From kevin.thiele at BIGPOND.COM Thu Sep 25 16:25:15 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 25 Sep 2003 16:25:15 Subject: Name for the Standard Message-ID: Whaddya mean, I like it! ----- Original Message ----- From: Eric.Zurcher at CSIRO.AU To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Thursday, September 25, 2003 10:49 AM Subject: Re: Name for the Standard Just be careful that it doesn't get corrupted to: Generalised Object Descriptive DAta Markup Notation. Eric Zurcher CSIRO Livestock Industries Canberra, Australia Eric.Zurcher at csiro.au -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Friday, 19 September 2003 8:47 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Re: Name for the Standard Got it! - we think that SDD will be pretty general, huh? Then Generalised Object Description Markup Language - an acronym to die for, surely. -k --Boundary_(ID_PAVf19Rtf3D8mu8n0wHKAA) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Whaddya mean, I like it!
----- Original Message -----
From: Eric.Zurcher at CSIRO.AU
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Sent: Thursday, September 25, 2003 10:49 AM
Subject: Re: Name for the Standard

Just be careful that it doesn't get corrupted to:

Generalised Object Descriptive DAta Markup Notation.
 

Eric Zurcher
CSIRO Livestock Industries
Canberra, Australia
Eric.Zurcher at csiro.au

-----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Friday, 19 September 2003 8:47 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Re: Name for the Standard

Got it! - we think that SDD will be pretty general, huh? Then Generalised Object
Description Markup Language - an acronym to die for, surely.

-k
From Eric.Zurcher at CSIRO.AU Thu Sep 25 10:49:32 2003 From: Eric.Zurcher at CSIRO.AU (Eric.Zurcher at CSIRO.AU) Date: Thu, 25 Sep 2003 10:49:32 Subject: Name for the Standard Message-ID: Just be careful that it doesn't get corrupted to: Generalised Object Descriptive DAta Markup Notation. Eric Zurcher CSIRO Livestock Industries Canberra, Australia Eric.Zurcher at csiro.au -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Friday, 19 September 2003 8:47 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Re: Name for the Standard Got it! - we think that SDD will be pretty general, huh? Then Generalised Object Description Markup Language - an acronym to die for, surely. -k ------_=_NextPart_001_01C382FE.829CCE68 Content-Type: text/html; charset="iso-8859-1"
Just be careful that it doesn't get corrupted to:

Generalised Object Descriptive DAta Markup Notation.
 

Eric Zurcher
CSIRO Livestock Industries
Canberra, Australia
Eric.Zurcher at csiro.au

-----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Friday, 19 September 2003 8:47 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Re: Name for the Standard

Got it! - we think that SDD will be pretty general, huh? Then Generalised Object
Description Markup Language - an acronym to die for, surely.

-k
From kevin.thiele at BIGPOND.COM Fri Sep 19 20:46:56 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Fri, 19 Sep 2003 20:46:56 Subject: Name for the Standard Message-ID: Got it! - we think that SDD will be pretty general, huh? Then Generalised Object Description Markup Language - an acronym to die for, surely. -k --Boundary_(ID_idN6RJazOgWmB7i6oKGcMA) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Got it! - we think that SDD will be pretty general, huh? Then Generalised Object
Description Markup Language - an acronym to die for, surely.

-k
From kmedina at ALEXIA.LIS.UIUC.EDU Fri Sep 19 16:12:56 2003 From: kmedina at ALEXIA.LIS.UIUC.EDU (Karen E. Medina) Date: Fri, 19 Sep 2003 16:12:56 Subject: GOD ML - Thiele's creation Re: Name for the Standard In-Reply-To: <045b01c37e9b$7cbfc880$3ba38b90@presario> Message-ID: GOD ML (by Kevin Thiele) What a creation. -karen medina On Fri, 19 Sep 2003, Kevin Thiele wrote: > Got it! - we think that SDD will be pretty general, huh? Then Generalised Object > Description Markup Language - an acronym to die for, surely. > > -k From heidorn at ALEXIA.LIS.UIUC.EDU Fri Sep 19 09:02:18 2003 From: heidorn at ALEXIA.LIS.UIUC.EDU (Bryan Heidorn) Date: Fri, 19 Sep 2003 9:02:18 Subject: Name for the Standard In-Reply-To: <045b01c37e9b$7cbfc880$3ba38b90@presario> Message-ID: Millions have already died for the books on this acronym, but I think you are onto something. If you can understand an organism well enough to describe it well, you are closer to your Generalized Object Description. -- Bryan At 08:46 PM 9/19/03 +1000, you wrote: >Got it! - we think that SDD will be pretty general, huh? Then Generalised >Object >Description Markup Language - an acronym to die for, surely. > >-k -- -------------------------------------------------------------------- P. Bryan Heidorn Graduate School of Library and Information Science pheidorn at uiuc.edu University of Illinois at Urbana-Champaign MC-493 (V)217/ 244-7792 Rm. 221, 501 East Daniel St., Champaign, IL 61820-6212 (F)217/ 244-3302 http://alexia.lis.uiuc.edu/~heidorn Calendar: http://calendar.yahoo.com/pbheidorn Visit the Biobrowser Web site at http://www.biobrowser.org From jrc at ANBG.GOV.AU Thu Sep 18 10:28:45 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 18 Sep 2003 10:28:45 Subject: update on names In-Reply-To: <013801c37d75$ef7a2130$7aa38b90@presario> Message-ID: >Hey - maybe we don't need a name for the standard - just a number! hexadecimal, octal or binary? jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kevin.thiele at BIGPOND.COM Thu Sep 18 09:46:10 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 18 Sep 2003 9:46:10 Subject: update on names Message-ID: Re: update on namesHey - maybe we don't need a name for the standard - just a number! ----- Original Message ----- From: Peter Stevens To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Thursday, September 18, 2003 7:47 AM Subject: Re: update on names Really - I think proponents of the PhyloCoide shoudl come to this list for inspiration :) P. update to 18-09-03: BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft) BioDescML (Chuck Miller) BiODML (Chuck Miller) BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html) BioTaxML (Chuck Miller) BiOTML (Chuck Miller) BODDS (Karen Medina) CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/) ExSDD (Stan Blum) DescML (Jim Croft) DescriptionML (Karen Medina) PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst) SDD (Structured Descriptive Data - port unclaimed?) SDBO (Rich Pyle) SSDDBO (Rich Pyle) TDML (Guillaume Rousse) TaxDescML (Guillaume Rousse) xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz) XBio (Julian Humphries) XSDD (Bob Morris and Stan Blum) Xtax (Julian Humphries) --Boundary_(ID_rAbrD+1M8Tv8PWYnbleE/A) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT Re: update on names
Hey - maybe we don't need a name for the standard - just a number!
 
----- Original Message -----
Sent: Thursday, September 18, 2003 7:47 AM
Subject: Re: update on names

Really - I think proponents of the PhyloCoide shoudl come to this list for inspiration :)


P.



update  to 18-09-03:
 
BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft)
BioDescML (Chuck Miller)
BiODML (Chuck Miller)
BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html)
BioTaxML (Chuck Miller)
BiOTML (Chuck Miller)
BODDS (Karen Medina)
CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/)
ExSDD (Stan Blum)
DescML (Jim Croft)
DescriptionML (Karen Medina)
PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst)
SDD (Structured Descriptive Data - port unclaimed?)
SDBO (Rich Pyle)
SSDDBO (Rich Pyle)
TDML (Guillaume Rousse)
TaxDescML (Guillaume Rousse)
xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz)
XBio (Julian Humphries)
XSDD (Bob Morris and Stan Blum)
Xtax (Julian Humphries)

From kevin.thiele at BIGPOND.COM Thu Sep 18 07:14:27 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 18 Sep 2003 7:14:27 Subject: Name for the standard Message-ID: RE: Name for the standard----- Original Message ----- From: Chuck.Miller at MOBOT.ORG To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Thursday, September 18, 2003 4:01 AM Subject: Re: Name for the standard As an aside, won't all three of these languages need to fit together or follow some consistent conventions to ultimately to feed data into a complete GBIF data repository or global search service? For instance, don't they all include taxon name data? Yes, at the moment we're not worrying too much about that, but obviously when we include a taxon name, place name, authority, reference etc these will all need to be harmonised with existing standards. From kevin.thiele at BIGPOND.COM Thu Sep 18 07:11:39 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 18 Sep 2003 7:11:39 Subject: update on names Message-ID: update to 18-09-03: BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft) BioDescML (Chuck Miller) BiODML (Chuck Miller) BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html) BioTaxML (Chuck Miller) BiOTML (Chuck Miller) BODDS (Karen Medina) CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/) ExSDD (Stan Blum) DescML (Jim Croft) DescriptionML (Karen Medina) PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst) SDD (Structured Descriptive Data - port unclaimed?) SDBO (Rich Pyle) SSDDBO (Rich Pyle) TDML (Guillaume Rousse) TaxDescML (Guillaume Rousse) xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz) XBio (Julian Humphries) XSDD (Bob Morris and Stan Blum) Xtax (Julian Humphries) --Boundary_(ID_aOicZT4qKlE4RIRt88Z54Q) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
update  to 18-09-03:
 
BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft)
BioDescML (Chuck Miller)
BiODML (Chuck Miller)
BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html)
BioTaxML (Chuck Miller)
BiOTML (Chuck Miller)
BODDS (Karen Medina)
CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/)
ExSDD (Stan Blum)
DescML (Jim Croft)
DescriptionML (Karen Medina)
PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst)
SDD (Structured Descriptive Data - port unclaimed?)
SDBO (Rich Pyle)
SSDDBO (Rich Pyle)
TDML (Guillaume Rousse)
TaxDescML (Guillaume Rousse)
xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz)
XBio (Julian Humphries)
XSDD (Bob Morris and Stan Blum)
Xtax (Julian Humphries)
From kevin.thiele at BIGPOND.COM Thu Sep 18 07:00:06 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 18 Sep 2003 7:00:06 Subject: Name for the standard Message-ID: See my previous email - what's so special about higher-level taxonomic concepts cf specimens? The character space created to describe a taxon can also be used perfectly well to describe a specimen of that taxon (and vice versa) in most cases. In fact, it could not be any other way, when you think about it. -k ----- Original Message ----- From: "P. Bryan Heidorn" To: Sent: Wednesday, September 17, 2003 9:05 PM Subject: Re: Name for the standard > As an information scientists and not a "taxonomists" in the systematics use of > the world, but certainly a taxonomists in the Library Science use of the word, > e.g. Dewey Decimal Classification (DDC) I think the work practice now is to > describe higher level taxonomic concepts independent of the raw data the > specimen. It is the description of a class of objects not the object > themselves. Even at the species level the taxonomists is not claiming to have > seen all of the individuals, just enough to make generalizations. So I think > this generalization needs to be addressed by SDD. It would be icing on the > cake if SDD could deal with the relationship to instance data as well. > > Bryan > >===== Original Message From TDWG - Structure of Descriptive Data > ===== > >> 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 at bishopmuseum.org > >http://www.bishopmuseum.org/bishop/HBS/pylerichard.html > > -- > -------------------------------------------------------------------- > P. Bryan Heidorn Graduate School of Library and Information Science > pheidorn at uiuc.edu University of Illinois at Urbana-Champaign > (V)217/ 244-7792 501 East Daniel St., Champaign, IL 61820-6212 > (F)217/ 244-3302 http://alexia.lis.uiuc.edu/~heidorn > http://calendar.yahoo.com/pbheidorn From ram at CS.UMB.EDU Wed Sep 17 20:43:59 2003 From: ram at CS.UMB.EDU (Robert A. Morris) Date: Wed, 17 Sep 2003 20:43:59 Subject: update on names In-Reply-To: <6.0.0.22.0.20030918102721.01c7a890@155.187.10.10> Message-ID: You needn't ask, because as frequently observed on the net, there are only 10 kinds of people in the world. Those who understand binary numbers and those who don't. Jim Croft wrote: >> Hey - maybe we don't need a name for the standard - just a number! > > > hexadecimal, octal or binary? > > jim > > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From peter.stevens at MOBOT.ORG Wed Sep 17 17:47:39 2003 From: peter.stevens at MOBOT.ORG (Peter Stevens) Date: Wed, 17 Sep 2003 17:47:39 Subject: update on names In-Reply-To: <008801c37d60$572f5cc0$7aa38b90@presario> Message-ID: >Really - I think proponents of the PhyloCoide shoudl come to this >list for inspiration :) P. >update to 18-09-03: > >BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D >->DELTA ->Jim Croft) >BioDescML (Chuck Miller) >BiODML (Chuck Miller) >BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html) >BioTaxML (Chuck Miller) >BiOTML (Chuck Miller) >BODDS (Karen Medina) >CAML (Jim Croft) (taken - see >http://www.vision.fhg.de/~veenhuis/CAML/) >ExSDD (Stan Blum) >DescML (Jim Croft) >DescriptionML (Karen Medina) >PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst) >SDD (Structured Descriptive Data - port unclaimed?) >SDBO (Rich Pyle) >SSDDBO (Rich Pyle) >TDML (Guillaume Rousse) >TaxDescML (Guillaume Rousse) >xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz) >XBio (Julian Humphries) >XSDD (Bob Morris and Stan Blum) >Xtax (Julian Humphries) --============_-1148287228==_ma============ Content-Type: text/html; charset="us-ascii" Re: update on names
Really - I think proponents of the PhyloCoide shoudl come to this list for inspiration :)


