December 1999 - tdwg-content

Re: (XML) XML?
by Leigh Dodds 07 Dec '99

07 Dec '99

> Over the past couple of days I've partially implemented an export function > to produce Leigh's XDELTA documents (as a simple example of a possible XML > format) for the data in Lucid keys. Would it be possible to see this code, or at least the resulting XML files? I'd like to put a lengthier example in with the XDELTA documentation than I currently have. Note that some of the verbosity in XDELTA (i.e. the length of the tag names) was derived from the requirement to make the format as 'readable' as possible. So that it wasn't opaque to a user how their data was stored, and also potentially allowing hand-authoring. > what could we do with such data as XML that we couldn't do with > the data as a simple structured file as above? At the basic data level I'd say nothing. A data format is a data format. You could put the whole thing into a complicated CSV (comma separated value) format if you wanted. Apart from the lauded benefits of interoperability and the other XML hype, I see one of the big advantages of XML is that because so much of the information is explicitly tagged you are able to add additional layers above that of processing the plain data. For example an RDF application layer might allow one to make inferences about a data set (or sets) that would be otherwise difficult with a format that is more context based. There are also advantages regarding extensibility (and again this is just a personal view). Take the DELTA comment structure. It includes all sorts of different information and has been used to encode different types of information during the lifetime of the format. When it comes to processing that data the application needs to be much more aware of this type of legacy usage. Explicitly tagging data mitigates some of these problems (but not all, XML isn't a magic bullet by any means). As a user of an application it wouldn't matter to me whether my data is in XML or some other format. Until I decide to use another application. Can it use this format? Will I lose any data? Can my colleague use my data in his/her application? Has all my data been rendered obsolete because the latest version of this package has changed the file format (i.e. the Microsoft Word syndrome). I believe careful application of XML can help in these cases. But you're right to question it at this stage - the initial focus needs to be on design and data modelling... > A final point. It seems to me that the discussion so far has been > dominated by computer nuts (no offence intended, we need you!) ...which I hope to be able to help with, as well as providing any XML and/or programming support. I'm really keen to hear from the domain experts out there who can provide hard usage facts. I'll duck back into my shell now! :) Cheers, L.

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Re: (RQT) character/state/comment
by Leigh Dodds 07 Dec '99

07 Dec '99

> Often, DELTA uses "characters", "states", and "comments" in the following > manner: (Using XDELTA here instead of DELTA-CLASSIC because to me it's a > bit more clear) :) Nice to see it has some uses anyway! > <character number="8"> > <description>outer edge of front wing</description> > <comment>shape</comment> > <multi type="unordered"> > <state number="1">convex</state> > <state number="2">straight</state> > <state number="3">concave</state> > <state number="4">irregular</state> > </multi> > </character> > > It was pointed out that "shape" is more than just a comment, but a > critical piece of data, a "property", which modifies the character and > perhaps even restricts the states to various types. Mike seemed to > indicate that there would be a way to make this explicit in DELTA, though > I don't recall what the mechanism was. As a first cut I just transferred everything from DELTA comments into XDELTA comments, although it was quite obvious that the 'comment' component of DELTA was overloaded depending on context (a legacy problem I guess, and one which raises the prospect of 'extensibility' as a requirement of the new format). In the above example the character description is discussing the 'shape' property of the 'outer edge of front wing' character. An alternate possible encoding would have been the 'shape' property of the 'outer edge' property of the 'front wing' character. I'd say that both are equally valid, just that the latter is normalised to a great extent. However there would appear to be some problems with assuming an morphological bias to the data model - i.e. a butterfly has wings which have shape... because its hard to draw the correct distinctions (see Gregors posting on 1/12 entitled Character and item hierarchy). Therefore attempting to normalise properties might lead to varying and inconsistent results. DELTA already allows dependencies between characters - such that if a specific state has been selected for a character, other characters are ignored (i.e. no wings, ignore anything to do with wings). Is there any other dependency relationships that might be required, or additional information about such a relationship? Restricting states to particular options depending on the property in question (e.g. leaf and/or wing shape) leads back to the prior discussion on accepted standards for character description. Defining, and agreeing upon these standard notations/descriptions are a fundamental part of specifying this new format, and one that isn't solved simply by deciding to use XML (for example). Its part of the fundamental design and modelling, and is therefore something that should be addressed early on. Cheers, L.

