
> bleview.html
> >
>
http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencecontributo
r%
> 7Etype%7Etableview.html
> >
>
http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferenceparty%7Ety
pe
> %7Etableview.html
> >
>
http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencejournal%7E
ty
> pe%7Etableview.html
> >
>
http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencealtident%7
Et
> ype%7Etableview.html
> >
> > Bob
> >
> >
> >
> > On Thu, 1 Dec 2005, Robert Liu wrote:
> >
> >> Although the citation components of both EML and TCS (v0953) are
> >> conceptually based on EndNote, they are quite different in
structure
> and
> >> contents. EML categorizes citations into several types, such as
> Article,
> >> Book, Book Chapter, AudioVisual, Presentation, Map and so on. While
TCS
> >> (v0953) has only one class - PublicationDetailedType as an
all-purpose
> >> container for different types of literatures. I guess this
difference
> is
> >> due to the different application purpose of EML and TCS. As a
generic
> >> schema for ecological meta data, EML should be designed to handle
any
> >> possible kind of literatures used in ecological world. TCS was
designed
> to
> >> handle taxonomic concepts which have a relatively smaller set of
> literature
> >> types that can be confidently used as taxon concept reference, such
as
> >> monographs, books and journal articles.
> >>
> >> For reference component in ConceptMapper, I'd like to follow the
idea
> of
> >> EML in the design of user interface and follow the idea of TCS in
the
> >> design of backend database. Users will appreciate a cleaned
interface
> with
> >> only required elements for each specific type of literatures. While
as
> a
> >> developer, it will be time-saving and energy-efficient to deal with
a
> >> single table.
> >>
> >> Based on EML 2.0.1 and TCS v0953, I generated a schema for
> ConceptMapper
> >> with 3 types of literatures which I think are the most often used
ones.
> >>
> >>
> >> 1. Categorized for user interface:
> >>
> >> [journal article]
> >> Author
> >> Year
> >> Title
> >> Journal title
> >> Volume
> >> Issue
> >> Publisher
> >> PlacePublished
> >> DatePublished
> >> Pages
> >> ISBN_ISSN
> >> URL
> >>
> >> [book chapter]
> >> Author
> >> Year
> >> Title
> >> Book title
> >> Editor
> >> Edition
> >> Volume
> >> NumberOfVolumes
> >> TotalPages
> >> Publisher
> >> PlacePublished
> >> DatePublished
> >> Pages
> >> ISBN_ISSN
> >> URL
> >>
> >> [book]
> >> Author
> >> Year
> >> Title
> >> Edition
> >> Volume
> >> NumberOfVolumes
> >> TotalPages
> >> Publisher
> >> PlacePublished
> >> DatePublished
> >> ISBN_ISSN
> >> URL
> >>
> >> 2. Mixed for database
> >> PubType: publication type, could be journal article, book chapter
or
> book
> >> Author
> >> Year
> >> Title
> >> InTitle: Journal title/Book title
> >> Editor
> >> Edition
> >> Volume
> >> NumberOfVolumes
> >> Issue
> >> TotalPages
> >> Publisher
> >> PlacePublished
> >> DatePublished
> >> Pages
> >> ISBN_ISSN
> >> URL
> >>
> >> It is just a tentative try. Your comments will be highly
appreciated.
> >>
> >> Xianhua
> >>
> >> Matt Jones <jones at nceas.ucsb.edu> wrote: 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:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ...
> >>>>>>>>>
> >>>>>>>>> cn55
> >>>>>>>>> ...
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> or...
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> 55
> >>>>>>>>> 5 mi west of Lawrence
> >>>>>>>>> Kansas
> >>>>>>>>> Douglas
> >>>>>>>>> United States
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> - 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
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>
----------------------------------------------------------------------
> >>>
> >>>> -
> >>>>
> >>>>>>>> -
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> 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
> >>>
> >>> be
> >>>
> >>>>>>> read, copied or disclosed to anyone else outwith the
University
> >>>>>>> without the permission of the sender.
> >>>>>>> It is your responsibility to ensure that this message and any
> >>>>>>> attachments are scanned for viruses or other defects. Napier
> >>>>>>> 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.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>
====================================================================
> >>>
> >>>>> 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
be
> read,
> >>> copied or disclosed to anyone else outwith the University without
the
> >>> permission of the sender.
> >>> It is your responsibility to ensure that this message and any
> attachments
> >>> are scanned for viruses or other defects. Napier 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.
> >>> _______________________________________________
> >>> Seek-taxon mailing list
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> >>>
http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-
> taxon
> >>
> >> --
> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >> 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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> >> 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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