P.



update  to 18-09-03:
 
BioDDS (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft)
BioDescML (Chuck Miller)
BiODML (Chuck Miller)
BioML (Jim Croft) (taken - see xml.coverpages.org/bioml.html)
BioTaxML (Chuck Miller)
BiOTML (Chuck Miller)
BODDS (Karen Medina)
CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/)
ExSDD (Stan Blum)
DescML (Jim Croft)
DescriptionML (Karen Medina)
PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst)
SDD (Structured Descriptive Data - port unclaimed?)
SDBO (Rich Pyle)
SSDDBO (Rich Pyle)
TDML (Guillaume Rousse)
TaxDescML (Guillaume Rousse)
xDELTA (don't know who to give the port to for this one - maybe Mike Dallwitz)
XBio (Julian Humphries)
XSDD (Bob Morris and Stan Blum)
Xtax (Julian Humphries)

From jrc at ANBG.GOV.AU Wed Sep 17 17:25:34 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 17 Sep 2003 17:25:34 Subject: Name for the standard In-Reply-To: Message-ID: >This is the part I'm having trouble understanding. What is being >"Described" are characters....correct? well, maybe... depends on how abstract you want to be... but I think I would be inclined towards recording characters and their states to describe the main game: a taxon. You can get there by describing specimens, but you do not have to. >While it is true that researchers >have traditionally used character descriptions as a "short-hand" attempt to >delineate taxonomic concepts; Using the perspective above, character description is the tool and not the work... Characters can be described in the absence of a taxon. A taxon can be described by the aggregate of the characters/states (described elsewhere) it does (or does not) possess. >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. At this point it is very easy to lapse metaphysical... perhaps organs are part of the organism but characters are an artificial human construct... :) [ Over the bottle of fine port one of us is going to win, we can solve this one relatively quickly... ] >When a taxonomist describes a character in the context of a taxon >concept, [ Thinks... Do characters always have to be defined in the context of a taxon? ] >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. This is probably quite a defensible assertion... the fact that taxonomy exists at all is that we can generalize like this... >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. Or, the organ and its attributes belongs to an organism... the character and its states belongs to the human who defined it... >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. I agree - taxon description, documentation and identification, especially as implemented in products such as Delta and Lucid, extends what we do far beyond what could be considered taxonomy in the narrow sense. >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. yes - we have another project running here covering a key to Orchid genera. In this case we are not even scoring species level taxa, but we are trying to cover the full range of variation in the genus and we are recording which specimens have been used in this assessment so we can al least go back and rescore if taxonomists change their minds (never! I hear you say). The argument is that if we actually scored the specimens all we would have to do is recompile the key - nice, but unacceptably more work for our budget... >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. but they are the best kind... >SDBO? >(Standard for Description of Biological Objects) or just DBO? nothing like a TLA to make it sound as though you know what you are doing... >DBOML? >(Description of Biological Objects Markup Language) or just BOML... >BODML? >(Biological Object Description Markup Language) see previous... >None very sexy, though... seen worse... jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kevin.thiele at BIGPOND.COM Wed Sep 17 16:07:21 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Wed, 17 Sep 2003 16:07:21 Subject: Name for the standard Message-ID: Well, in practice (though perhaps not in philosophy) there isn't actually any great difference between describing a specimen and "describing" a taxon - in the former case we're describing a real thing (we don't actually use describe the characters of the object, rather we use characters to describe), in the latter case we're describing a 'platonic ideal' - an idealised 'object'. In the same way we describe a triangle as being a three sided figure and we describe the angles as equalling 180 degrees, but what we're actually describing is a platonic triangle, not any real one. The platonic taxon can be handled in exactly the same way as a real object - we can say that a real specimen has leaves 10-15 cm long, and the taxon to which it belongs has leaves 8-18 cm long - easy. In Lucid we are implementing a system for coding specimens, and specimens merely become twigs on the taxon tree. We don't even seem to find that we need to specify that this node of the tree is a specimen and that node is a taxon. 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. SDD still needs to visit specimen coding, but I think when we do we'll find that it's trivial. As to the scope of SDD, you're right that it should be possible in principle to use it to describe the morphology of a widget, a soil, a nematode, or perhaps even an asteroid. In practice, though, I doubt that it will be useful for us to specifically scope SDD beyond the taxonomic domain - probably the hardest domain to deal with anyway, so the ultimate challenge. I quite like SDBO. Is there a courier service from Lisbon to Hawaii? Cheers - k ----- Original Message ----- From: "Richard Pyle" To: Sent: Wednesday, September 17, 2003 2:32 PM Subject: Re: Name for the standard > > 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 From humphries at MAIL.UTEXAS.EDU Wed Sep 17 14:50:47 2003 From: humphries at MAIL.UTEXAS.EDU (Julian H) Date: Wed, 17 Sep 2003 14:50:47 Subject: Name for the standard In-Reply-To: Message-ID: My 2 cents is that "descriptive" doesn't need to be part of the resulting name, at least not part of the acronym or codon that is used for the resulting standard. Most folks want biology to be part of the name. How about "XBio" ? Nothing like it shows up in any of the xml coverage I can find (it is used for a variety of smallscale software projects). It doesn't have to actually stand for any literal phrase (I like the New Mexico District Court XML Interface (XCI) ) which has a similar derived structure, but at any rate could be "XML for Biology". Xbio is easy to pronounce, somewhat distinctive, contemporary sounding and short. Julian P.S. Xtax is also pretty interesting as a acronym, nice pairing of x's and also easy to say and remember. Julian Humphries DigiMorph.Org Geological Sciences University of Texas at Austin Austin, TX 78712 512-471-3275 --=====================_172449812==.ALT Content-Type: text/html; charset="us-ascii" My 2 cents is that "descriptive" doesn't need to be part of the resulting name, at least not part of the acronym or codon that is used for the resulting standard.  Most folks want biology to be part of the name.

How about "XBio" ?  Nothing like it shows up in any of the xml coverage I can find (it is used for a variety of smallscale software projects).  It doesn't have to actually stand for any literal phrase (I like the New Mexico District Court XML Interface (XCI) ) which has a similar derived structure, but at any rate could be "XML for Biology".   Xbio is easy to pronounce, somewhat distinctive, contemporary sounding and short.

Julian

P.S. Xtax is also pretty interesting as a acronym, nice pairing of x's and also easy to say and remember.



Julian Humphries
DigiMorph.Org
Geological Sciences
University of Texas at Austin
Austin, TX 78712
512-471-3275

From jrc at ANBG.GOV.AU Wed Sep 17 13:29:46 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 17 Sep 2003 13:29:46 Subject: Name for the standard In-Reply-To: Message-ID: >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 at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From Chuck.Miller at MOBOT.ORG Wed Sep 17 13:01:12 2003 From: Chuck.Miller at MOBOT.ORG (Chuck.Miller at MOBOT.ORG) Date: Wed, 17 Sep 2003 13:01:12 Subject: Name for the standard Message-ID: >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... Leaving out "structured data", how about Biological Object Description Markup Language - BiODML. We could then have Biological Object Taxonomy Markup Language - BiOTML and Biological Object Collection Markup Languag - BiOCML (now either Darwin Core/DiGIR or ABCD?). As an aside, won't all three of these languages need to fit together or follow some consistent conventions to ultimately to feed data into a complete GBIF data repository or global search service? For instance, don't they all include taxon name data? Chuck -----Original Message----- From: Jim Croft [mailto:jrc at ANBG.GOV.AU] Sent: Tuesday, September 16, 2003 10:30 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Re: Name for the standard >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 at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ ------_=_NextPart_001_01C37D45.AE274350 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Name for the standard

>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...

Leaving out "structured data", how about = Biological Object Description Markup Language - BiODML.

We could then have Biological Object Taxonomy Markup = Language - BiOTML and Biological Object Collection Markup Languag - = BiOCML (now either Darwin Core/DiGIR or ABCD?).

As an aside, won't all three of these languages need = to fit together or follow some consistent conventions to ultimately to = feed data into a complete GBIF data repository or global search = service?  For instance, don't they all include taxon name = data?     

Chuck

-----Original Message-----
From: Jim Croft [mailto:jrc at ANBG.GOV.AU]
Sent: Tuesday, September 16, 2003 10:30 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Re: Name for the standard


>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 at anbg.gov.au ~ 02-62465500 ~ = www.anbg.gov.au/jrc/ ~

