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Re: (XML)Pedagogy
by Gregor Hagedorn 29 Nov '99

29 Nov '99

Thanks for your talk about XML. I have several questions: o Are Vocabulary and Namespace synonymous terms? o What is XML-DATA? o Reading about RDF and Dublin Core as RDF application I was left confused as to what acutally is a resource. It usually seems to be assumed that it is a document, but this impression may only be due to the examples. Thus, in a file with several item descriptions could: - Each item be a resource, for which a creator/editor etc. is described using DublinCore? - Could even the characters information within an item have different authors? (And if yes: Is it wise to do this?) - Is there a limit to a hierarchy of RDF objects in an XML file? > You can copy-and-paste this into an example.html file, and see it in > Internet Explorer 5, or Mozilla, or any XHTML+CSS1 compliant browser. Note: I assume that Mozilla does not apply to Netscape 4.7, which did not seem to be able to display the code you appended > * how and why mix several vocabularies, I would be very interested in this one. thanks Gregor ---------------------------------------------------------- Inst. for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Gregor Hagedorn Net: G.Hagedorn(a)bba.de 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: (XML)Pedagogy
by Leigh Dodds 29 Nov '99

29 Nov '99

> o Are Vocabulary and Namespace synonymous terms? Not quite, and I'd actually say that the term 'vocabulary' might be a little off base - I'd prefer 'schema' based on the previous example, and common usage: A vocabulary (or schema) is the syntax for your XML file. It defines what are the legal elements and attributes, and how they can be combined. A namespace (declaration) indicates that a particular XML element or attribute belongs to a particular schema (vocabulary). This means that you can build an XML document based on more than one schema (vocabulary) and qualify the elements/attributes to denote which schema they derive from. This is obviously useful if two schema have elements/attributes of the same name - you can explicitly state which version you are using. The Namespace Recommendation can be found at : http://www.w3.org/TR/REC-xml-names/ > o What is XML-DATA? See http://www.w3.org/TR/1998/NOTE-XML-data-0105/ XML-DATA is one of many proposed schema languages which includes XML Schemas, SOX and DSD. I'd suggest that XML Schemas is likely to become the standard simply because its further along the review process. > > * how and why mix several vocabularies, > > I would be very interested in this one. As are a lot of XML developers! Its hoped that the next version of the Schemas spec will address these issues. http://www.lists.ic.ac.uk/hypermail/xml-dev/xml-dev-Nov-1999/0916.html Cheers, L.

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Item description data in XML (XML)
by Robert A. (Bob) Morris 29 Nov '99

29 Nov '99

Gregor Hagedorn writes: >[...] > Probably a stylesheet could determine whether only the free text with > hidden markup is visible, only the data, or both? > > Any ideas, perhaps any technical suggestions, how to achieve that? > XSLT, now an official W3 Recommendation, is the language for transforming XML documents into other XML documents. From the point of view of XSLT, document nodes include text, XML elements, element attributes, comments, and a few other things. This makes it particularly easy to hide or reveal either the text or the markup, or the attributes in various combinations. Bob Morris

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(RQT) 250 000 species in my hand
by Jean-Marc Vanel 28 Nov '99

28 Nov '99

In a CD of course. And not in 5 years... There is a strong necessity to have an exhaustive coverage of species. A telephone directory with only 1/100 of the persons is useless. Science is not only a matter of doing publications to advance careers. It has social implications. If an information of high quality is available on the Net, it will greatly advance the cause of nature conservation. It will also advance the cause of descriptive biology and field biology, and help to raise funds (which go to molecular biology mainly). The paradox is that there is a growing sympathy in the general public for ecology, nature conservation, biodiversity, etc. But at the same time there is growing ignorance in Natural History. However there is a hunger to learn and understand that isn't satisfied by books. But the answers aren't at hand. With current floras and descriptions properly computerized, with the web, and some logic programming and image pattern recognition, we can remedy that. It seems that descriptive biology needs help from computer scientists, not only database and knowledge management, but also image processing (see other posts about "Types of data"). More on those matters at http://jmvanel.free.fr/ . Cheers Jean-Marc Vanel

