September 2003 - tdwg-content

Re: Name for the standard
by P. Bryan Heidorn 16 Sep '03

16 Sep '03

I think in theory the SDD spec could be used to describe anything that can be broken into characteristics and states. That can certainly go beyond biology as DELTA did in some cases. I believe that, "Structure of Descriptive Data" handles that idea. It can be a description of anything. The description may itself be grounded in instance data from the world (specimens) that have been abstracted or summarized. The taxonomy component is needed to specify what it is that is being described. In the realm of biology it would seem to be worth some effort to be domain specific in this part to make sure we can capture this reference to a "taxonomic concept." >===== Original Message From TDWG - Structure of Descriptive Data <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> ===== >>In the note below and in previous notes, there seems to be an emphasis >>on SDD in the contect of "taxonomy"; but wouldn't it be more appropriate to >>place the emphasis more in the context of biological objects (e.g., >>specimens), rather than abstract concepts (taxa)? > >you are right, in part. Although the SDD activity is undertaken by >taxonomists, it extends beyond the core of taxonomy and nomenclature to >delineation and description of the objects themselves (taxa mostly, to a >lesser extent specimens). In fact, existing programs in this area such as >DELTA and LUCID handle nomenclature and taxonomy data extremely poorly... > >>Even though the >>descriptive data may be applied directly to taxon concepts without an >>explicit reference to specific specimens/objects, ultimately the characters >>themselves that are being described are attached to a physical organism -- >>whether or not the specific physical organism is explicitly identified, or >>merely implied. > >we we may be getting into the philosophical realm here... Our Rainforest >Key project actually scored recorded individual specimens for each >taxon... most DELTA and LUCID implementations amalgamate and abstract this >to the level of taxon or taxon concept and score at this level... > >of course, SDD should ideally handle both approaches... > >>Ultimately, this is about a Standard for Structured Data to Describe >>Biological Objects -- isn't it? > >I think that is what we are talking about... you could leave out >'structured data' too and it will still make sense... > >jim > >~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: Name for the standard
by Richard Pyle 16 Sep '03

16 Sep '03

> Note also that, for efficiency, different features are described at > different levels of the tree. Thus, whether the ovary is superior or > inferior is often most efficiently coded at family level, whether > the leaves > are opposite or alternate may best be coded at genus level, what > colour the > flowers are at species level, and how long the seeds are may be best at > specimen level. Ultimately, you're right, all coded features 'inherit' to > the ends of the tree (the specimens) but it would be inefficient > to code, or > to store, the data there. This is exactly the answer I needed -- thanks. So yes, for obvious practical reasons, described characters can apply directly to taxonomic concepts. But I guess the one lingering point I have is that the descriptive data is not *necessarily* used only in the context of taxonomy, and as such perhaps should not be confined to a taxonomic context by whatever moniker is finally selected. I think that a taxon could be thought of as a "Bioliogical Object", so that might be a more encompassing term. But then again, if you don't want to confine it to living objects, then the "Biological" could be discarded. > I quite like SDBO. Is there a courier service from Lisbon to Hawaii? Nah -- just think warm thoughts next month in Portugal (wish I could attend, but alas, cannot). Aloha, Rich

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Re: Name for the standard
by Richard Pyle 16 Sep '03

16 Sep '03

> I think in theory the SDD spec could be used to describe > anything that can be > broken into characteristics and states. That can certainly go > beyond biology > as DELTA did in some cases. I believe that, "Structure of > Descriptive Data" > handles that idea. It can be a description of anything. The > description may > itself be grounded in instance data from the world (specimens) > that have been > abstracted or summarized. If the intent is to maintain it so generalized that it can be used in any context, including abiotic ones (in the same sense that DiGIR is specifically intended to be "Generic", not necessarily limited to biological datasets), then I agree -- stick with "SDD". > The taxonomy component is needed to specify what it is that is being > described. In the realm of biology it would seem to be worth some > effort to be domain specific in this part to make sure we can capture this > reference to a "taxonomic concept." I guess that lies at the heart of my original question. I've been under the impression that descriptive data about, for example, certain characteristics of a leaf, are related to the tree from which the leaf fell, moreso than the abstract taxonomic concept in which some taxonomist might include that tree within. In that sense, I see "taxonomy" as a field that may very well be a (the?) primary consumer of such descriptive data, but not necessarily what the descriptive data is specifically endeavoring to describe. I don't want to belabor this point, but I just would like to understand whether taxonomic concepts are considered by this group as the direct objects that are being described; or whether the descriptive data really apply to individual (or sets of individual) organisms, which may or may not be viewed within the context of a taxonomic concept. Again, my apologies if this is drifting too far from the focus of this discussion. Aloha, Rich Richard L. Pyle Ichthyology, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html