From jrc at ANBG.GOV.AU Wed Sep 17 08:50:29 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 17 Sep 2003 8:50:29 Subject: Fwd: Re: simple instance Message-ID: I am sorry - I had not realized the discussion had moved off list... :( was just replying mindlessly to email as it came in... :) jim >Date: Wed, 17 Sep 2003 08:45:00 +1000 >To: "G. Hagedorn" >From: Jim Croft >Subject: Re: simple instance > >>Bob very bravely defended our decision and I think it is more or less >>correct, > >It was not meant to be an attack... just expressing a bit of concern that >non-SDD people are going to look at it and freak out at the specification >overhead... > >>but your reaction concerns me, because this is socialogical >>and a question of acceptance. > >that is why I made the comments... if our specification is so complex in >its implementation that people can not understand or install it they will >not become engaged in our noble cause... > >>The specification (= "schema" with comments) of html >>is not, it is huge. >>Doing is very short. However, that means >>we have to put the specification (= "schema") elsewhere. > >As a general rule, argument by analogy is not a good thing to do, but in >this case I think the comparison is apt... > >The reason HTML took off is that it was simple enough to understand the >code and implied DTD, and it was not allowed to fail from the users >perspective - you could put in as many or as few tags as you liked, even >leave out the all important and half the closing tags, and it would >still not bomb out on the browser... I believe it was this level of fault >tolerance that ensured its unquestionable success. > >SGML on the other hand was impenetrable to the average human, or >scientist, and was almost a complex as SDD and as a result has almost >vanished from the everyday information management lexicon. It was >undeniably a better environment to do what we were trying to achieve, but >there was not way we were going to be able to give it the level of social >acceptance to enable it to take off like HTML did... > >and then along came XML which offered the power of SGML with the >simplicity of HTML... we had to be the opportunity to be as simple or as >complex as we want... > >and here we are... :) > >>The SDD design principle is to allow the user to define things. That >>means we not only have the leaves and simple, we also need to define >>that. That makes it a lot more complicated. > >perhaps were should look a bit more closely at the word 'allow'. As it >stands at the moment, are we allowing, or compelling people to define >everything, multiple times? > >Is there a compromise position? can we specify the standard to different >backwardly compatible levels depending on the degree of compulsion we >might want for a particular instance? > >>Audience definitions: a single audience definition will do according >>to our current definition. You must define one, however. > >why? can't we have a general audience definition implied by default? > >>You can also >>include a fairly complete set of audience definitions which should be >>readily available at the end of this effort. Both is fine. > >Or we could leave it to be user definable? is it linear? perhaps a >3,5,7,10 level of audience sophistication from stupid to genius is ok? :) > >>If I receive a dataset from an editor that does not care about >>statistical parameters (unable to express numeric statements) and >>want to edit this with another application, adding numeric >>statements, I somehow have to have a mechanism to add the basic >>infrastructure to become able to do this. This is an extra step, >>which we could avoid by simple for SDD version 1 require a fixed set >>of minimal statistical parameters to be present in each file. For >>processors not really supporting it, this would in fact be a singe >>xinclude statement to some globally stored SDD template file. > >This is fine if we live in Bob's utopian machine to machine world, but >until we get there we have these human things to deal with... we need to >be able to present a series of initial and intermediate steps in using SDD >that people can understand and implement or all we will have is a nice >specification that suffers the same fate as SGMwho... > >Even if it going to be machine talking to machine, and ultimately that is >what it needs to do, a human has to interpret what we have invented and >instruct the machines accordingly. Unfortunately 99 our of 100 people >working on descriptive data do not have the level if computing savvy of a >Bob or a Gregor - for the most part they are taxonomists who know about >organisms and we can't, and shouldn't, try to turn them into >programmers. we need to provide something to the well meaning taxonomist >who want to do the right thing. If we give them the schema and instance >we are talking about, most will take one look and walk away... > >>Reason 1. silly but true: xmlspy does not display attributes in the >>schema view directly, you are have to click on an element and then >>look in a separate window. We therefore overlooked things that were >>hidden in attributes. > >yep, you are right - that is silly - I remember the discussion now... :) > >>Reason 2. We kept moving things between elements and attributes. Some >>things just have to be elements (because they contain further >>structure), many things we could choose. After some indecision I >>increasingly found that I have the best feeling of simply saying: >>key/keyref in attributes, the rest elements. > >I think it was Guillaume who had a good definition - if it was data it >belonged in an element, if was metadata, data about the data, then it was >an attribute... don't know if this is right, but it seemed to make a lot >of sense at the time and stuck in my brain to the extent that I have not >looked at a schema the same way since... :) > >jim > >~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kevin.thiele at BIGPOND.COM Wed Sep 17 06:56:28 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Wed, 17 Sep 2003 6:56:28 Subject: Name for the standard Message-ID: 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" To: 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 at 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! From heidorn at ALEXIA.LIS.UIUC.EDU Wed Sep 17 06:05:51 2003 From: heidorn at ALEXIA.LIS.UIUC.EDU (P. Bryan Heidorn) Date: Wed, 17 Sep 2003 6:05:51 Subject: Name for the standard Message-ID: As an information scientists and not a "taxonomists" in the systematics use of the world, but certainly a taxonomists in the Library Science use of the word, e.g. Dewey Decimal Classification (DDC) I think the work practice now is to describe higher level taxonomic concepts independent of the raw data the specimen. It is the description of a class of objects not the object themselves. Even at the species level the taxonomists is not claiming to have seen all of the individuals, just enough to make generalizations. So I think this generalization needs to be addressed by SDD. It would be icing on the cake if SDD could deal with the relationship to instance data as well. Bryan >===== Original Message From TDWG - Structure of Descriptive Data ===== >> 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 at bishopmuseum.org >http://www.bishopmuseum.org/bishop/HBS/pylerichard.html -- -------------------------------------------------------------------- P. Bryan Heidorn Graduate School of Library and Information Science pheidorn at uiuc.edu University of Illinois at Urbana-Champaign (V)217/ 244-7792 501 East Daniel St., Champaign, IL 61820-6212 (F)217/ 244-3302 http://alexia.lis.uiuc.edu/~heidorn http://calendar.yahoo.com/pbheidorn From heidorn at ALEXIA.LIS.UIUC.EDU Tue Sep 16 22:25:35 2003 From: heidorn at ALEXIA.LIS.UIUC.EDU (P. Bryan Heidorn) Date: Tue, 16 Sep 2003 22:25:35 Subject: Name for the standard Message-ID: 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 ===== >>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 at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From deepreef at BISHOPMUSEUM.ORG Tue Sep 16 20:57:07 2003 From: deepreef at BISHOPMUSEUM.ORG (Richard Pyle) Date: Tue, 16 Sep 2003 20:57:07 Subject: Name for the standard In-Reply-To: <030401c37ce2$0feb2e30$68a38b90@presario> Message-ID: > 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 From deepreef at BISHOPMUSEUM.ORG Tue Sep 16 20:42:24 2003 From: deepreef at BISHOPMUSEUM.ORG (Richard Pyle) Date: Tue, 16 Sep 2003 20:42:24 Subject: Name for the standard In-Reply-To: <3F6231F1@cricket.lis.uiuc.edu> Message-ID: > 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 at bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html From deepreef at BISHOPMUSEUM.ORG Tue Sep 16 18:32:28 2003 From: deepreef at BISHOPMUSEUM.ORG (Richard Pyle) Date: Tue, 16 Sep 2003 18:32:28 Subject: Name for the standard In-Reply-To: <6.0.0.22.0.20030917125615.01c3b658@155.187.10.10> Message-ID: > 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 From deepreef at BISHOPMUSEUM.ORG Tue Sep 16 16:36:19 2003 From: deepreef at BISHOPMUSEUM.ORG (Richard Pyle) Date: Tue, 16 Sep 2003 16:36:19 Subject: Name for the standard Message-ID: 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 at bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html > -----Original Message----- > From: TDWG - Structure of Descriptive Data > [mailto:TDWG-SDD at LISTSERV.NHM.KU.EDU]On Behalf Of Kevin Thiele > Sent: Tuesday, September 16, 2003 10:56 AM > To: TDWG-SDD at 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" > To: > 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 at 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! From G.Hagedorn at BBA.DE Tue Sep 16 14:53:19 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Tue, 16 Sep 2003 14:53:19 Subject: Name for the standard In-Reply-To: <00e301c37bf6$c19a1de0$daa38b90@presario> Message-ID: Kevin wrote: > yes, I agree that SDD (Standard for Descriptive Data) would do - I was > just looking for something a little more exciting. Cheers - k .... I disagree :-) that "Standard for Descriptive Data"-standard would do, I therefore propose "Structured Descriptive Data"-standard. I absolutely agree with you about searching something more exciting. There is a general name grabbing of most-general and all-encompassing names (like BioML, which is really indecent...). Since we think about the generalization from Biological to other collected objects all the time and try to avoid too specifically biological jargon, we actually have some justification following suit and grab DescriptionML ? (for which Google returns 1 hit, which interestingly does not contain the term, I even checked the html source...) Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 Often wrong but never in doubt! From jrc at ANBG.GOV.AU Tue Sep 16 13:24:13 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Tue, 16 Sep 2003 13:24:13 Subject: Name for the standard In-Reply-To: <00e301c37bf6$c19a1de0$daa38b90@presario> Message-ID: >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 at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kevin.thiele at BIGPOND.COM Tue Sep 16 11:01:28 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Tue, 16 Sep 2003 11:01:28 Subject: Name for the standard Message-ID: 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" To: 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 at 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! From ram at CS.UMB.EDU Tue Sep 16 09:58:11 2003 From: ram at CS.UMB.EDU (Robert A. Morris) Date: Tue, 16 Sep 2003 9:58:11 Subject: DescriptoinML might be too broad Re: Name for the standard In-Reply-To: Message-ID: 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 From marija.markovic at ABBOTT.COM Tue Sep 16 09:06:50 2003 From: marija.markovic at ABBOTT.COM (marija.markovic at ABBOTT.COM) Date: Tue, 16 Sep 2003 9:06:50 Subject: DescriptoinML might be too broad Re: Name for the standard Message-ID: I agree. Ask any linguist, and they'll tell you: "it looks just like HPSG (head-driven phrase structure grammar)". :) "Robert A. Morris" Sent by: TDWG - Structure of Descriptive Data 09/16/2003 08:58 AM Please respond to TDWG - Structure of Descriptive Data To: TDWG-SDD at 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 --=_alternative 004DEA9B86256DA3_= Content-Type: text/html; charset="us-ascii"
I agree. Ask any linguist, and they'll tell you: "it looks just like HPSG (head-driven phrase structure grammar)".
:)




"Robert A. Morris" <ram at CS.UMB.EDU>
Sent by: TDWG - Structure of Descriptive Data <TDWG-SDD at LISTSERV.NHM.KU.EDU>

09/16/2003 08:58 AM
Please respond to TDWG - Structure of Descriptive Data

       
        To:        TDWG-SDD at 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

From kmedina at ALEXIA.LIS.UIUC.EDU Tue Sep 16 08:49:55 2003 From: kmedina at ALEXIA.LIS.UIUC.EDU (Karen E. Medina) Date: Tue, 16 Sep 2003 8:49:55 Subject: DescriptoinML might be too broad Re: Name for the standard In-Reply-To: <3F6723DF.15238.59F3277@localhost> Message-ID: All xml is descriptive. > DescriptionML ? From G.Hagedorn at BBA.DE Mon Sep 15 17:27:45 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Mon, 15 Sep 2003 17:27:45 Subject: Name for the standard In-Reply-To: <5.2.1.1.0.20030911093852.01604aa0@155.187.10.10> Message-ID: > >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 at 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! From G.Hagedorn at BBA.DE Mon Sep 15 16:43:41 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Mon, 15 Sep 2003 16:43:41 Subject: XDELTA / RDF In-Reply-To: Message-ID: Leigh Dodds wrote: > btw, where would look for an update/docs on the new > standard? I'm curious whether any consideration was > given to using RDF, which provides a good framework > for collating data about resources from multiple sources > and using multiple vocabularies. (For docs see http://160.45.63.11/Projects/TDWG-SDD/index.html. The minutes and xsd draft changes from Paris are not finished yet by me, however. Also Kevin is writing some introduction to the whole of SDD, that hopefully makes it easier to understand.) The application of RDF to SDD has been repeatedly discussed -- and is currently avoided. It probably would be a good thing, everybody agrees so, but most do not understand it well enough to really work with it or profit from the definitional documents. I failed to understand them. So we decided to try without RDF, rather than debating little understood things. Any review of our results from you would be great. If you can, come to Lisbon! Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at 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! From jrc at ANBG.GOV.AU Thu Sep 11 23:23:54 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 11 Sep 2003 23:23:54 Subject: BODDS Re: Name for the standard In-Reply-To: Message-ID: >>>There is a plant ontology consortium (POC) that is involved in >>>trying to rationalise terminology used by Arabidopsis, Zea and >>>Oryza people, and by extension (I hope) more gererally in fl. pl. Have they published anything? URL? jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Thu Sep 11 09:45:02 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 11 Sep 2003 9:45:02 Subject: BODDS Re: Name for the standard In-Reply-To: Message-ID: >BODDS -Biological Ontological Descriptive Data Standard. It sounds kinda >sexy when you say BODDS outloud. Or very juvenile. Or both. well, if the shoe fits, I suppose we should wear it... or we could just call it Biological Ontology... :) nah... that one stinks... jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Thu Sep 11 09:41:38 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 11 Sep 2003 9:41:38 Subject: Name for the standard In-Reply-To: <010401c377eb$3f009ad0$ee9f8a90@presario> Message-ID: >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'? >By the way, I'd better correct my last email. Make that a cheap bottle of >Portugues port. Well! That is one way to ensure that it stays as SDD! jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From Leszek at MISSOURI.EDU Thu Sep 11 09:30:35 2003 From: Leszek at MISSOURI.EDU (Vincent, Leszek) Date: Thu, 11 Sep 2003 9:30:35 Subject: BODDS Re: Name for the standard Message-ID: > -----Original Message----- > From: Jim Croft [mailto:jrc at ANBG.GOV.AU] > Sent: Thursday, September 11, 2003 8:24 AM > To: TDWG-SDD at LISTSERV.NHM.KU.EDU > Subject: Re: BODDS Re: Name for the standard > > > >>>There is a plant ontology consortium (POC) that is > involved in trying > >>>to rationalise terminology used by Arabidopsis, Zea and > Oryza people, > >>>and by extension (I hope) more gererally in fl. pl. > > Have they published anything? URL? > > jim > > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ > ==================================== Hi TDWG folk, "Has the Plant Ontology Consortium published anything? URL" Yes - for that info. & a whole lot more visit www.plantontology.org. Regards, - Leszek Vincent xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox P. Leszek D. Vincent Ph.D., FLS Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall, University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850; Ph/Fax (Home): (573) 441-1228; Email: Leszek at missouri.edu Yahoo! Messenger: leszekvincent Plant Systematist on the Maize Mapping Project - NSF award 9872655 - (http://www.maizemap.org/ and http://www.agron.missouri.edu/) Associate Curator, Dunn-Palmer Herbarium (UMO) Research Associate, Missouri Botanical Garden, USA xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox From kevin.thiele at BIGPOND.COM Thu Sep 11 08:30:46 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 11 Sep 2003 8:30:46 Subject: Name for the standard Message-ID: 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. Of course, if we use SDD in the end, then the bottle of port is unclaimed. By the way, I'd better correct my last email. Make that a cheap bottle of Portugues port. -k ----- Original Message ----- From: "Jim Croft" To: Sent: Thursday, September 11, 2003 7:43 AM Subject: Re: Name for the standard > >By the way, there's a bottle of fine Portuguese port for whoever comes up > >with the final name. Of course, if no-one can come up with anything, the > >SDD group at Lisbon will have to drink the port as consolation. > > just our of interest, what was wrong with SDD? Is it really something that > needs a catchy name to market to the outside world? Won't it just become > part of the information infrastructure that everyone takes for granted? > > jim > > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Thu Sep 11 07:45:23 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 11 Sep 2003 7:45:23 Subject: Name for the standard In-Reply-To: <005601c377e0$1f610ee0$ee9f8a90@presario> Message-ID: >Jim your skills are wasted. Get a real job! Unfortunately these days it is the real job that is wasting my skills... :( jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Thu Sep 11 07:43:52 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Thu, 11 Sep 2003 7:43:52 Subject: Name for the standard In-Reply-To: <005701c377e0$202c2710$ee9f8a90@presario> Message-ID: >By the way, there's a bottle of fine Portuguese port for whoever comes up >with the final name. Of course, if no-one can come up with anything, the >SDD group at Lisbon will have to drink the port as consolation. just our of interest, what was wrong with SDD? Is it really something that needs a catchy name to market to the outside world? Won't it just become part of the information infrastructure that everyone takes for granted? jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From peter.stevens at MOBOT.ORG Thu Sep 11 07:33:41 2003 From: peter.stevens at MOBOT.ORG (Peter Stevens) Date: Thu, 11 Sep 2003 7:33:41 Subject: BODDS Re: Name for the standard In-Reply-To: <5.2.1.1.0.20030911094241.0160c820@155.187.10.10> Message-ID: >>There is a plant ontology consortium (POC) that is involved in >>trying to rationalise terminology used by Arabidopsis, Zea and >>Oryza people, and by extension (I hope) more gererally in fl. pl. Peter S. >>BODDS -Biological Ontological Descriptive Data Standard. It sounds kinda >>sexy when you say BODDS outloud. Or very juvenile. Or both. > >well, if the shoe fits, I suppose we should wear it... > >or we could just call it Biological Ontology... :) > >nah... that one stinks... > >jim > > >~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kevin.thiele at BIGPOND.COM Thu Sep 11 07:29:28 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 11 Sep 2003 7:29:28 Subject: Name for the standard Message-ID: RE: Name for the standardso far, we have: BioDDS - (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft) BioDescML - (Chuck Miller) BioML - (Jim Croft) (taken - see xml.coverpages.org/bioml.html) BioTaxML - (Chuck Miller) CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/) ExSDD - (Stan Blum) DescML - (Jim Croft) PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst) TDML - (Guillaume Rousse) TaxDescML - (Guillaume Rousse) xDELTA - (don't know who to give the port to for this one - maybe Mike Dallwitz) XSDD - (Bob Morris and Stan Blum) Keep them coming. There hasn't been so much traffic on the list for years! -k --Boundary_(ID_yfEW066RZTc+GaTySEakgw) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT RE: Name for the standard
so far, we have:
 