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Re: (RQT)Limits of the Discussion.[features+other disciplines]
by Jean-Marc Vanel 27 Nov '99

27 Nov '99

"Stuart G. Poss" wrote:: > Are existing methods and this discussion restricted to "morphological characters"? ... > ... begin the much needed dialog among disciplines that > are not defined by the taxa themselves. 1. About the concept of features see 1rst post of this discussion, and my post "feature-property-value" 2.About other disciplines see my post "Re: The end of DELTA?", about how an entomologist might refer to a plant accessible on the net, not only simply linking to it like an HTML hyperlink, but ASSERTING SOMETHING about this plant, thus ADDING INFORMATION about this plant without changing anything on the plant's site. (RQT) means requirements (see Gregor Hagedorn's post, "First level topics on this list (GEN)"; every post should bear a tag among RQT, XML, GEN).

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GEN RE: Types of Quantitative Data - Outline Methods
by Robert A. (Bob) Morris 27 Nov '99

27 Nov '99

Stuart G. Poss writes: > Date: Sat, 27 Nov 1999 10:47:58 -0700 >[...] > Elliptical Fourier transforms >[... good reference list including Kuhl and Giardina 1982] and also Fourier Descriptors and Their Applications in Biology by Pete E. Lestrel (Editor), Cambridge University Press, 1997. As I recall, this has a paper using Kuhl and Giardina to identify many species of oak and maple trees algorithmically. As a biologically naive outsider, I would have thought that there is an interesting problem of authority for statistical characters not much different from other authority questions, namely how/where/who/when were the statistical parameters estimated. My impression about Elliptical Fourer Descriptors---which I think is a neat idea---is that the literature is mostly devoted to showing that they work, and not to otherwise collecting parameter estimates. A student of mine implemented Kuhl and Giardina in matlab and my recollection is that you can make EFD's independent of size and orientation, so sloppy scanning can do pretty well. However, fall came to New England, the semester and her interestd waned and we never tested her implementation. If I'm right that this is robust to size and orientation, then it would be a cute citizen science application. People could send their leaf images to a central server, and hordes of biology students could then quickly (or slowly) assign a species in furtherence of the parameter estimate. David Hearn is doing something like this at http://ag.arizona.edu/~dhearn/help/PlantID.html.

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(XML)Pedagogy
by Jean-Marc Vanel 27 Nov '99

27 Nov '99

(XML) means a post about XML (see Gregor Hagedorn's post, "First level topics on this list (GEN)"; every post should bear a tag among RQT, XML, GEN). By the way, this kind of tagging is much in the spirit of XML. Even in an HTML text, you can mark up a sentence, a paragraph, or words, with tags like <requirement>, <opinion>, <example>, <reference-to-article>, etc. To identify this family of tags (called a vocabulary), it is better (though not mandatory) to indicate that this fragment of HTML text is using this vocabulary (say, in this example, called authoring-discussion). Here is a complete example: <HTML xmlns:disc="urn:authoring-discussion" > <STYLE> disc\:opinion{color:red; font-size:large;} </STYLE> <P> Everybody agrees that ......; but I think that <disc:opinion>modelizing amphibians is very important and a very special case</disc:opinion>. </P> </HTML> You can copy-and-paste this into an example.html file, and see it in Internet Explorer 5, or Mozilla, or any XHTML+CSS1 compliant browser. For your conveniance, this file is joined to the post. Notes: N1 xmlns is a reserved word meaning "XML namespace"; the string following = can be: * a URN, that is an Unique Resource Name, (see RFC 2396, it's only required to remain globally unique and persistent ) as in this example, * or an URL (Uniform Resource Locator), that is something retrievable on the Internet, like http://www.w3.org/DTD/authoring-discussion.dtd , which in our example would contain a formal description of the vocabulary, a DTD (XML Data Type Definition) or another syntax like XML Schema. N2 This is a CSS1 style; complete specification in http://www.w3.org/TR/REC-CSS1 There many topics more about XML, like: * how and why mix several vocabularies, * how to format and query an XML document (XSLT), * what's going on in the business and scientific domains around XML * relations beetwen XML and HTML, * XML and the Web: the so-called semantic Web. If time and popular demand are here, I could write more on this. Cheers Jean-Marc