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Re: Name for the standard
by Richard Pyle 16 Sep '03

16 Sep '03

> you are right, in part. Although the SDD activity is undertaken by > taxonomists, it extends beyond the core of taxonomy and nomenclature to > delineation and description of the objects themselves (taxa mostly, to a > lesser extent specimens). This is the part I'm having trouble understanding. What is being "Described" are characters....correct? While it is true that researchers have traditionally used character descriptions as a "short-hand" attempt to delineate taxonomic concepts; the bottom line is that characters are intrinsically part of actual living, breathing (respirating) physical beings -- not the concepts (represented by names) that are intended to circumscribe a set of individual organisms deemed to belong to a common taxon. When a taxonomist describes a character in the context of a taxon concept, what is really being asserted is that the character as described is shared by the primary type specimen of the name used to represent the concept, as well as the primary type specimens of any/all names deemed to be synonymous, as well as a wide swath of other individual organisms, a tiny fraction of which have been collected and curated in Museums; the vast majority of which live out their lives in their natural environment. In my mind, characters belong to individual organisms -- to associate them directly with taxon concepts (by way of the implied existence of individual organisms that share the character) is merely a short-hand convenience. Maybe this is getting off track, but my basic point is that if "SDD" is to be qualified in any way, I think it should be qualified in terms of general biology, or biological objects; not necessarily taxonomy. > we we may be getting into the philosophical realm here... Dear God, no!.... :-) > Our Rainforest > Key project actually scored recorded individual specimens for each > taxon... most DELTA and LUCID implementations amalgamate and > abstract this > to the level of taxon or taxon concept and score at this level... > > of course, SDD should ideally handle both approaches... I agree...but in my optimized view of the data management world, I'd like to see characters linked with taxa via implied (if not real) specimens, even if no specific physical specimen can be cited. But if this is getting too philosophical for the issue at hand, I'll gladly step back to my previous status of quiet observer, so as not to clutter the list with tangential issues. > >Ultimately, this is about a Standard for Structured Data to Describe > >Biological Objects -- isn't it? > > I think that is what we are talking about... you could leave out > 'structured data' too and it will still make sense... SDBO? (Standard for Description of Biological Objects) DBOML? (Description of Biological Objects Markup Language) BODML? (Biological Object Description Markup Language) None very sexy, though... Aloha, Rich

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Re: Name for the standard
by Richard Pyle 16 Sep '03

16 Sep '03

I've been quietly following this discussion, and have a general question to ask. In the note below and in previous notes, there seems to be an emphasis on SDD in the contect of "taxonomy"; but wouldn't it be more appropriate to place the emphasis more in the context of biological objects (e.g., specimens), rather than abstract concepts (taxa)? Even though the descriptive data may be applied directly to taxon concepts without an explicit reference to specific specimens/objects, ultimately the characters themselves that are being described are attached to a physical organism -- whether or not the specific physical organism is explicitly identified, or merely implied. Thus, when searching for another moniker to reference what we now refer to as "SDD", I suggest that options along the lines of "Bio..." are preferable to those along the lines of "Taxo...". Ultimately, this is about a Standard for Structured Data to Describe Biological Objects -- isn't it? I doubt that "SSDDBO" will win the hearts of many (or a shot at the bottle of cheap Portugues port). Personally, I'm partial to the previously-suggested "BODDS". Aloha, Rich Richard L. Pyle Natural Sciences Database Coordinator, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html > -----Original Message----- > From: TDWG - Structure of Descriptive Data > [mailto:TDWG-SDD@LISTSERV.NHM.KU.EDU]On Behalf Of Kevin Thiele > Sent: Tuesday, September 16, 2003 10:56 AM > To: TDWG-SDD(a)LISTSERV.NHM.KU.EDU > Subject: Re: Name for the standard > > > Do people in general think that we need to specify that we're > working in the > taxonomic domain - something that the name SDD doesn't - or can we be > extremely general. Perhaps it's the case that SDD will be able to be used > for descriptions outside the taxonomic domain, and we should embrace this > (whether anyone else embraces us is another matter entirely) - k > > ----- Original Message ----- > From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> > To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> > Sent: Tuesday, September 16, 2003 10:53 PM > Subject: Re: Name for the standard > > > > Kevin wrote: > > > yes, I agree that SDD (Standard for Descriptive Data) would do - I was > > > just looking for something a little more exciting. Cheers - k > > > > .... I disagree :-) that "Standard for Descriptive Data"-standard > > would do, I therefore propose "Structured Descriptive Data"-standard. > > I absolutely agree with you about searching something more exciting. > > > > There is a general name grabbing of most-general and all-encompassing > > names (like BioML, which is really indecent...). Since we think about > > the generalization from Biological to other collected objects all the > > time and try to avoid too specifically biological jargon, we actually > > have some justification following suit and grab > > > > DescriptionML ? > > > > (for which Google returns 1 hit, which interestingly does not contain > > the term, I even checked the html source...) > > > > Gregor > > ---------------------------------------------------------- > > Gregor Hagedorn (G.Hagedorn(a)bba.de) > > Institute for Plant Virology, Microbiology, and Biosafety > > Federal Research Center for Agriculture and Forestry (BBA) > > Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 > > 14195 Berlin, Germany Fax: +49-30-8304-2203 > > > > Often wrong but never in doubt!