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Re: (XML) XML?
by Mauro J. Cavalcanti 07 Dec '99

07 Dec '99

Susan B. Farmer wrote: > How programmable *is* a Palm Pilot? There is also implementations of the Smalltalk language for the PalmPilot. One of them is Pocket Smalltalk. This system will be freely available for noncommercial uses. A $40 "registration" fee is required if you want to write commercial or shareware programs in Pocket Smalltalk. It can be found at http://www.tiac.net/users/ajb/pocketst/index.html There is also a port of the very nice Squeak Smalltalk for Windows CE: http://www.sugarWeb.com/Miniatures/Files/WinCE/WceToday.htm Comments on Java programming: "Java programming is like teenage sex .... -Everyone talks about it all of the time (but they don't realy know where they talking about); -Everyone claims to be doing it; -Everyone thinks everyone else is doing it; -Those few who are actually doing it: -Are not practicing it safely; -Are doing it poorly, and -Are sure it will be better next time." [From a post on comp.lang.smalltalk] Hope this helps... ;-)) Best wishes, -- + - - - - - - - - - - - - Mauro J. Cavalcanti - - - - - - - - - - - - + | Setor de Paleovertebrados, Departamento de Geologia e Paleontologia | | Museu Nacional do Rio de Janeiro | | Quinta da Boa Vista, 20940-040, Rio de Janeiro, RJ, BRASIL | | E-mail: maurobio(a)acd.ufrj.br | | Home Page: http://read.at/digitax/personal.html | + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + "Life is complex. It consists of real and imaginary parts."

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Re: Symbolism
by Una Smith 07 Dec '99

07 Dec '99

Robert A. (Bob) Morris wrote: >My question: is it uniquely American for a political jursidiction to >have an official insect? And what role does an official insect >actually play, other than to be designated? These are good questions for the Usenet newsgroup sci.bio.entomology.misc. Una Smith una.smith(a)yale.edu

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Symbolism (Idle query)
by Robert A. (Bob) Morris 06 Dec '99

06 Dec '99

Anax junius, locally known as the Green Darner Dragonfly, was designated the official insect of the state of Washington in 1997. (See http://www.americasflowers.com/kids/wakids.html for the other official symbols of Washington state, including the state bird, the state fruit, the state fish, and the state folk song). As of December 4, 1999 there were 14,797 signatures on a petition to make A. junius the state insect of Michigan (http://members.aol.com/YESnetwk/Progress.html). My question: is it uniquely American for a political jursidiction to have an official insect? And what role does an official insect actually play, other than to be designated? By the way, of 124 pages on the web mentioning A. junius, I could only find two that told me what it might eat for dinner, which is what sent me looking in the first place. --Bob

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Re: (XML) XML?
by Dave Vieglais 06 Dec '99

06 Dec '99

> I know little about Palm Pilot. But we should avoid being > tied to proprietary systems and API, which doesn't prevent to > work on Palm Pilot, having a compatibility API layer for > proprietary calls. It seems that a lot can be done a standard > browser, using Javascript, DOM, XSLT, with small applets to > provide the rest of functionalities. Internet Explorer 5 will > probably be soon XSLT-compliant, and Mozilla > (www.mozilla.org) is advancing, having a modular, open-source > architecture, and support for XML and CSS. Problem with PDA's is that they do not support full versions of browsers (no scripting, etc, well Win CE devices will do JavaScript, but do not support the XML DOM). Probably the simplest app that could be built to run on both systems that connected to the remote database on a base station via a serial connection would use custom IO on the serial port talking to a custom app on the base station. I believe serial IO libraries are similar enough on the windows CE devices and Palm Pilots that the underlying structure of such an app would be quite similar on both platforms, but the interface programming (i.e. the GUI) would be *quite* different. > > Dave Vieglais a écrit : > > > Palm Pilots are eminently programmable. > > With standard tools? C, C++, Java (limited), BASIC (limited), and a couple other goofy scripting languages. Typically compile on a desktop and upload to the PDA. > > > Add a GPS... Add in a couple more data collection devices- > and capture quantitative information at the same time- > temperature, humidity, canopy gap fraction, even fish-eye > photos (if you're into that sort of thing)... > > Can you connect all those things on a palm pilot ? Technically yes. Actually, not yet. There is a single serial port on PDA's, so multiple serial devices require an RS232 switch, and custom programming to support it. You can certainly connect one device at a time though. Dave V.

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Re: (XML) XML?
by Jean-Marc Vanel 05 Dec '99

05 Dec '99

Wellcome in this list! It seems that we are on the same wavelength, see my vision in : http://jmvanel.free.fr/call.htm I know little about Palm Pilot. But we should avoid being tied to proprietary systems and API, which doesn't prevent to work on Palm Pilot, having a compatibility API layer for proprietary calls. It seems that a lot can be done a standard browser, using Javascript, DOM, XSLT, with small applets to provide the rest of functionalities. Internet Explorer 5 will probably be soon XSLT-compliant, and Mozilla (www.mozilla.org) is advancing, having a modular, open-source architecture, and support for XML and CSS. Dave Vieglais a écrit : > Palm Pilots are eminently programmable. With standard tools? > Add a GPS... Add in a couple more data collection devices- and capture quantitative information at the same time- temperature, humidity, canopy gap fraction, even fish-eye photos (if you're into that sort of thing)... Can you connect all those things on a palm pilot ? > Sounds like a fun project to me. Have you the time and/or sponsorship and/or skills to do that? > The real key is datasets that are readily interoperable- that's what XML can provide. Don't worry, datasets will come within a few month, using a simple linguistic approach to parse existing floristic texts (see http://jmvanel.free.fr/Samples/parsing.htm). Cheers Jean-Marc