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GEN RE: Types of Quantitative Data - Outline Methods
by Stuart G. Poss 27 Nov '99

27 Nov '99

Gregor wrote: > > > Does anybody know about good parameterization of shapes, so they can > > be stored in more objective forms? > To which Don responded: > > Wouldn't the most objective representation of shape be given by a set of > coordinates for points placed around the outline? If orientation of the > object is important, then give landmark coordinates too eg. mark the organ > base and apex. From that info, parameters such as object area, perimeter > length, circularity (perimeter length*perimeter length/area), centroid, > longest and shortest axes, aspect ratios etc. can be calculated. > > You'd also be able to standardise your outlines (eg. using Bookstein's > transformation) and compare against reference shapes (eg elliptic fourier > analysis), pairwise comaprisons using (thin plate splines) or fit to average > shape using Procrustes metric. > > Feature extraction from digital images (eg defining the object outline, > sampling of points around outline)and calculation of the shape parameters > and export to spreadsheet is virtually automatic in packages like OPTIMAS. > James Rolf's NTsysPC will perform the basic standardisations, thin plate > splines and EFA. > > don Approaches to evaluating OUTLINES include: Freeman Chain Code Encoding Chris Meacham's MorphoSys package uses a Freeman Chain Code to automatically identify and encode points along the perimeter of a target object using video digitization, as well as along the edge of holes within it. There is a published citation for this, but I can not find it at the moment. This is not a parametric technique since it generates a point set for which no parameters must be either calculated. Median or Symmetrical Axis Blum, H. 1967. A transformation for extracting new descriptors of shape, pp. 362-380, In: Whaten-Dunn, E, Models for the perception of speech and visual form, MIT Press, Cambridge, MA, 470 pp. Straney, D. O. 1990. Median Axis Methods in Morphometrics, pp. 179-200, In: Rohlf, F. J. and F. L. Bookstein, Proceedings of Michigan Morphometrics Workshop. Special Publication Number 2, The University of Michigan Museum of Zoology, Ann Arbor, 380 pp. Fourier Analysis using Polar Coordinates Kaesler, R. L. and J. A. Waters. 1972. Fourier analysis of the ostracode margin. Geol. Soc. Amer. Bull., 83:1169-1178. Younker, J. L. and R. Ehrlich. 1977. Fourier biometrics: harmonic amplitudes as multivariate shape descriptors: Syst. Zool., 26:336-342. Elliptical Fourier transforms Kuhl, F. P. and C. R. Giardina. 1982. Elliptic Fourier features of a closed contour. Computer Graphiccs and Image Processing. 18:236-258. Rohlf, F. J. and J. W. Archie. 1984. A Comparions of Fourier methods for the description of wing shape in mosquitos (Diptera: Culicidae). Syst. Zol., 33:302-317. Eigenshape analysis: Lohmann, G. P. 1984. Eigenshape analysis of microfossils: A general morphometric procedure for describing changes in shape. Math. Geol., 15(6):659-672. Lohmann, G. P. and P. N. Schweitzer. 1990. On Eigenshape Analysis, pp. 147-166, In: Rohlf, F. J. and F. L. Bookstein, Proceedings of Michigan Morphometrics Workshop. Special Publication Number 2, The University of Michigan Museum of Zoology, Ann Arbor, 380 pp. Bezier Curves Engles, H. 1986. A least squares methods for estimation of Bezier curves and surface and its applicability to multivariate analysis. Mathemaical Biosciences, 79:155-170. Cubic Splines Evans, D. G., P. N. Schweitzer, and M. S. Hanna. 1985. Parametric cubic splines and geological shape descriptions. Mathematical Geology, 17:611-624. Fractals Barnsley, M. F. , V. Ervin, D. Hardin, and J. Lancaster. 1986. Solution of an inverse problem for fractals and other sets. Proceedings of the National Academy of Sciences USA, 83:1975-1977.