BioDDS - (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft)
BioDescML - (Chuck Miller)
BioML - (Jim Croft) (taken - see xml.coverpages.org/bioml.html)
BioTaxML - (Chuck Miller)
CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/)
ExSDD - (Stan Blum)
DescML - (Jim Croft)
PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst)
TDML - (Guillaume Rousse)
TaxDescML - (Guillaume Rousse)
xDELTA - (don't know who to give the port to for this one - maybe Mike Dallwitz)
XSDD - (Bob Morris and Stan Blum)
 
Keep them coming. There hasn't been so much traffic on the list for years!
 
-k
From kevin.thiele at BIGPOND.COM Thu Sep 11 07:11:31 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 11 Sep 2003 7:11:31 Subject: Name for the standard Message-ID: RE: Name for the standardAn excellent suggestion - perhaps we need to set up a TDWG working group to consider this and report in 12 months time. By the way, there's a bottle of fine Portuguese port for whoever comes up with the final name. Of course, if no-one can come up with anything, the SDD group at Lisbon will have to drink the port as consolation. -k ----- Original Message ----- From: Chuck.Miller at MOBOT.ORG To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Thursday, September 11, 2003 3:43 AM Subject: Re: Name for the standard How many XML schemas are currently in work within TDWG(Collections, SDD, Economic Botany, Geography, Spatial Data) and GBIF(DADI, ECAT, and DIGIT)? Is there a way to unify them under some more universal schemaML naming approach? This seems like a unique moment in time to start a precedent. The GBIF Biodiversity Data Architecture document is replete with models of interfaces and web services that will all require new XML schemas to be created--each needing a name. GBIF also intends to add schemas for taxa, literature, gazeteers, indexes, providers, etc. Is there a way to be more universal in naming these schemas? The simple names like BioML, TaxML, etc. have already been used and are probably too general anyway. (OmniML?) One approach could be to concatentate dipthongs or something to create a schema of ML names. For example, BioDescML, BioTaxML, BioLitML. Or BioDML, BioTML, BioLML. Or GBIFDescML. Or TDWGDescML. Chuck Miller -----Original Message----- From: Jim Croft [mailto:jrc at ANBG.GOV.AU] Sent: Tuesday, September 09, 2003 8:53 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Re: Name for the standard is DescML taken? jim >jrc> So what is it to be? BioML? > >preoccupied, although there in no strict registration mechanism except >its flavour in namespace. http://xml.coverpages.org/bioml.html ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ --Boundary_(ID_AKb4cMiBMTJZRGQV88Cc0A) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT RE: Name for the standard
An excellent suggestion - perhaps we need to set up a TDWG working group to consider this and report in 12 months time.
 
By the way, there's a bottle of fine Portuguese port for whoever comes up with the final name. Of course, if no-one can come up with anything, the SDD group at Lisbon will have to drink the port as consolation.
 
-k
----- Original Message -----
Sent: Thursday, September 11, 2003 3:43 AM
Subject: Re: Name for the standard

How many XML schemas are currently in work within TDWG(Collections, SDD, Economic Botany, Geography, Spatial Data) and GBIF(DADI, ECAT, and DIGIT)?  Is there a way to unify them under some more universal schemaML naming approach?  This seems like a unique moment in time to start a precedent. 

The GBIF Biodiversity Data Architecture document is replete with models of interfaces and web services that will all require new XML schemas to be created--each needing a name. GBIF also intends to add schemas for taxa, literature, gazeteers, indexes, providers, etc. 

Is there a way to be more universal in naming these schemas?

The simple names like BioML, TaxML, etc. have already been used and are probably too general anyway. (OmniML?)

One approach could be to concatentate dipthongs or something to create a schema of ML names.  For example, BioDescML, BioTaxML, BioLitML.  Or BioDML, BioTML, BioLML.  Or GBIFDescML.  Or TDWGDescML. 

Chuck Miller  

-----Original Message-----
From: Jim Croft [mailto:jrc at ANBG.GOV.AU]
Sent: Tuesday, September 09, 2003 8:53 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Re: Name for the standard


is DescML taken?

jim

>jrc> So what is it to be?  BioML?
>
>preoccupied, although there in no strict registration mechanism except
>its flavour in namespace. http://xml.coverpages.org/bioml.html

~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

From kevin.thiele at BIGPOND.COM Thu Sep 11 07:04:26 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Thu, 11 Sep 2003 7:04:26 Subject: Name for the standard Message-ID: Jim your skills are wasted. Get a real job! ----- Original Message ----- From: "Jim Croft" To: Sent: Wednesday, September 10, 2003 7:46 AM Subject: Re: Name for the standard > >How about BIODDS - BIOlogical Descriptive Data Standard? > > or BDDS... > > but the data is probably a given in this day and age so we could get away > with BDS... > > .... > > but most people would probably refer to it as the 'BD standard' so we could > shorten it further to BD... > > and if we do the job properly and at the right level there is no reason why > it needs to be restricted to biology, so it could be the D standard... or D > > or Descriptive Ontology Integrating Taxonomy: DO IT > > Got it! ... Descriptive Environment for Large Taxonomic Arrays... > > now, where did I put those pills... > > jim > > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Wed Sep 10 23:25:59 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 23:25:59 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) In-Reply-To: <200309101201.11251.rousse@ccr.jussieu.fr> Message-ID: >CAML is already a (excellent) programming language, see >http://caml.inria.fr/index-eng.html Damn... all the good ones are taken... story of my life... jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From kmedina at ALEXIA.LIS.UIUC.EDU Wed Sep 10 17:47:12 2003 From: kmedina at ALEXIA.LIS.UIUC.EDU (Karen E. Medina) Date: Wed, 10 Sep 2003 17:47:12 Subject: BODDS Re: Name for the standard In-Reply-To: <005601c377e0$1f610ee0$ee9f8a90@presario> Message-ID: BODDS -Biological Ontological Descriptive Data Standard. It sounds kinda sexy when you say BODDS outloud. Or very juvenile. Or both. I'd kinda liked the idea of doing something in latin. -karen medina On Thu, 11 Sep 2003, Kevin Thiele wrote: > Jim your skills are wasted. Get a real job! > > ----- Original Message ----- > From: "Jim Croft" > To: > Sent: Wednesday, September 10, 2003 7:46 AM > Subject: Re: Name for the standard > > > > >How about BIODDS - BIOlogical Descriptive Data Standard? > > > > or BDDS... > > > > but the data is probably a given in this day and age so we could get away > > with BDS... > > > > .... > > > > but most people would probably refer to it as the 'BD standard' so we > could > > shorten it further to BD... > > > > and if we do the job properly and at the right level there is no reason > why > > it needs to be restricted to biology, so it could be the D standard... or > D > > > > or Descriptive Ontology Integrating Taxonomy: DO IT > > > > Got it! ... Descriptive Environment for Large Taxonomic Arrays... > > > > now, where did I put those pills... > > > > jim > > > > > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ > --------------------------->>>>>***<<<<<--------------------------- Karen E Medina Sometimes reachable through: 217/244-2757 From rousse at CCR.JUSSIEU.FR Wed Sep 10 15:32:10 2003 From: rousse at CCR.JUSSIEU.FR (Guillaume Rousse) Date: Wed, 10 Sep 2003 15:32:10 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) In-Reply-To: <5.2.1.1.0.20030910232021.00b7de10@155.187.10.10> Message-ID: Ainsi parlait Jim Croft : > >CAML is already a (excellent) programming language, see > >http://caml.inria.fr/index-eng.html > > Damn... all the good ones are taken... I forgot to say the camel symbol itself was already used by the Perl communauty :-P http://www.perl.org/ -- Suppressive fires -- won't -- Murphy's Military Laws n?3 From buchen at BIO2.COLUMBIA.EDU Wed Sep 10 14:36:52 2003 From: buchen at BIO2.COLUMBIA.EDU (Cornelia Buchen-Osmond) Date: Wed, 10 Sep 2003 14:36:52 Subject: Name for the standard Message-ID: RE: Name for the standardxDELTA was Leigh Dobbs invention as far as I understand. Dr Cornelia B?chen-Osmond Biosphere 2 Center 32540 S. Biosphere Road P.O. Box 689 Oracle, AZ 85623 U.S.A. Please note that our phone numbers have changed. Phone +1 (520) 838-5126 Fax +1 (520) 838-6214 email: buchen at bio2.columbia.edu ICTVdB - The Universal Virus Database home at Bio2 http://ictvdb.bio2.edu/ mirror in the USA http://www.ncbi.nlm.nih.gov/ICTVdb/ mirror in the UK http://www.ictvdb.iacr.ac.uk/ mirror in China http://ictvdb.mirror.ac.cn/ ----- Original Message ----- From: Kevin Thiele To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Wednesday, September 10, 2003 2:29 PM Subject: Re: Name for the standard so far, we have: BioDDS - (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft) BioDescML - (Chuck Miller) BioML - (Jim Croft) (taken - see xml.coverpages.org/bioml.html) BioTaxML - (Chuck Miller) CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/) ExSDD - (Stan Blum) DescML - (Jim Croft) PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst) TDML - (Guillaume Rousse) TaxDescML - (Guillaume Rousse) xDELTA - (don't know who to give the port to for this one - maybe Mike Dallwitz) XSDD - (Bob Morris and Stan Blum) Keep them coming. There hasn't been so much traffic on the list for years! -k ------=_NextPart_000_000A_01C377A8.F97F5AB0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Name for the standard
xDELTA was Leigh Dobbs invention as far as I understand.
 
