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Re: SDD standard - kinds of description
by Stan Blum 20 Jul '00

20 Jul '00

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Original charge and URLs to other docs
by Stan Blum 20 Jul '00

20 Jul '00

At 09:17 AM 7/20/00 +1000, Kevin Thiele wrote: >Bob Allkin, > >Gregor Hagedorn's original posting to the list explains the brief we >received from TDWG. That would be a good starting point - you can get it >(and all previous list correspondence) downloaded by sending the >appropriate message to the server {can anyone tell Bob what that message is?} There is a welcome message by Gregor Hagedorn at http://usobi.org/archives/cgi-bin/wa.exe?A1=ind9911d&L=tdwg-sdd#19 You can see a number of other important (organizing) messages from Gregor if you go to the root of the SDD archive ( http://usobi.org/archives/tdwg-sdd.html ), then to "November 1994, Week 4" at the bottom, then select browse by author, etc... Also see the TDWG page for this subgroup http://www.tdwg.org/sddhome.html -Stan

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Re: Expression of continuing interest
by Susan B. Farmer 20 Jul '00

20 Jul '00

I'm still here as well. Haven't read the attached file yet -- teaching general botany in the summer is a Real Trip. Susan Susan Farmer sfarmer(a)goldsword.com Botany Department, University of Tennessee http://www.goldsword.com/sfarmer/Trillium

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Re: Expression of continuing interest
by John C. Turnbull 20 Jul '00

20 Jul '00

I'm still here and ready to contribute in any way I can. ----- Original Message ----- From: "Kevin Thiele" <kevin.thiele(a)PI.CSIRO.AU> To: <TDWG-SDD(a)USOBI.ORG> Sent: Tuesday, July 18, 2000 1:12 PM Subject: Expression of continuing interest > To: other contributors on the SDD list > > Yes, I'm still out here, I'm a taxonomist and I'm still interested in > contributing to the requirements analysis. > > <Please reply to this message to register that you're still out there> >

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Re: Expression of continuing interest
by Donovan Sharp 20 Jul '00

20 Jul '00

I'm still here Donovan Kevin Thiele wrote: > To: other contributors on the SDD list > > Yes, I'm still out here, I'm a taxonomist and I'm still interested in > contributing to the requirements analysis. > > <Please reply to this message to register that you're still out there>

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Re: Expression of continuing interest
by Bryan Heidorn 20 Jul '00

20 Jul '00

Just a couple of brief comments. I agree as well with most of Starts thoughtful comments. It is even worth putting into my keep folder on this issue to review whenever I make the mistake of thinking I've covered all of the bases. The other comment is that I don't think that it is useful to think of this as a standard that data must be stored in by anyone. It is better thought of as a gateway like Z39.50 (and ZBIG). Your data on your computer stays in whatever format is best for your application, it is only when you want to share that data that you provide the "standard" view of the data. It is also not necessary that we specify any particular set of characters or character states. What be need is a mechanism for having one computer (agent 1) ask the other computer (Agent 2), "Hey you, what data do you have?" Reply from Agent 2, "I have plant morphology data, some specimens with images,... and I can give them to you in Format X. Want 'um?" Agent 1, "Sure, what characters to you have encoded?" Agent 2, "I have Angiosperm Macrobiology set 1 Version 1.2 and Microbiology Set 2 Version 13.3." Agent 1, "I'll have the Angiosperm set, for species X, Y and Z. Thank you." Agent 2, "<taxonid>....</taxonid><morphology><plantheightmaximun units=m Authority=Caldwell98>5</plantheightmaximum><plantheightminimum units=m Authority=Caldwell98>2</plantheightminimum>....</morphology>..... There needs to be a little authorization conversation between the computers before this to make sure that Agent 1 had access to all of the data that agent 2 can provide... This sort of thing is done in Z39.50 and other protocols all of the time. SpeciesAnalyst does it for some data. The format of the data on Agent 2's disk is anything at all, an MySQL database, flat files, whatever. It is just the gateway software that knows the standard. I assume that for now what we need to focus on is providing a framework so that some Angiosperm expert could create a "sub-standard" definition "Angiosperm Macrobiology set 1 ". Right? Having said that, I am off for the lake county of Michigan. Back in a week. I hope you all have this figured out by the time I return. Cheers, Bryan -- -------------------------------------------------------------------- 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

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Re: SDD standard - purpose
by Kevin Thiele 20 Jul '00

