[seek-taxon] TCS help: Placeholder question (tentative version for ConceptMapper)
Robert Liu
robertliu325 at yahoo.com
Mon Dec 5 06:49:20 PST 2005
Michael & Bob:
Thank you for your comments. I have added a field to the reference table to hold the whole reference. I think it is good for user to have an option to enter a reference as a whole string instead of parsing it out into separate components.
Xianhua
Michael Lee <mikelee at email.unc.edu> wrote:
Xianhua,
The key difference VegBank made was in adding a somewhat redundant field
called fullText.
http://vegbank.org/vegdocs/dbdictionary/dd~table~reference~field~fulltext~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%7Etableview.html
> http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencecontributor%7Etype%7Etableview.html
> http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferenceparty%7Etype%7Etableview.html
> http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencejournal%7Etype%7Etableview.html
> http://vegbank.org/vegdocs/dbdictionary/dd%7Etable%7Ereferencealtident%7Etype%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 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*
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>> ----------------------------------------------------------------------
>>>
>>>> -
>>>>
>>>>>>>> -
>>>>>>>>
>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>>> 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/
>>>>>>>>
>>>
>>> ====================================================================
>>>
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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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>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>> jones at nceas.ucsb.edu SIP #: 1-747-626-7082
>> National Center for Ecological Analysis and Synthesis (NCEAS)
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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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