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Re: Name for the standard
by Gregor Hagedorn 16 Sep '03

16 Sep '03

Kevin wrote: > yes, I agree that SDD (Standard for Descriptive Data) would do - I was > just looking for something a little more exciting. Cheers - k .... I disagree :-) that "Standard for Descriptive Data"-standard would do, I therefore propose "Structured Descriptive Data"-standard. I absolutely agree with you about searching something more exciting. There is a general name grabbing of most-general and all-encompassing names (like BioML, which is really indecent...). Since we think about the generalization from Biological to other collected objects all the time and try to avoid too specifically biological jargon, we actually have some justification following suit and grab DescriptionML ? (for which Google returns 1 hit, which interestingly does not contain the term, I even checked the html source...) Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 Often wrong but never in doubt!

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Re: Name for the standard
by Jim Croft 16 Sep '03

16 Sep '03

>yes, I agree that SDD (Standard for Descriptive Data) would do - I was just >looking for something a little more exciting. Cheers - k and just what could possibly be more exciting than that? jim ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: Name for the standard
by Kevin Thiele 16 Sep '03

16 Sep '03

Gregor, yes, I agree that SDD (Standard for Descriptive Data) would do - I was just looking for something a little more exciting. Cheers - k ----- Original Message ----- From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> Sent: Tuesday, September 16, 2003 1:27 AM Subject: Re: Name for the standard > > >SDD stands for Structure of Descriptive Data - doesn't seem to me to > > >do the job, and I just thought it would be sensible for the standard > > >to have a different name from the group. > > > couldn't you just redefine the final product as 'Standard for > > Descriptive Data', or if you want to be really creative and out there, > > 'Descriptive Data Standard'? > > > The workgroup name "Structure of descriptive data" was originally > explicitly chosen to describe an analysis process, rather than the > proposed standard. > > However, there is already some history of calling our thing > "Structured Descriptive Data (SDD)". Used e.g. by Kevin Thiele, Bryan > Heidorn, Donald Hobern... ! > > I think SDD may be a good option for a new standard name if no other > term is really convincing. However, I also like Chucks idea of > putting all TDWG/GBIF standards under a common roof very much. > Without the TDWG subgroup 12 month later no decision yet extension, > of course. > > Gregor > ---------------------------------------------------------- > Gregor Hagedorn (G.Hagedorn(a)bba.de) > Institute for Plant Virology, Microbiology, and Biosafety > Federal Research Center for Agriculture and Forestry (BBA) > Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 > 14195 Berlin, Germany Fax: +49-30-8304-2203 > > Often wrong but never in doubt!

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Re: DescriptoinML might be too broad Re: Name for the standard
by Robert A. Morris 16 Sep '03

16 Sep '03

No XML is descriptive. It's all syntactic. Hah, hah, just serious. Karen E. Medina wrote: >All xml is descriptive. > > >> DescriptionML ? >> >> -- Robert A. Morris, Professor of Computer Science University of Massachusetts at Boston 100 Morrissey Blvd; Boston, MA 02125 http://www.cs.umb.edu/~ram http://www.cs.umb.edu/efg phone: (+1)617-287-6466 fax: (+1)617-287-6433

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Re: DescriptoinML might be too broad Re: Name for the standard
by marija.markovic＠ABBOTT.COM 16 Sep '03

16 Sep '03

I agree. Ask any linguist, and they'll tell you: "it looks just like HPSG (head-driven phrase structure grammar)". :) "Robert A. Morris" <ram(a)CS.UMB.EDU> Sent by: TDWG - Structure of Descriptive Data <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> 09/16/2003 08:58 AM Please respond to TDWG - Structure of Descriptive Data To: TDWG-SDD(a)LISTSERV.NHM.KU.EDU cc: Subject: Re: DescriptoinML might be too broad Re: Name for the standard No XML is descriptive. It's all syntactic. Hah, hah, just serious. Karen E. Medina wrote: >All xml is descriptive. > > >> DescriptionML ? >> >> -- Robert A. Morris, Professor of Computer Science University of Massachusetts at Boston 100 Morrissey Blvd; Boston, MA 02125 http://www.cs.umb.edu/~ram http://www.cs.umb.edu/efg phone: (+1)617-287-6466 fax: (+1)617-287-6433

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