Dr Cornelia B?chen-Osmond
Biosphere 2 Center
32540 S. Biosphere Road
P.O. Box 689
Oracle, AZ 85623
U.S.A.
Please note that our phone numbers have changed.
Phone  +1 (520) 838-5126
Fax        +1 (520) 838-6214
email:   buchen at bio2.columbia.edu
 
 
 
ICTVdB - The Universal Virus Database
home at Bio2             http://ictvdb.bio2.edu/
mirror in the USA      http://www.ncbi.nlm.nih.gov/ICTVdb/
mirror in the UK         http://www.ictvdb.iacr.ac.uk/
mirror in China          http://ictvdb.mirror.ac.cn/
----- Original Message -----
Sent: Wednesday, September 10, 2003 2:29 PM
Subject: Re: Name for the standard

so far, we have:
 
BioDDS - (Chuck Miller) (spinning off to BDDS -> BDS -> BD -> D ->DELTA ->Jim Croft)
BioDescML - (Chuck Miller)
BioML - (Jim Croft) (taken - see xml.coverpages.org/bioml.html)
BioTaxML - (Chuck Miller)
CAML (Jim Croft) (taken - see http://www.vision.fhg.de/~veenhuis/CAML/)
ExSDD - (Stan Blum)
DescML - (Jim Croft)
PanML (Nick Lander, who will undoubtedly pass the port to Richard Pankhurst)
TDML - (Guillaume Rousse)
TaxDescML - (Guillaume Rousse)
xDELTA - (don't know who to give the port to for this one - maybe Mike Dallwitz)
XSDD - (Bob Morris and Stan Blum)
 
Keep them coming. There hasn't been so much traffic on the list for years!
 
-k
From jrc at ANBG.GOV.AU Wed Sep 10 12:50:22 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 12:50:22 Subject: Name for the standard In-Reply-To: <1063161560.7717.2.camel@ibis> Message-ID: >A little bureaucratic ... You need to get out more often ... tell me about it... :( jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From Chuck.Miller at MOBOT.ORG Wed Sep 10 12:43:34 2003 From: Chuck.Miller at MOBOT.ORG (Chuck.Miller at MOBOT.ORG) Date: Wed, 10 Sep 2003 12:43:34 Subject: Name for the standard Message-ID: How many XML schemas are currently in work within TDWG(Collections, SDD, Economic Botany, Geography, Spatial Data) and GBIF(DADI, ECAT, and DIGIT)? Is there a way to unify them under some more universal schemaML naming approach? This seems like a unique moment in time to start a precedent. The GBIF Biodiversity Data Architecture document is replete with models of interfaces and web services that will all require new XML schemas to be created--each needing a name. GBIF also intends to add schemas for taxa, literature, gazeteers, indexes, providers, etc. Is there a way to be more universal in naming these schemas? The simple names like BioML, TaxML, etc. have already been used and are probably too general anyway. (OmniML?) One approach could be to concatentate dipthongs or something to create a schema of ML names. For example, BioDescML, BioTaxML, BioLitML. Or BioDML, BioTML, BioLML. Or GBIFDescML. Or TDWGDescML. Chuck Miller -----Original Message----- From: Jim Croft [mailto:jrc at ANBG.GOV.AU] Sent: Tuesday, September 09, 2003 8:53 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Re: Name for the standard is DescML taken? jim >jrc> So what is it to be? BioML? > >preoccupied, although there in no strict registration mechanism except >its flavour in namespace. http://xml.coverpages.org/bioml.html ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ ------_=_NextPart_001_01C377C3.0ED257E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Name for the standard

How many XML schemas are currently in work within = TDWG(Collections, SDD, Economic Botany, Geography, Spatial Data) and = GBIF(DADI, ECAT, and DIGIT)?  Is there a way to unify them under = some more universal schemaML naming approach?  This seems like a = unique moment in time to start a precedent. 

The GBIF Biodiversity Data Architecture document is = replete with models of interfaces and web services that will all = require new XML schemas to be created--each needing a name. GBIF also = intends to add schemas for taxa, literature, gazeteers, indexes, = providers, etc. 

Is there a way to be more universal in naming these = schemas?

The simple names like BioML, TaxML, etc. have already = been used and are probably too general anyway. (OmniML?)

One approach could be to concatentate dipthongs or = something to create a schema of ML names.  For example, BioDescML, = BioTaxML, BioLitML.  Or BioDML, BioTML, BioLML.  Or = GBIFDescML.  Or TDWGDescML. 

Chuck Miller  

-----Original Message-----
From: Jim Croft [mailto:jrc at ANBG.GOV.AU]
Sent: Tuesday, September 09, 2003 8:53 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Re: Name for the standard


is DescML taken?

jim

>jrc> So what is it to be?  BioML?
>
>preoccupied, although there in no strict = registration mechanism except
>its flavour in namespace. http://xml.coverpages.org/bioml.html

~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ = www.anbg.gov.au/jrc/ ~

From ghw at ANBG.GOV.AU Wed Sep 10 12:39:22 2003 From: ghw at ANBG.GOV.AU (Greg Whitbread) Date: Wed, 10 Sep 2003 12:39:22 Subject: Name for the standard In-Reply-To: <5.2.1.1.0.20030910115205.02204658@155.187.10.10> Message-ID: A little bureaucratic ... You need to get out more often ... On Wed, 2003-09-10 at 11:52, Jim Croft wrote: > is DescML taken? > > jim > > >jrc> So what is it to be? BioML? > > > >preoccupied, although there in no strict registration mechanism > >except its flavour in namespace. > >http://xml.coverpages.org/bioml.html > > ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ -- Greg Whitbread ANBG/CPBR/ANH From jrc at ANBG.GOV.AU Wed Sep 10 12:10:56 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 12:10:56 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) In-Reply-To: Message-ID: >Similarly, we could honour Richard Pankhurst with PanXML, which should >cover most things we might use it for. or Comprehensive Abstraction Markup Language - CAML or Comprehensive Annotation Markup Language - CAML both pronounced 'camel' ... in honour of its design process... jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From rousse at CCR.JUSSIEU.FR Wed Sep 10 12:01:11 2003 From: rousse at CCR.JUSSIEU.FR (Guillaume Rousse) Date: Wed, 10 Sep 2003 12:01:11 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) In-Reply-To: <5.2.1.1.0.20030910115419.021e07d0@155.187.10.10> Message-ID: Ainsi parlait Jim Croft : > >Similarly, we could honour Richard Pankhurst with PanXML, which should > >cover most things we might use it for. > > or Comprehensive Abstraction Markup Language - CAML > or Comprehensive Annotation Markup Language - CAML > > both pronounced 'camel' ... in honour of its design process... CAML is already a (excellent) programming language, see http://caml.inria.fr/index-eng.html And annotation or abstraction isn't specific to systematics moreover. -- The more work you have to get done, the more likely it is to rain. -- Precipitation Precepts n?1 From jrc at ANBG.GOV.AU Wed Sep 10 11:52:56 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 11:52:56 Subject: Name for the standard In-Reply-To: <20030910.073115.126572349.nozomi@biol.tsukuba.ac.jp> Message-ID: is DescML taken? jim >jrc> So what is it to be? BioML? > >preoccupied, although there in no strict registration mechanism >except its flavour in namespace. >http://xml.coverpages.org/bioml.html ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From nozomi at BIOL.TSUKUBA.AC.JP Wed Sep 10 11:21:52 2003 From: nozomi at BIOL.TSUKUBA.AC.JP (Nozomi Ytow) Date: Wed, 10 Sep 2003 11:21:52 Subject: Name for the standard In-Reply-To: <5.2.1.1.0.20030910115205.02204658@155.187.10.10> Message-ID: jrc> is DescML taken? Not yet, according to an oracle of google. CAML is preoccupied: http://www.vision.fhg.de/~veenhuis/CAML/ http://caml.inria.fr/ Cheers, JMS -- Dr. Nozomi "James" Ytow www.nomencurator.org From nozomi at BIOL.TSUKUBA.AC.JP Wed Sep 10 10:19:55 2003 From: nozomi at BIOL.TSUKUBA.AC.JP (Nozomi Ytow) Date: Wed, 10 Sep 2003 10:19:55 Subject: XDELTA In-Reply-To: <5.2.1.1.0.20030909174634.035bc758@mail.calacademy.org> Message-ID: sblum> This one could be xDELTA (!). See http://www.ldodds.com/delta/ http://freshmeat.net/projects/xdelta/?topic_id=52 Cheers, JMS -- Dr. Nozomi "James" Ytow Institute of Biological Sciences / Gene research center University of Tsukuba Tsukuba, Ibaraki 305-8572 Japan From jrc at ANBG.GOV.AU Wed Sep 10 09:30:32 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 9:30:32 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) Message-ID: messaged from Liz Kolster who is having a few techincal difficulties with her subscription... is the listmaster listening? jim >I give a second on Stan's suggestion, ExSDD! Well Done Stan, >Liz. ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From ldodds at INGENTA.COM Wed Sep 10 09:25:40 2003 From: ldodds at INGENTA.COM (Leigh Dodds) Date: Wed, 10 Sep 2003 9:25:40 Subject: XDELTA In-Reply-To: <20030910.101955.122623282.nozomi@biol.tsukuba.ac.jp> Message-ID: > sblum> This one could be xDELTA (!). > > See > > http://www.ldodds.com/delta/ I don't make any particular claims to the name though, so (re-)use it as you see fit. btw, where would look for an update/docs on the new standard? I'm curious whether any consideration was given to using RDF, which provides a good framework for collating data about resources from multiple sources and using multiple vocabularies. Cheers, L. From nickl at CALM.WA.GOV.AU Wed Sep 10 09:18:49 2003 From: nickl at CALM.WA.GOV.AU (Lander, Nicholas) Date: Wed, 10 Sep 2003 9:18:49 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) Message-ID: > This one could be xDELTA (!). I do like the fact that it would honor one of the pioneers in this field. Don't Dalwitz's papers go back to 1980? In chip-years that's a long time! < Similarly, we could honour Richard Pankhurst with PanXML, which should cover most things we might use it for. Nicholas Lander Western Australian Herbarium (PERTH) From jrc at ANBG.GOV.AU Wed Sep 10 07:58:41 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 7:58:41 Subject: Name for the standard In-Reply-To: <200309092346.18175.rousse@ccr.jussieu.fr> Message-ID: >All domain-specific XML standard are kind of fooML: >MathML >GeoML >So i'd suggest to keep it that way. If the product that we are creating is serious and encompasses all of its domain and I hope it is, I would agree with this fully... So what is it to be? BioML? jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From jrc at ANBG.GOV.AU Wed Sep 10 07:46:51 2003 From: jrc at ANBG.GOV.AU (Jim Croft) Date: Wed, 10 Sep 2003 7:46:51 Subject: Name for the standard In-Reply-To: Message-ID: >How about BIODDS - BIOlogical Descriptive Data Standard? or BDDS... but the data is probably a given in this day and age so we could get away with BDS... .... but most people would probably refer to it as the 'BD standard' so we could shorten it further to BD... and if we do the job properly and at the right level there is no reason why it needs to be restricted to biology, so it could be the D standard... or D or Descriptive Ontology Integrating Taxonomy: DO IT Got it! ... Descriptive Environment for Large Taxonomic Arrays... now, where did I put those pills... jim ~ Jim Croft ~ jrc at anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ From nozomi at BIOL.TSUKUBA.AC.JP Wed Sep 10 07:31:15 2003 From: nozomi at BIOL.TSUKUBA.AC.JP (Nozomi Ytow) Date: Wed, 10 Sep 2003 7:31:15 Subject: Name for the standard In-Reply-To: <5.2.1.1.0.20030910075512.014f8b48@155.187.10.10> Message-ID: jrc> So what is it to be? BioML? preoccupied, although there in no strict registration mechanism except its flavour in namespace. http://xml.coverpages.org/bioml.html Cheers, JMS -- Dr. Nozomi "James" Ytow Institute of Biological Sciences / Gene research center University of Tsukuba Tsukuba, Ibaraki 305-8572 Japan From kevin.thiele at BIGPOND.COM Wed Sep 10 07:10:55 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Wed, 10 Sep 2003 7:10:55 Subject: Name for the standard Message-ID: MessageBest yet - any improvements anyone? ----- Original Message ----- From: Chuck.Miller at MOBOT.ORG To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Wednesday, September 10, 2003 1:10 AM Subject: Re: Name for the standard Kevin, Don't forget biological. How about BIODDS - BIOlogical Descriptive Data Standard? Chuck Miller Missouri Botanical Garden -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Tuesday, September 09, 2003 1:32 AM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Name for the standard I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms? relevant keywords include taxonomy descriptions XML markup language transform there are surely more. Cheers - k --Boundary_(ID_hH3oAbKyBc4pS3cY7qCw8g) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT Message
Best yet - any improvements anyone?
----- Original Message -----
Sent: Wednesday, September 10, 2003 1:10 AM
Subject: Re: Name for the standard

Kevin,
Don't forget biological. 
 