20 Jul '00

Bob Allkin, Gregor Hagedorn's original posting to the list explains the brief we received from TDWG. That would be a good starting point - you can get it (and all previous list correspondence) downloaded by sending the appropriate message to the server {can anyone tell Bob what that message is?} This is my take on your questions. >- who will use this, Potentially anyone who needs to capture and manage descriptive data, but this will have to wait on development of appropriate tools. Initially, and in a more limited scope, it will serve as an interchange format between existing programs e.g. Lucid, DELTA, XID etc (assuming the developers of those programs come to the party and write I/O functions. >- to store what types of information I think initially we need to be flexible enough to be able to store any type of morphological or anatomical data. Some chemical descriptive data could fit in here as well, at least simple "chemical A: present/absent" statements. I suppose the main thing we seem to be leaving out for the time being is genome, sequence and protein data - too specialised for our present purpose? >- for what kinds of description (for identification as with DELTA) for >cladistics, for publishing to other audiences Initially, I think we should aim at descriptions and interactive ID. This is a problematical area, that I think should be explored more. The idea of massaging one data file into two or more different products (e.g. natural-language and keys) is very attractive, but surprisingly problematical, since the structure of data needed for the two purposes is often subtly different. Of course, doing just this is the basis of the DELTA system, but we may need to do it in a more sophisticated way. As for cladistics, this is more problematical. In the early days of the list there was much enthusiasm about our standard subsuming NEXUS. I think I'm right in thinking that the NEXUS people thought this was a bit of a joke - NEXUS is widely used, is widely supported and seems to be highly successful, while ours doesn't even exist yet! The problems inherent in the multiple-product model become even more alarming when you try to maintain one data file for both description/identification and phylogenetic analysis. My personal view is that we should leave cladistics out of the scope at least for the time being. Anyone else out there want to comment on this? >- to do what (for exchanging data between different databases, as a public >format upon which independent applications will run). Initially, as an interchange format for existing applications, but if it works, hopefully a new generation of applications will flow. >I'd appreciate it if someone could point me at a summary of your previous >deliberations on this. Other contributors - is this a fair summary? Cheers - k

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Re: Expression of continuing interest
by Kevin Thiele 20 Jul '00

20 Jul '00

At 06:58 PM 18/7/00 -0500, Bryan Heidorn wrote: >I do not see how we can avoid mixing data in a treatment. I'll need to go back >and reread Bob's comments on that. Generally I don't see how we can have a >standard that requires all fields to be reduced to finite states. Some things >will just need to be unprocessed (by the computer) text. You mean like the "Text" character type of DELTA?, or unparsed textual notes attached to characters/states/taxa/data items? Cheers - k

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Re: SDD standard - kinds of description
by Kevin Thiele 20 Jul '00

20 Jul '00

At 11:56 PM 18/7/00 -0300, Bob Allkin wrote: >Kevin >your document makes interesting reading. Further to my earlier email on >purpose I see how morphological descriptive data (such as DELTA handles - >which may well be the primary aim) would fit within your described format. > >IF your aim were for this format also to serve for: > >1) description of distribution (a hierarchical descriptor - with attributes >attached to each substate such as native/introduced/etc) > >2) description of use [e.g. taxon- plantpart(eg leaf) - forwhom (eg >children) - forwhat (eg sorethroat) - how (eg infusion)] > >3) description of ecology - requiring links between two "descriptors" (eg. >plant A is a tree at altitude X BUT plant A is a bush at altitude Y) > > then Im less clear how these would be accomodated. Is there elsewhere a >set of descriptor/state structures that I could see? You're right that the structure at the moment does not accommodate some data types well. It uses the standard structure of a character list where each character has a list of states and taxa are scored for those states. Distribution data particularly could use a more sophisticated approach - sometimes we can fit distribution into this (e.g. Character = "Which continent?" States = "Australia", "Antarctica" etc.) But can we do better? Can you suggest a way to accommodate your suggestions?

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Re: Expression of continuing interest / what needs to be done
by Stinger 19 Jul '00

19 Jul '00

Still here too, although I have been silent lately. I am in reasonably good agreement with Stuart Poss on what needs to be done with relation to data structures and standards - good work Stuart. I will add, briefly, that the issues, in my mind are clearly being debated beyond their level of resolution in that I really don't think that we should be wasting our time trying to figure out sets of descriptors for specific taxa, the inherent data hierarchy and descriptive extensibility are the important things. As much as I would like not to admit it, I have not yet been convinced that DELTA cannot function for us as the basis for taxonomic data structure. We will never regulate descriptor terminology because creative careful observation and the creative and clear semantics involved in communicating those observations completely is the basis of all observational biology. The strength of Systematics as a science is really in our diversity of ways of making observations and communicating them. Do we need this? I think yes. We need to expand it. With respect to what needs to be done by TDWG in the big picture. My priority is in developing reliable authority files. Our efforts at making reliable and updateable authority files for many groups and types of data are in their infancy and every database is suffering because of it. Content and structure are both important and we have heard from several clearly gifted thinkers on structure. I think that we need to put some more enegry, as a group, into ways to generate more and better content. Cheers, Stinger -- Gerald "Stinger" Guala, Ph.D. Keeper of the Herbarium Systematist Fairchild Tropical Garden 11935 Old Cutler Rd. Miami, FL 33156 http://www.ftg.fiu.edu/

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