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Re: update on names
by Peter Stevens 17 Sep '03

17 Sep '03

>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/>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)

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Re: Name for the standard
by Jim Croft 17 Sep '03

17 Sep '03

>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(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: Name for the standard
by Kevin Thiele 17 Sep '03

17 Sep '03

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" <deepreef(a)BISHOPMUSEUM.ORG> To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> 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

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Re: Name for the standard
by Julian H 17 Sep '03

17 Sep '03

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 <http://xml.coverpages.org/xci.html>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

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Re: Name for the standard
by Jim Croft 17 Sep '03

17 Sep '03

>In the note below and in previous notes, there seems to be an emphasis >on SDD in the contect of "taxonomy"; but wouldn't it be more appropriate to >place the emphasis more in the context of biological objects (e.g., >specimens), rather than abstract concepts (taxa)? you are right, in part. Although the SDD activity is undertaken by taxonomists, it extends beyond the core of taxonomy and nomenclature to delineation and description of the objects themselves (taxa mostly, to a lesser extent specimens). In fact, existing programs in this area such as DELTA and LUCID handle nomenclature and taxonomy data extremely poorly... >Even though the >descriptive data may be applied directly to taxon concepts without an >explicit reference to specific specimens/objects, ultimately the characters >themselves that are being described are attached to a physical organism -- >whether or not the specific physical organism is explicitly identified, or >merely implied. we we may be getting into the philosophical realm here... Our Rainforest Key project actually scored recorded individual specimens for each taxon... most DELTA and LUCID implementations amalgamate and abstract this to the level of taxon or taxon concept and score at this level... of course, SDD should ideally handle both approaches... >Ultimately, this is about a Standard for Structured Data to Describe >Biological Objects -- isn't it? I think that is what we are talking about... you could leave out 'structured data' too and it will still make sense... jim ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: Name for the standard
by Chuck.Miller＠MOBOT.ORG 17 Sep '03

17 Sep '03

>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@ANBG.GOV.AU] Sent: Tuesday, September 16, 2003 10:30 PM To: TDWG-SDD(a)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(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Fwd: Re: simple instance
by Jim Croft 17 Sep '03

17 Sep '03

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" <G.Hagedorn(a)bba.de> >From: Jim Croft <jrc(a)anbg.gov.au> >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 <leaves><simple/></leaves> 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 <html> 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(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: Name for the standard
by Kevin Thiele 17 Sep '03

17 Sep '03

Do people in general think that we need to specify that we're working in the taxonomic domain - something that the name SDD doesn't - or can we be extremely general. Perhaps it's the case that SDD will be able to be used for descriptions outside the taxonomic domain, and we should embrace this (whether anyone else embraces us is another matter entirely) - k ----- Original Message ----- From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> Sent: Tuesday, September 16, 2003 10:53 PM Subject: Re: Name for the standard > Kevin wrote: > > yes, I agree that SDD (Standard for Descriptive Data) would do - I was > > just looking for something a little more exciting. Cheers - k > > .... I disagree :-) that "Standard for Descriptive Data"-standard > would do, I therefore propose "Structured Descriptive Data"-standard. > I absolutely agree with you about searching something more exciting. > > There is a general name grabbing of most-general and all-encompassing > names (like BioML, which is really indecent...). Since we think about > the generalization from Biological to other collected objects all the > time and try to avoid too specifically biological jargon, we actually > have some justification following suit and grab > > DescriptionML ? > > (for which Google returns 1 hit, which interestingly does not contain > the term, I even checked the html source...) > > Gregor > ---------------------------------------------------------- > Gregor Hagedorn (G.Hagedorn(a)bba.de) > Institute for Plant Virology, Microbiology, and Biosafety > Federal Research Center for Agriculture and Forestry (BBA) > Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 > 14195 Berlin, Germany Fax: +49-30-8304-2203 > > Often wrong but never in doubt!

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Re: Name for the standard
by P. Bryan Heidorn 17 Sep '03

17 Sep '03

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

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

16 Sep '03

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

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