How about BIODDS - BIOlogical Descriptive Data Standard?
 
Chuck Miller
Missouri Botanical Garden
 
 -----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Tuesday, September 09, 2003 1:32 AM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Name for the standard

I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms?
 
relevant keywords include
 
taxonomy
descriptions
XML
markup
language
transform
 
there are surely more.
 
Cheers - k
From rousse at CCR.JUSSIEU.FR Tue Sep 9 23:46:18 2003 From: rousse at CCR.JUSSIEU.FR (Guillaume Rousse) Date: Tue, 9 Sep 2003 23:46:18 Subject: Name for the standard In-Reply-To: <002b01c37716$e91b4450$8da38b90@presario> Message-ID: Ainsi parlait Kevin Thiele : > MessageBest yet - any improvements anyone? All domain-specific XML standard are kind of fooML: MathML GeoML So i'd suggest to keep it that way. >>How about BIODDS - BIOlogical Descriptive Data Standard? Biological Descriptive isn't very adequate here. Are we supposed to describe populations ? genomes ? cells ? Just because bioinformatics usually means molecular biology only shouldn't lead us to the same kind of attitude. BTW, could people please use standard mail practice to quote only what is relevant and insert your replies thereafter ? It makes long thread reading way easier... -- Guillaume Rousse Facings tend to be sewn to the wrong side -- Murphy's Laws of Sewing n?12 From maurobio at ACD.UFRJ.BR Tue Sep 9 22:29:08 2003 From: maurobio at ACD.UFRJ.BR (Mauro J. Cavalcanti) Date: Tue, 9 Sep 2003 22:29:08 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) Message-ID: Stan Blum gravada: > Actually, I liked Jim's "D", or even better still, DELTA. Didn't Mauro > Calvalcanti and others try to establish "Open-DELTA"? This one could be > xDELTA (!). I do like the fact that it would honor one of the pioneers in > this field. Don't Dalwitz's papers go back to 1980? In chip-years that's > a long time! It is actually "Free DELTA" - as DELTA, the format, has since the beginning been conceived as an open standard for data exchange. See the GNU Project at www.gnu.org for clarifications of the terms "free" and "open" software. [], -- + - - - - - - - - - - - - Mauro J. Cavalcanti - - - - - - - - - - - - + | Programa de P?s-Gradua??o em Zoologia | | Museu Nacional/Universidade Federal do Rio de Janeiro | | Quinta da Boa Vista, 20940-040, Rio de Janeiro, RJ, BRASIL | | E-mail: maurobio at acd.ufrj.br | | Homepage: http://www.maurobio.cjb.net | + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + "Life is complex. It consists of real and imaginary parts." From kevin.thiele at BIGPOND.COM Tue Sep 9 22:10:42 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Tue, 9 Sep 2003 22:10:42 Subject: Name for the standard Message-ID: I agree, description is an essential part. But, of course, it doesn't need to be an english-sounding acronym - something Latinate would be nice...k ----- Original Message ----- From: "Guillaume Rousse" To: Sent: Tuesday, September 09, 2003 10:00 PM Subject: Re: Name for the standard Ainsi parlait Kevin Thiele : > Dear Nick - I'd thought of TaxML and had rejected it as too boring - so was > enormously amused to find that tax inspectors think it's just the ticket > :-) Better avoid taxonomic word alone, as this standard address descriptive data only. Something such as TDML, or TaxDescML, for Taxonomic Description Markup Language, would be better IMHO. -- If you take more than your fair share of objectives, you will get more than your fair share of objectives to take -- Murphy's Military Laws n?45 From kevin.thiele at BIGPOND.COM Tue Sep 9 21:51:44 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Tue, 9 Sep 2003 21:51:44 Subject: Name for the standard Message-ID: Dear Nick - I'd thought of TaxML and had rejected it as too boring - so was enormously amused to find that tax inspectors think it's just the ticket :-) Cheers - k ----- Original Message ----- From: Lander, Nicholas To: TDWG-SDD at LISTSERV.NHM.KU.EDU Sent: Tuesday, September 09, 2003 6:24 PM Subject: Re: Name for the standard Kevin What a pity TaXML has been bagged by the Tax Inspectors :-( Nicholas -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Tuesday, 9 September 2003 2:32 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Name for the standard I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms? relevant keywords include taxonomy descriptions XML markup language transform there are surely more. Cheers - k --Boundary_(ID_G6iUFEMGwxcAxg2ixu49fg) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Dear Nick - I'd thought of TaxML and had rejected it as too boring - so was enormously amused to find that tax inspectors think it's just the ticket :-)
 
Cheers - k
----- Original Message -----
Sent: Tuesday, September 09, 2003 6:24 PM
Subject: Re: Name for the standard

Kevin
 
What a pity TaXML has been bagged by the Tax Inspectors :-(
 
Nicholas
-----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Tuesday, 9 September 2003 2:32 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Name for the standard

I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms?
 
relevant keywords include
 
taxonomy
descriptions
XML
markup
language
transform
 
there are surely more.
 
Cheers - k
From sblum at CALACADEMY.ORG Tue Sep 9 18:07:33 2003 From: sblum at CALACADEMY.ORG (Stan Blum) Date: Tue, 9 Sep 2003 18:07:33 Subject: Fwd: Rejected posting to TDWG-SDD@LISTSERV.NHM.KU.EDU (fwd) In-Reply-To: <5.2.1.1.0.20030910092856.02174900@155.187.10.10> Message-ID: >>I give a second on Stan's suggestion, ExSDD! Well Done Stan, >>Liz. Actually, I liked Jim's "D", or even better still, DELTA. Didn't Mauro Calvalcanti and others try to establish "Open-DELTA"? This one could be xDELTA (!). I do like the fact that it would honor one of the pioneers in this field. Don't Dalwitz's papers go back to 1980? In chip-years that's a long time! -Stan From ram at CS.UMB.EDU Tue Sep 9 17:37:48 2003 From: ram at CS.UMB.EDU (Robert A. (Bob) Morris) Date: Tue, 9 Sep 2003 17:37:48 Subject: Name for the standard In-Reply-To: <5.2.1.1.0.20030909142749.00b1d008@mail.calacademy.org> Message-ID: Best yet, but XSDD has the same pronounciation and evokes XML Bob Stan Blum writes: > Date: Tue, 9 Sep 2003 14:34:10 -0700 > From: Stan Blum > To: TDWG-SDD at listserv.nhm.ku.edu > Subject: Re: Name for the standard > > At 07:10 AM 9/10/2003 +1000, Kevin Thiele wrote: > >Best yet - any improvements anyone? > > > ExSDD (pronounced "Ex eS Dee Dee" or "ExcessDD" = exchange structure for > descriptive data > > -Stan (not implying that the standard is excessive ;-) > From kevin.thiele at BIGPOND.COM Tue Sep 9 16:32:25 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Tue, 9 Sep 2003 16:32:25 Subject: Name for the standard Message-ID: I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms? relevant keywords include taxonomy descriptions XML markup language transform there are surely more. Cheers - k --Boundary_(ID_6AoNQgDXsyu0WZnvgFsV3Q) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms?
 
relevant keywords include
 
taxonomy
descriptions
XML
markup
language
transform
 
there are surely more.
 
Cheers - k
From nickl at CALM.WA.GOV.AU Tue Sep 9 16:24:09 2003 From: nickl at CALM.WA.GOV.AU (Lander, Nicholas) Date: Tue, 9 Sep 2003 16:24:09 Subject: Name for the standard Message-ID: Kevin What a pity TaXML has been bagged by the Tax Inspectors :-( Nicholas -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Tuesday, 9 September 2003 2:32 PM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Name for the standard I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms? relevant keywords include taxonomy descriptions XML markup language transform there are surely more. Cheers - k ------_=_NextPart_001_01C376AB.BDAAAA47 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Kevin
 
What a pity TaXML has been bagged by the Tax Inspectors :-(
 
Nicholas
-----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Tuesday, 9 September 2003 2:32 PM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Name for the standard

I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms?
 
relevant keywords include
 
taxonomy
descriptions
XML
markup
language
transform
 
there are surely more.
 
Cheers - k
From sblum at CALACADEMY.ORG Tue Sep 9 14:34:10 2003 From: sblum at CALACADEMY.ORG (Stan Blum) Date: Tue, 9 Sep 2003 14:34:10 Subject: Name for the standard In-Reply-To: <002b01c37716$e91b4450$8da38b90@presario> Message-ID: At 07:10 AM 9/10/2003 +1000, Kevin Thiele wrote: >Best yet - any improvements anyone? ExSDD (pronounced "Ex eS Dee Dee" or "ExcessDD" = exchange structure for descriptive data -Stan (not implying that the standard is excessive ;-) From rousse at CCR.JUSSIEU.FR Tue Sep 9 14:00:38 2003 From: rousse at CCR.JUSSIEU.FR (Guillaume Rousse) Date: Tue, 9 Sep 2003 14:00:38 Subject: Name for the standard In-Reply-To: <002801c376c8$cb0b2d70$b8a48b90@presario> Message-ID: Ainsi parlait Kevin Thiele : > Dear Nick - I'd thought of TaxML and had rejected it as too boring - so was > enormously amused to find that tax inspectors think it's just the ticket > :-) Better avoid taxonomic word alone, as this standard address descriptive data only. Something such as TDML, or TaxDescML, for Taxonomic Description Markup Language, would be better IMHO. -- If you take more than your fair share of objectives, you will get more than your fair share of objectives to take -- Murphy's Military Laws n?45 From Chuck.Miller at MOBOT.ORG Tue Sep 9 10:10:08 2003 From: Chuck.Miller at MOBOT.ORG (Chuck.Miller at MOBOT.ORG) Date: Tue, 9 Sep 2003 10:10:08 Subject: Name for the standard Message-ID: Kevin, Don't forget biological. How about BIODDS - BIOlogical Descriptive Data Standard? Chuck Miller Missouri Botanical Garden -----Original Message----- From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM] Sent: Tuesday, September 09, 2003 1:32 AM To: TDWG-SDD at LISTSERV.NHM.KU.EDU Subject: Name for the standard I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms? relevant keywords include taxonomy descriptions XML markup language transform there are surely more. Cheers - k ------_=_NextPart_001_01C376E4.751EF510 Content-Type: text/html; charset="iso-8859-1" Message
Kevin,
Don't forget biological. 
 
How about BIODDS - BIOlogical Descriptive Data Standard?
 