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Re: (XML) XML?
by Dave Vieglais 04 Dec '99

04 Dec '99

Palm Pilots are eminently programmable. But they only have a few (2-8) meg of RAM depending on the model. So, they'll never hold a very large data set. There are a few options- upload an appropriate portion of the dataset to the device, carry the data with you in a format that can be easily loaded into the Palm Pilot, or provide the device with a connection to another device that stores enough data. There are several wireless solutions available, with transmission ranges from a hundred or so feet to a few miles, to global (cellular or satellite). A custom solution (custom software, off-the-shelf components) could probably be worked out with a laptop as base station, radio modem for connectivity, and a happy Palm Pilot/ windows CE user in the field. Add a GPS, a database back in the base station, and a bunch of field observations could be collected quickly and easily, with one point of data entry. Add in a couple more data collection devices- and capture quantitative information at the same time- temperature, humidity, canopy gap fraction, even fish-eye photos (if you're into that sort of thing)... Sounds like a fun project to me. The real key is datasets that are readily interoperable- that's what XML can provide. Dave V. > > *snip* I've got to catch up on my back reading ... > > But I saw this and *had* to respond! > > > > >Example 2: Say I want to run NaviKey on my Palm Pilot*. > The device has > >limited resources and I would prefer to use very small files > if at all > >possible. > > > >As you say, these problems will all go away someday. > > > >Best, > > > >-Noel Cross > > > >*I only wish it were possible -- A few people have actually > asked for this > >capability, as it would be handy to use such as program in the field. > > > > It's probably not that far off. I found the program that Larry Morse > first did for interactive specimen identification before I > entered Grad > School. It takes 64K to run. (At the time it probably had a limit of > 64K for data too -- and that stretched the limits of the > computer.) Most > of your hand-help calculators have a memory of at least 64K now. > How programmable *is* a Palm Pilot? > > Susan Farmer > sfarmer(a)goldsword.com > Botany Department, University of Tennessee > http://www.goldsword.com/sfarmer/Trillium

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(RQT) character/state/comment
by Noel Cross 04 Dec '99

04 Dec '99

Hi all, Getting back to requirements, one thing that came up at the TDWG meeting was what I think of as the character/state/comment issue. Often, DELTA uses "characters", "states", and "comments" in the following manner: (Using XDELTA here instead of DELTA-CLASSIC because to me it's a bit more clear) <character number="8"> <description>outer edge of front wing</description> <comment>shape</comment> <multi type="unordered"> <state number="1">convex</state> <state number="2">straight</state> <state number="3">concave</state> <state number="4">irregular</state> </multi> </character> It was pointed out that "shape" is more than just a comment, but a critical piece of data, a "property", which modifies the character and perhaps even restricts the states to various types. Mike seemed to indicate that there would be a way to make this explicit in DELTA, though I don't recall what the mechanism was. Should this be explored as a possible requirement? How might this be issue best be resolved? -Noel

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Re: (XML) XML?
by Jean-Marc Vanel 04 Dec '99

04 Dec '99

My synthetic answer to Kevin Thiele's question: Why XML? * it is the ultimate standard for exchange of data of any kind: textual, database, knowledge representation, etc; this standard is quickly growing and there is no doubt it will succeed, accompanying the growth of Internet; * it is extendible, allowing to be very formal or very unformal, as needed, * lots of free tools and standards exist for parsing, viewing, transforming, querying, * it is possible to apply the same techniques on the client browser or on the server, thus adding flexibility. See the main links on XML on http://jmvanel.free.fr/XML.htm And now the figures about the "verbosity" of XML: My XML example (a single plant species from the flora of China) compresses from 2500 bytes to 1090 (57%): http://jmvanel.free.fr/Samples/DisplayDescriptions/species_example.xml An Xdelta example (Lepidoptera) on Leigh Dodds' site compresses from 50500 bytes to 3600 (93%), because it has a large number of repeted tags. I used winzip. Now we see that we can have all plant species on a CD (650 Mb), even without compression: 2500 bytes * 250 000 species = 625 Mb And on a DVD you can have 10 times more! And also on Internet with the new HTTP 1.1 protocol, the files can be compressed during transmission. Still 2 more arguments: the verbose repeted tags are not repeted when the XML file has been parsed and is in memory; the last argument is financial: today you can buy a 10 000 Mega-bytes disk for 200 US$ , and it will decrease. So file size is NO problem for taxonomy with XML. You must understand that it's the small price to pay for extensibility and interoperability. Noel Cross wrote : > On Thu, 2 Dec 1999, Kevin Thiele wrote: > > > Over the past couple of days I've partially implemented an export function > > to produce Leigh's XDELTA documents (as a simple example of a possible XML > > format) for the data in Lucid keys. I have a key to families of flowering > > plants of Australia (240 taxa, 166 characters, 600 states). The data I'm > > using are simple - basically a score matrix, a list of taxa and a list of > > characters. The file sizes in three formats for these data are: > > > > LucID 166 kb > > DELTA 240 kb > > XML c3 Mb > > > > And this is only the most basic XML!.

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