[SEEK-Taxon] LinneanCore Wiki

franz@nceas.ucsb.edu franz at nceas.ucsb.edu
Thu Nov 4 14:22:46 PST 2004 

Hi Rich et al.:

   I will jump in just to present *my* perspective on the name/concept/nominal
concept issue. I think within SEEK Taxon we are in substantive agreement about this.

   As I understand, part of the motivation to with strictly nomenclatural issues
as if they were something unique has to do with the notion that, when changing a
name due only to abidence with Code rules, there is no altering/creating of a
definition (circumscription, diagnosis) implied. No implied definition
creation/change - no concept. We cannot follow that reasoning simply because the
new names nevertheless are published by someone, at a certain time, in a certain
publication, and the use and reuse of that name/publication will have a fate
different from that of the publication containing (e.g.) the new synonym.

   In short, instances of rule abidance are properly modelled in the TCS JUST AS
IF they were concepts with deeper definitions. The trade-off is taxonomic
meaning vs. fair data management, and the latter wins. No fair data management
and the origin of data becomes intractable. This is worse than attaching a
"sec." to a nomenclatural emendation. It is that simple.

   Furthermore, because many units the TCS must handle and redestribute ONLY
have a name provided by the source from which they come, we have something lie
"nominal concepts." Meaning, there is in essence just the name we are
transporting electronically, followed by the "sec." provider. Again, even
lacking a deeper definition, these name instances will have their own
idiosyncratic fates and they are enriched, reused, redistributed, etc. To
capture those origis and fates, they receive a "sec." Fair and sustainable
information management outtrumps taxonomic transparency and meaning - again.

   Because TCS/SEEK is such a dynamic, information-importing and -expoiting
environment, it is a major challenge for us to keep thing with different origins
separate and internally consistent. That is why nomenclatural emendations and
"just names" are treated just like concepts. There is no room for name instances
lacking any association with a provider authority.

Cheers,

Nico



Quoting Richard Pyle <deepreef at bishopmuseum.org>:

> 
> Hi Jessie,
> 
> Thanks -- you are right, LC does go beyond the ABCD field set in trying to
> identify discrete name objects, with internal nomenclatural linkages (*NOT*
> implied conceptual relationships).  My *strong* hope is that LC objects
> will
> be, by definition, TCS "Nominal"-type objects, and will only exist in the
> context of a TCS Nominal-type wrapper (not as objects that exist outside of
> TCS).  When you have the time, please try to contribute to that section of
> the Wiki discussion.
> 
> One thing that would be a great help would be if you or Robert or someone
> else could send us a few (2 or 3) instance-cases of TCS "Nominal"-type
> records, using the ABCD element set.  That way we can have some concrete
> examples of TCS instances to test our ideas about wrapping LC instances
> within TCS instances.  We are also working on some test-case examples that
> we can send back to you folks.
> 
> Does there exist somewhere on the web, or can someone send me, a detailed
> explanation of the "Nominal" type (aka "Nomenclatural" type) of TCS
> instance?
> 
> Thanks, and I hope the SEEK meeting is going well (despite the atmosphere
> of
> global mourning).
> 
> Aloha,
> Rich
> 
> -----Original Message-----
> From: Kennedy, Jessie [mailto:J.Kennedy at napier.ac.uk]
> Sent: Thursday, November 04, 2004 10:45 AM
> To: Richard Pyle
> Cc: seek-taxon at ecoinformatics.org
> Subject: RE: [SEEK-Taxon] LinneanCore Wiki
> 
> 
> Hi Rich
> 
> I was on holiday in NZ since TDWG and am now in a seek meeting this week -
> I'm back at work next week and will have a good look at the LC wiki site
> then and make comment.
> >From the Sunday meeting at TDWG I guess I'm concerned that LC turns into
> more than a set of fields as was in ABCD i.e. objects with relationships
> between them - as I explained I think you can do that with TCS - but will
> think carefully on what has been said/proposed before responding further.
> 
> later,
> 
> Jessie
> 
> 
> 
> From: seek-taxon-admin at ecoinformatics.org on behalf of Richard Pyle
> Sent: Thu 04/11/2004 20:29
> To: Dave Vieglais
> Cc: seek-taxon at ecoinformatics.org
> Subject: RE: [SEEK-Taxon] LinneanCore Wiki
> 
> 
> 
> 
> Ah!  O.K. -- then I think the concerns can be dispelled.  In fact, one of
> the central themes in the discussions so far has been to ensure that
> elelments that are a matter for TCS are *NOT* built into LC.  I'm not
> entirely sure what context you're using the term "business rules", but we
> are certainly discussing the rules which apply to the creation and
> objective
> synonymy of Code-regulated names (ICBN, ICZN, etc.) -- which I think of as
> sort of "business rules" -- but it is very clear to all the LC folk that LC
> does *NOT* deal with concepts at all, or rules related to mapping of
> concepts to other concepts, etc.  Only stuff like basionyms, nomenclatural
> authorships, etc., that relate to producing a string of characters to be
> used as a textual label, that TCS could then attach to concept instances.
> 
> I hope that adequately alleviates concerns (if not, let me know so I can
> help guide/restrict/re-shape LC accordingly).  Of course, anyone/everyone
> is
> welcome to monitor/participate in the LC Wiki discussion (URL below).
> 
> I suspect that after LC matures a little bit, we will need to come back to
> this group and discuss how LC will fit (seamlessly) into TCS.  I think the
> only TCS elements that would be affected are "NameSimple" and the contents
> of "NameDetailed".  I also hope that Jessie and Robert will monitor the LC
> Wiki, to make sure we do not stray and/or overlap/conflict with TCS (I'm
> already doing my best to avoid that, but would still appreciate their
> guidance & oversight).
> 
> Aloha,
> Rich
> 
> > -----Original Message-----
> > From: Dave Vieglais [mailto:vieglais at ku.edu]
> > Sent: Thursday, November 04, 2004 5:18 AM
> > To: Richard Pyle
> > Cc: seek-taxon at ecoinformatics.org
> > Subject: Re: [SEEK-Taxon] LinneanCore Wiki
> >
> >
> > Hi Rich,
> > thanks for the detailed explanation.
> >
> > Developing a more extensive "data type" for holding nomenclatural data
> > makes a lot of sense.  There was a bit of concern that the development
> > of the Linnean Core was going beyond that and including business rules
> > for taxonomy, and so starting to overlap, and possibly conflict /
> > duplicate / confuse with the role of the TCS.
> >
> > cheers,
> >    Dave V.
> >
> > Richard Pyle wrote:
> > > Hi Dave,
> > >
> > > In a nutshell, the LinneanCore group is working on a more
> > robust version of
> > > what now falls within the "NameDetailed" part of the TCS schema.  At
> the
> > > moment, TCS just "borrows" the ABCD nomenclatural elements for this;
> but
> > > several of us at Christchurch felt that Jerry Cooper's draft
> > "LinnaeanCore"
> > > (later amended to "LinneanCore") schema was a better approach