Chuck Miller
Missouri Botanical Garden
 
 -----Original Message-----
From: Kevin Thiele [mailto:kevin.thiele at BIGPOND.COM]
Sent: Tuesday, September 09, 2003 1:32 AM
To: TDWG-SDD at LISTSERV.NHM.KU.EDU
Subject: Name for the standard

I'm trying to write an introduction and primer for the SDD standard, and it strikes me that we don't actually have a name for the thing we're trying to create. SDD is short for the Structure of Descriptive Data, and is an acronym only for the subgroup, not for the standard. Anyone out there with a facility with acronyms?
 
relevant keywords include
 
taxonomy
descriptions
XML
markup
language
transform
 
there are surely more.
 
Cheers - k
From dewey at KU.EDU Mon Sep 8 11:32:45 2003 From: dewey at KU.EDU (Rob Dewhirst) Date: Mon, 8 Sep 2003 11:32:45 Subject: Important change to TDWG-SDD mailing list Message-ID: TDWG-SDD Subscribers: The email and web addresses for this list have changed, as of this message. To submit messages to the TDWG-SDD list for others to read, send them to TDWG-SDD at LISTSERV.NHM.KU.EDU. The new web address for viewing archives and managing your subscription is: To send commands to the LISTSERV (unsubscribe, etc) send them to LISTSERV at LISTSERV.NHM.KU.EDU No action needs to be taken by you except to send all future submissions to the new email address TDWG-SDD at LISTSERV.NHM.KU.EDU If you need further clarification, please reply to me directly. Rob Dewhirst Listserv Admin KU Biodiversity Research Institute robd at ku.edu From Steve at Wed Sep 3 17:22:12 2003 From: Steve at (Steve at ) Date: Wed, 3 Sep 2003 17:22:12 Subject: Special states Message-ID: Yes, Kevin's interpretation is the same as the way I see it. But this is only a small part of what Gregor presented in his last email. I really don't understand where all the other stuff fits into this. I get the feeling Gregor has designed the entire system and is now feeding us little bits at a time (currently "special states"). When we suggest alternatives Gregor seems to respond "No, that won't work because all the rest of it will break". I find this very frustrating as we seem to be going around in circles. I don't know what the solution is, but I'm pretty sure this isn't it. Steve ------_=_NextPart_001_01C371EC.18133DF1 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message
Yes, Kevin's interpretation is the same as the way I see it.  But this is only a small part of what Gregor presented in his last email.  I really don't understand where all the other stuff fits into this.  I get the feeling Gregor has designed the entire system and is now feeding us little bits at a time (currently "special states").  When we suggest alternatives Gregor seems to respond "No, that won't work because all the rest of it will break".  I find this very frustrating as we seem to be going around in circles.  I don't know what the solution is, but I'm pretty sure this isn't it.
 
Steve
 
 
From kevin.thiele at BIGPOND.COM Wed Sep 3 15:12:33 2003 From: kevin.thiele at BIGPOND.COM (Kevin Thiele) Date: Wed, 3 Sep 2003 15:12:33 Subject: Special states Message-ID: Let me see if I have this right: Gregor wants to have a set of 'special states', globally applicable, that one can use to "score" the fact that e.g. one is not going to score a particular taxon x character: Leaf shape ovate elliptic obovate not scored (won't be scored) not scored (will score later) not scored (can't be coded) {note- these "special states" won't actually appear in the character list like this - they'll be defined separately, but the effect will be the same} Taxon x: code as "not scored (will score later)" Steve Shattuck wants instead to have a modifying flag that can be set for the taxon x character cell in the data matrix, which flags that this cell is not going to be scored. Leaf shape ovate elliptic obovate Taxon x: not coded (flagged as "will score later") It strikes me that 1. in some ways these two suggestions are very similar (whether the thing goes into the taxon x character cell or is attached to it is immaterial from a data point of view). 2. the real difference is in where their values are defined. Gregor's "special states" are defined in the instance document, while Steve's flags are (I assume) defined in the schema. Does this make a difference? Cheers - k --Boundary_(ID_QWCMY/60gUPVKM6Hx77hvg) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Let me see if I have this right:
 
Gregor wants to have a set of 'special states', globally applicable, that one can use to "score" the fact that e.g. one is not going to score a particular taxon x character:
 
Leaf shape
    ovate
    elliptic
    obovate
    not scored (won't be scored)
    not scored (will score later)
    not scored (can't be coded)
 
{note- these "special states" won't actually appear in the character list like this - they'll be defined separately, but the effect will be the same}
 Taxon x: code as "not scored (will score later)"
 
Steve Shattuck wants instead to have a modifying flag that can be set for the taxon x character cell in the data matrix, which flags that this cell is not going to be scored.
 
Leaf shape
    ovate
    elliptic
    obovate
 Taxon x: not coded (flagged as "will score later")
 
It strikes me that
1. in some ways these two suggestions are very similar (whether the thing goes into the taxon x character cell or is attached to it is immaterial from a data point of view).
2. the real difference is in where their values are defined. Gregor's "special states" are defined in the instance document, while Steve's flags are (I assume) defined in the schema.
 
Does this make a difference?
 
Cheers - k
From Steve at Wed Sep 3 13:05:41 2003 From: Steve at (Steve at ) Date: Wed, 3 Sep 2003 13:05:41 Subject: Special states: stepping back to the generalized character definition and coding model Message-ID: I'm afraid this doesn't make much sense to me so I'll have to let the rest of you sort it out. When you come up with a solution we'll see if we can implement it in the morphology section of BioLink. Sorry about that, Steve Steve Shattuck CSIRO Entomology steve.shattuck at csiro.au -----Original Message----- From: Gregor Hagedorn To: TDWG-SDD at USOBI.ORG Sent: 9/2/2003 9:36 PM Subject: Special states: stepping back to the generalized character definition and coding model Steve Shattuck wrote: > For "Special States", another way to look at it is that this doesn't > really relate to a character but to the coding of a given character > for a given taxon. It is really the status of the coding of that > character for a taxon. Instead of storing it as a part of the > character (by creating a new state for the character) why not create a > new element for this information and attach it to the taxon by > character intersection (or "cell", or "taxon description"). Call it > "Coding Status" with an enumerated list of "Coded" (meaning the taxon > has been coded for this character), "Not yet coded" (meaning it will > be coded when I get around to it), "Not to be coded" (meaning it can > be coded but I not going to) and "Can't be coded". Then add a text > attribute to this element to allow an explanation of what's going on > for the coding of this character for this taxon ("I haven't yet coded > this character because suitable material of this taxon is currently > unavailable"). This would seem to meet the needs of computer > processing (through a defined, machine-readable enumerated list), > extensibility (by supporting additions to this list such as "Coded but > unreliable") and a full, human-readable explanation of what's going on > (in the text comment). I agree on the need to add an option for annotation text and to keep the "coding status/missing data indicator" list relatively short. I also can basically accept your list, except that the last example usually applies to a coded state, not the character, i.e. one state may be coded unreliably, the other ok. Currently we propose to use uncertainty modifiers (probably, perhaps, etc.) for this case. This is similar to the "by-misinterpretation" mechanism originally proposed by Kevin, now proposed in SDD to be handled through a coding modifier on an existing state. General question to all: Any examples where having uncertainty/unreliability should apply to the entire character rather than to the states, i.e. where if implemented as a modifier this would always have to be added to all states? I wonder whether the "Coded" option is redundant. This should be evident if no other CodingStatus is present and data are coded. Except for redundancy (and therefore the need to enforce a rule that "Coded" requires categorical or numerical data to be indeed coded; else it would be a "lie"), I have no problem with it. > We need to take a step back before we can move forward. I am quite willing to take that step back. Let my try to explain the reasoning why I think it is a good idea to generalize "coding status/missing data indicators" to be handled akin to categorical states: The current SDD model for categorical characters is: 1. It is possible to defined shared state sets globally. Example: color-states: red, green, blue, ... 2. The character definition list allows to define a) local states b) refer to 0 to several shared state sets (= inherit them) alpha) as a whole set beta) restricting the inheritance to states specified in an enumeration (Note: if the shared definition is expanded, alpha automatically inherits the new character, beta not) 3. The item descriptions always refers to states defined in the character definition list, never to global/shared definitions directly. ---------- I view this as a structural generalization, and tried to model statistical parameters like min/mean/max/s.d./s.e./sample size etc. accordingly: 1. Global measures define the semantics of for the first version of SDD perhaps 30 parameters. In the first SDD version to keep it simply, the list would not yet be exandable, but it is modeled such that it is easily expandable later on. Statistical parameters already carry descriptive attributes that allows for most purposes to interpret them without referring the state code. 2. Within a numeric character in Terminology: character definition it is possible to select only specific parameters. 3. in the item description only parameters selected by the designer of the terminology can be used. ---------- Now in that admittedly confusing "special state" paper from March I tried to figure out whether we should really (as implemented in Brazil) use this same generalization for "special states" or "coding status/missing data indicators" 1. A shared state set defining special states with fixed codes (i.e. not user expandable in the first SDD version, but since all information is already in the data, easily expandable in future versions. 2. Within a character in Terminology: define which of these status/indicator states are to be enabled for a given character. 3. The item descriptions always refers to states defined in the character definition list, never to global/shared definitions directly. ---------- You propose to handle them separately. What would be the advantages and disadvantages? Please add to the list if I overlook something: Advantages: a) avoid confusion in the definition of the terminology between normal categorical states and "coding status/missing data indicators". These things are structurally related in that both are specific to a given character when the character is coded, but yield information from different (although non-overlapping!) knowledge domains, viz. biology for character states and knowledge meta data for "coding status/missing data indicators". Disadvantages: a) the list is fixed and changes to the software are required if the next SDD version extends another coding status. b) reports can be generated only in the language of the program. If the data are in German, but the software is English, the software must add a special feature to translate the reporting of this information into German. c) when collating/compiling data from children, "coding status/missing data indicators" must be handled identical with normal data. That means especially, that the "coding status/missing data indicators" must support multiple concurrent states: Item 1, character 1: state 1 Item 2, character 1: coding status "excluded/scoped out" Item 3, character 1: coding status: "Not applicable" if these 3 items are species within a genus, the compiled genus description would be: genus item, character 1: state 1, or "excluded/scoped out", or "Not applicable" In which type of report this information would be made visible is another question, i.e. a difference between the types of states remains. However, it would be clearly inappropriate to summarize this into just "state 1". Note that I was especially delighted to see that probably the entire question of character scoping automatically falls into place, without any additional structural complexity, if "scoped out" can be inherited as a default value from the taxonomic parents! This is my only excuse that I included preliminary notes on the issue of default states in the special state paper, which made the paper a lot more confusing! --------------- This is my list, and on the basis of this list I would prefer to keep the structural generalization, rather than implementing a completely different mechanism. However, it is definitely good to take that step back and rethink this. To all: please respond if I currently overlook issues here! However, even if "coding status/missing data indicators" are handled analogous to shared categorical states and statistical parameters, this does not mean, they have to be in one xml element. Whether a database would store them in one table (would make sense to me) is quite independent of this. So, we could have (as an example, not necessarily the acutal schema): Terminology SharedStates StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates CharacterDefinition StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates Description Character keyref=... StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates ---- Or: Terminology SharedStates StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates CharacterDefinition Description Character keyref=... ------ Which is preferable? ------ Technical aside regarding the second version: I still don't fully understand the implications of using the latter subtyping ("substitution group"?) version in regard to key/keyref constraints. One thing is: is it possible to force the schema that xs:type is required? It seems that this is only optional, and that if it is not present it is up to the consuming application to figure out which subtype is acutally used. However, whereas the CharacterDefininition subtypes (StatisticalParametersDef) differ in their complex content and can be recognized, the StatisticalParameterRef do not differ EXCEPT in the keyref constraint. My guess is that therefore the above does not work in xml schema, but please comment if you have insight on this! Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at 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! From G.Hagedorn at BBA.DE Wed Sep 3 12:55:57 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Wed, 3 Sep 2003 12:55:57 Subject: Special states In-Reply-To: <662FF5A611597C41987B05E11DFE359226CBDF@exact3-cbr.act.csiro.au> Message-ID: Steve wrote: > Yes, Kevin's interpretation is the same as the way I see it. But this > is only a small part of what Gregor presented in his last email. I > really don't understand where all the other stuff fits into this. I > get the feeling Gregor has designed the entire system and is now > feeding us little bits at a time (currently "special states"). When > we suggest alternatives Gregor seems to respond "No, that won't work > because all the rest of it will break". I find this very frustrating > as we seem to be going around in circles. I don't know what the > solution is, but I'm pretty sure this isn't it. First: I do not have the solution and am feeding it! I am searching it together with you. On the other hand, I have some vague ideas what may work, and naturally these ideas influence me in the direction I am going. I tried to be very serious in stepping back and explaining why I consider it a progress that made in the Brazil discussion: The general sorting out of how to treat categorical states, numerical statistical parameter, and coding states in a model that supports extension in future SDD versions and multiple languages. Note that text characters or states and numerical value lists are not yet touched at all. Steve: can you be more specific about what "doesn't make much sense" to you? I often feel that my communication skills are inadequate. However, I really did not want to give the impression in the "stepping back to the generalized character definition..." posting "No, that won't work because all the rest of it will break". I truly welcome proposals that show alternative ways that are easier to grasp. However, the problems are connected. This is not specific to SDD. For example, you cannot talk in DELTA about character dependency and ignore how characters and states are modeled. The "Special states" which I am very grateful you criticized in so much detail, is embedded in the context of the Brazil proposal. In "stepping back" I tried to summarize the relevant context and throw the discussion open whether this should be changed. Steve, we need much more input and feedback from you and others. Tell me what do you propose to do that it is less frustrating? Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at 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! From G.Hagedorn at BBA.DE Wed Sep 3 12:55:06 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Wed, 3 Sep 2003 12:55:06 Subject: Special states In-Reply-To: <024601c371db$7db97af0$7ea38b90@presario> Message-ID: Kevin wrote: > It strikes me that > 1. in some ways these two suggestions are very similar (whether the > thing goes into the taxon x character cell or is attached to it is > immaterial from a data point of view). 2. the real difference is in > where their values are defined. Gregor's "special states" are defined > in the instance document, while Steve's flags are (I assume) defined > in the schema. > Does this make a difference? Two differences I see: a) The Brazil proposal allows the project designer to constrain which "missing data indicators = special states = CodingStatus" are available within a given character while scoring this character in an item description. This is why the "special states" occur indeed within a character definition: They are not defined there, but by referring to the global/shared definition level, they are _enabled_. What I find nice is that this uses the same kind of mechanism the inheritance of shared state sets uses: either inherit the full set for a given character, or restrict it to certain states. BUT: it is not necessary to do it like this. This is truly just my private attempt to get some structural generalization into the model. Also: I tried to raise the question of how important it is to be able to enable/disable certain special states. I find it useful if the list of special states has, say 5 options and you want to produce a web interface, but I am uncertain whether it is worth it. If it is a side-effect of having a structurally simple model, I welcome it, but otherwise I can just as well live with "missing data indicators = special states = CodingStatus" always enabled for all characters if we can reach a consensus about that. b) Second difference: special states do need a label/wording whenever they are reported. To achieve multilinguality this wording must be user-definable (i.e. by the designer of the project/the terminology). To me this points into the direction of putting it into the xml instance document, handling it like the state definitions. Again other solutions are possible. I am not fully happy with the way the Brazil model works, and it obviously confuses people. Perhaps one of the confusing things is that 1. SDD makes definitions 2. Project designer makes global/shared definitions 3. Project designer creates characters, referring to shared definitions (point 2 above), inheriting the properties of 0-several shared definitions, PLUS in the case of categorical states defines local states (but in the Brazil model not in the case of "statical parameters = global measures" or "special states") 4. The scientist using a designed project scores the descriptions based on the decisions of the designer of the terminology. Because SDD is able to constrain things through the schema, this 4 layer model is acutally NOT represented in the Brazil model (and the model could perhaps be made more understandable by changing that? I really don't know!). Instead, SDD definitions like "Special states" (or whatever better to call them) and "statistical parameters" are treated like point 2, but the designer has only limited choice. The xml schema requires the designer to have a given number of shared definitions for special states and statistical parameters present in that part. However, this contraction allows the designer to add labels to these required definition in new languages. I currently do not see a better solution for this, but I welcome any suggestion! Can anybody help me in making the explanations above or the questions poised in "stepping back" more intelligable? Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at 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! From G.Hagedorn at BBA.DE Tue Sep 2 13:36:54 2003 From: G.Hagedorn at BBA.DE (Gregor Hagedorn) Date: Tue, 2 Sep 2003 13:36:54 Subject: Special states: stepping back to the generalized character definition and coding model In-Reply-To: <662FF5A611597C41987B05E11DFE359226CBDE@exact3-cbr.act.csiro.au> Message-ID: Steve Shattuck wrote: > For "Special States", another way to look at it is that this doesn't > really relate to a character but to the coding of a given character > for a given taxon. It is really the status of the coding of that > character for a taxon. Instead of storing it as a part of the > character (by creating a new state for the character) why not create a > new element for this information and attach it to the taxon by > character intersection (or "cell", or "taxon description"). Call it > "Coding Status" with an enumerated list of "Coded" (meaning the taxon > has been coded for this character), "Not yet coded" (meaning it will > be coded when I get around to it), "Not to be coded" (meaning it can > be coded but I not going to) and "Can't be coded". Then add a text > attribute to this element to allow an explanation of what's going on > for the coding of this character for this taxon ("I haven't yet coded > this character because suitable material of this taxon is currently > unavailable"). This would seem to meet the needs of computer > processing (through a defined, machine-readable enumerated list), > extensibility (by supporting additions to this list such as "Coded but > unreliable") and a full, human-readable explanation of what's going on > (in the text comment). I agree on the need to add an option for annotation text and to keep the "coding status/missing data indicator" list relatively short. I also can basically accept your list, except that the last example usually applies to a coded state, not the character, i.e. one state may be coded unreliably, the other ok. Currently we propose to use uncertainty modifiers (probably, perhaps, etc.) for this case. This is similar to the "by-misinterpretation" mechanism originally proposed by Kevin, now proposed in SDD to be handled through a coding modifier on an existing state. General question to all: Any examples where having uncertainty/unreliability should apply to the entire character rather than to the states, i.e. where if implemented as a modifier this would always have to be added to all states? I wonder whether the "Coded" option is redundant. This should be evident if no other CodingStatus is present and data are coded. Except for redundancy (and therefore the need to enforce a rule that "Coded" requires categorical or numerical data to be indeed coded; else it would be a "lie"), I have no problem with it. > We need to take a step back before we can move forward. I am quite willing to take that step back. Let my try to explain the reasoning why I think it is a good idea to generalize "coding status/missing data indicators" to be handled akin to categorical states: The current SDD model for categorical characters is: 1. It is possible to defined shared state sets globally. Example: color-states: red, green, blue, ... 2. The character definition list allows to define a) local states b) refer to 0 to several shared state sets (= inherit them) alpha) as a whole set beta) restricting the inheritance to states specified in an enumeration (Note: if the shared definition is expanded, alpha automatically inherits the new character, beta not) 3. The item descriptions always refers to states defined in the character definition list, never to global/shared definitions directly. ---------- I view this as a structural generalization, and tried to model statistical parameters like min/mean/max/s.d./s.e./sample size etc. accordingly: 1. Global measures define the semantics of for the first version of SDD perhaps 30 parameters. In the first SDD version to keep it simply, the list would not yet be exandable, but it is modeled such that it is easily expandable later on. Statistical parameters already carry descriptive attributes that allows for most purposes to interpret them without referring the state code. 2. Within a numeric character in Terminology: character definition it is possible to select only specific parameters. 3. in the item description only parameters selected by the designer of the terminology can be used. ---------- Now in that admittedly confusing "special state" paper from March I tried to figure out whether we should really (as implemented in Brazil) use this same generalization for "special states" or "coding status/missing data indicators" 1. A shared state set defining special states with fixed codes (i.e. not user expandable in the first SDD version, but since all information is already in the data, easily expandable in future versions. 2. Within a character in Terminology: define which of these status/indicator states are to be enabled for a given character. 3. The item descriptions always refers to states defined in the character definition list, never to global/shared definitions directly. ---------- You propose to handle them separately. What would be the advantages and disadvantages? Please add to the list if I overlook something: Advantages: a) avoid confusion in the definition of the terminology between normal categorical states and "coding status/missing data indicators". These things are structurally related in that both are specific to a given character when the character is coded, but yield information from different (although non-overlapping!) knowledge domains, viz. biology for character states and knowledge meta data for "coding status/missing data indicators". Disadvantages: a) the list is fixed and changes to the software are required if the next SDD version extends another coding status. b) reports can be generated only in the language of the program. If the data are in German, but the software is English, the software must add a special feature to translate the reporting of this information into German. c) when collating/compiling data from children, "coding status/missing data indicators" must be handled identical with normal data. That means especially, that the "coding status/missing data indicators" must support multiple concurrent states: Item 1, character 1: state 1 Item 2, character 1: coding status "excluded/scoped out" Item 3, character 1: coding status: "Not applicable" if these 3 items are species within a genus, the compiled genus description would be: genus item, character 1: state 1, or "excluded/scoped out", or "Not applicable" In which type of report this information would be made visible is another question, i.e. a difference between the types of states remains. However, it would be clearly inappropriate to summarize this into just "state 1". Note that I was especially delighted to see that probably the entire question of character scoping automatically falls into place, without any additional structural complexity, if "scoped out" can be inherited as a default value from the taxonomic parents! This is my only excuse that I included preliminary notes on the issue of default states in the special state paper, which made the paper a lot more confusing! --------------- This is my list, and on the basis of this list I would prefer to keep the structural generalization, rather than implementing a completely different mechanism. However, it is definitely good to take that step back and rethink this. To all: please respond if I currently overlook issues here! However, even if "coding status/missing data indicators" are handled analogous to shared categorical states and statistical parameters, this does not mean, they have to be in one xml element. Whether a database would store them in one table (would make sense to me) is quite independent of this. So, we could have (as an example, not necessarily the acutal schema): Terminology SharedStates StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates CharacterDefinition StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates Description Character keyref=... StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates ---- Or: Terminology SharedStates StatisticalParameters MissingDataIndicators / or CodingStatus CategoricalStates CharacterDefinition Description Character keyref=... ------ Which is preferable? ------ Technical aside regarding the second version: I still don't fully understand the implications of using the latter subtyping ("substitution group"?) version in regard to key/keyref constraints. One thing is: is it possible to force the schema that xs:type is required? It seems that this is only optional, and that if it is not present it is up to the consuming application to figure out which subtype is acutally used. However, whereas the CharacterDefininition subtypes (StatisticalParametersDef) differ in their complex content and can be recognized, the StatisticalParameterRef do not differ EXCEPT in the keyref constraint. My guess is that therefore the above does not work in xml schema, but please comment if you have insight on this! Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn at 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! From Steve at Mon Sep 1 16:42:54 2003 From: Steve at (Steve at ) Date: Mon, 1 Sep 2003 16:42:54 Subject: Special states: What term to use instead? Message-ID: It's good to see you back Gregor, most welcome. For "Special States", another way to look at it is that this doesn't really relate to a character but to the coding of a given character for a given taxon. It is really the status of the coding of that character for a taxon. Instead of storing it as a part of the character (by creating a new state for the character) why not create a new element for this information and attach it to the taxon by character intersection (or "cell", or "taxon description"). Call it "Coding Status" with an enumerated list of "Coded" (meaning the taxon has been coded for this character), "Not yet coded" (meaning it will be coded when I get around to it), "Not to be coded" (meaning it can be coded but I not going to) and "Can't be coded". Then add a text attribute to this element to allow an explanation of what's going on for the coding of this character for this taxon ("I haven't yet coded this character because suitable material of this taxon is currently unavailable"). This would seem to meet the needs of computer processing (through a defined, machine-readable enumerated list), extensibility (by supporting additions to this list such as "Coded but unreliable") and a full, human-readable explanation of what's going on (in the text comment). I think this "problem" is directly related to a number of issues I raised in early March and Kevin expanded on in his email of 21 March. Until those issues are addressed I don't think we'll make any real progress and we will continue to be distracted by the detail while the bigger picture and ultimate goals of this project are overlooked. We need to take a step back before we can move forward. Thanks, Steve Steve Shattuck CSIRO Entomology Steve.shattuck at csiro.au