> > to managing
> > > purely nomenclatural information (I could list specific reasons
> > why we felt
> > > that the LC approach was preferable to the ABCD approach, if you're
> > > interested).  Bear in mind that the LC group is *only*
> > interested in Names
> > > data -- NOT concept data.  Virtually all of the LC discussion
> > members have
> > > agreed that all concept-related information should be excluded
> > from LC, and
> > > left to TCS.  Many (but not all....yet) of us feel strongly
> > that LC should
> > > not exist as stand-alone schema, but rather exist only in the
> > context of a
> > > TCS "wrapper".  In the case of TCS instances that are of "Nominal" (aka
> > > "Nomenclatural") type, the LC elements would constitute the
> > bulk of content.
> > > As far as I can tell, whatever comes of LC, it will not impact
> > any of the
> > > TCS elements outside of "NameDetailed" (except, perhaps, for
> > some comments
> > > about "NameSimple". Of course, if any of our discussions lead
> > to conclusions
> > > relevant to parts of TCS outside of "NameDetailed", we'll certainly
> make
> > > sure those comments get back to the SEEK taxon group).
> > >
> > > So...here are some bulleted points:
> > >    * LC is intended to replace the elements included within the TCS
> > > "NameDetailed" section (currently borrowed from ABCD)
> > >
> > >    * LC focuses mostly on issues related to Codes of
> > Nomenclature, and does
> > > not deal with concept information
> > >
> > >    * Most of the points of discussion on LC are topics that have not
> yet
> > > been adequately addressed (if at all) by the TCS group
> > >
> > >    * If those of us who feel that LC should only exist within a
> > TCS wrapper
> > > prevail in the LC discussions, LC could go a long way to
> > providing a pathway
> > > for nomenclators and name-only data holders to embrace TCS as a means
> of
> > > names-only data exchange (via TCS "Nominal"-type records).
> > >
> > > If you'd like more bulleted points, or more elaboration on any
> > of the points
> > > above, please let me know.  The bottom line is that I see LC as purely
> > > complementary to TCS; not a duplication of effort. Note that Jessie and
> > > Robert were both part of the main LC discussion in
> > Christchurch, and from my
> > > discussions with Jessie, I get the impression that she also
> > feels that what
> > > we are doing will support TCS ('though I may have misunderstood her --
> > > Jessie?)
> > >
> > > Aloha,
> > > Rich
> > >
> > > P.S. I know it's looking bleak, but don't write off Ohio just yet....
> > >
> > > Richard L. Pyle, PhD
> > > Natural Sciences Database Coordinator, Bishop Museum
> > > 1525 Bernice St., Honolulu, HI 96817
> > > Ph: (808)848-4115, Fax: (808)847-8252
> > > email: deepreef at bishopmuseum.org
> > > http://www.bishopmuseum.org/bishop/HBS/pylerichard.html
> > >
> > >
> > >>-----Original Message-----
> > >>From: Dave Vieglais [mailto:vieglais at ku.edu]
> > >>Sent: Tuesday, November 02, 2004 12:54 PM
> > >>To: Richard Pyle
> > >>Cc: Seek-Taxon
> > >>Subject: Re: [SEEK-Taxon] LinneanCore Wiki
> > >>
> > >>
> > >>Hi Rich,
> > >>I must ask - What's the point?  The discussion of the so called Linnean
> > >>Core seems to be a duplicate of the last couple of years of community
> > >>effort that have gone into the development of the TCS.  Could you help
> > >>me out a bit by providing a few bullet points to show why this
> > >>development is necessary and not already covered by the TCS?
> > >>
> > >>Thanks,
> > >>   Dave V.
> > >>
> > >>
> > >>
> > >>Richard Pyle wrote:
> > >>
> > >>>Hi All,
> > >>>
> > >>>I thought I'd forward to you the URL to the "LinneanCore" Wiki
> > >>
> > >>site.  For
> > >>
> > >>>those who weren't at TDWG in Christchurch, this came together
> > >>
> > >>around a group
> > >>
> > >>>of "name nerds" to hammer out an schema for taxonomic names.
> > >>
> > >>The intention
> > >>
> > >>>would be to have this schema drop directly into TCS "Names" section,
> > >>>replacing what is currently taken directly from ABCD.
> > >>>
> > >>>Some preliminary info is on the Wiki now, and I expect discussion to
> > >>>increase over the next few weeks:
> > >>>
> > >>>http://efgblade.cs.umb.edu/twiki/bin/view/UBIF/LinneanCore
> > >>>
> > >>>Aloha,
> > >>>Rich
> > >>>
> > >>>Richard L. Pyle, PhD
> > >>>Natural Sciences Database Coordinator, Bishop Museum
> > >>>1525 Bernice St., Honolulu, HI 96817
> > >>>Ph: (808)848-4115, Fax: (808)847-8252
> > >>>email: deepreef at bishopmuseum.org
> > >>>http://www.bishopmuseum.org/bishop/HBS/pylerichard.html
> > >>>
> > >>>
> > >>>_______________________________________________
> > >>>seek-taxon mailing list
> > >>>seek-taxon at ecoinformatics.org
> > >>>http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> > >>>
> > >
> > >
> > >
> > >
> 
> 
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