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Re: (XML) feature-property-value
by Noel Cross 26 Nov '99

26 Nov '99

Hello XML'ers, A few minor comments with regard to Jean-Marc's recent proposals which, on the whole, I find intriguing: On Fri, 26 Nov 1999, Jean-Marc Vanel wrote: > This feature-property-value triology is what I had in mind the first > time I read about Delta. > A few remarks: > > 1. the feature can be a hierarchy, like: > > leaf/lamina/abaxial_surface/vein_islands/indumentum/density I wouldn't have thought that "density" would be the feature, but rather the property, i.e.: feature = leaf/lamina/abaxial_surface/vein_islands/indumentum property = density value = (some value) > * we can turn the Flora of Australia GLOSSARY in a XML vocabulary in > XML Schema or RDF Schema syntax; each glossary entry should be > classified either as a feature, or a property, or a property-value; Would properties be reified into features (as is done in RDF), or will there be some other way to deal with properties of properties? Intensifiers such as "very", for example. > * the current type of characters of Delta (multistate=enumerate, > integer, real numeric, text) will become type information for > properties in our new Taxonomic XML Schema; there is a standard for > data types in the 2nd part of W3C's XML Schema recommandation; we > must avoid to re-invent the wheel; Note: the XML Schema part 2 of November 1999 is a Working Draft, not even a Proposed Recommendation, let a alone a Recommendation. > * the proposed XDELTA format (http://www.bath.ac.uk/~ccslrd/delta/) > is too much a direct translation of a Delta file; Of course, since its intent is to be a direct translation of the DELTA format, this is not exactly a failing of the XDELTA format. > * I propose to have 3 XML Namespaces for our different XML > vocabularies: > o biological descriptions (generalities) > o botany > o zoology I'm sure you don't mean to leave out Mycology, Bryology, etc. Best wishes, -Noel

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Nexus -- from a user
by Susan B. Farmer 26 Nov '99

26 Nov '99

Note that these comments are based on what is currently available in the current versions of Paup (more Paup 3.1.1 rather than Paup*) and MacClade that I've been using -- not the published standard. I can get the version number for the MacClade that I've been using, if that will help. You can have numeric characters in your data, but they must be "hard coded," (e.g., character #4 "number of leaves" with states "1. three," "2. four," etc. You can't put comments in your character matrix but you can put comments in your state names and character labels section. There's not an unlimited number of states. Paup will let you have about 36 I think, but MacClade allows less. I know I had to combine some of mine to get the data set into MacClade. Practically, unless you're modeling color (which I was) this is usually equivalent to an unlimited number of states, Character notes and illustrations only in MacClade. If you revert/convert to Paup, you loose all that information. Taxon and character names are limited to the number of characters. If I"m not mistaken this is only true in MacClade. Either that or MacClade is once again "shorter" than Paup. Multi-state characters -- they handle this wierd -- and differently. It used to be that they all had to be either AND or OR. And it's not even a true AND or OR type situation. It's mostly an OR, but not quite. (And I know that this is making *no* sense whatsoever!) Multiple states tend to be interpreted as uncertainty rather than polymorphism. YOu can now make that distinction, but it is still polymorphic rather than all of the above at the same time. Inapplicable is treated as missing. There's really no other way to do it. If you have an apealout plant, all the petal characters can either be treated as "missing" or you can have an extra state "not applicable." Then, you run into the problem of that extra state providing support that otherwise might not be there. I'm not aware of value probabilities in either Paup or MacClade. The same situation applies to taxon notes and taxon illustrations. Those are only good in MacClade. The typesetting markup in MacClade is only for HTML rather than typsetting. Anyway, I hope this helps. Maybe you can get some other experiential comments about Paup and MacClade. Susan Farmer sfarmer(a)goldsword.com Botany Department, University of Tennessee http://www.goldsword.com/sfarmer/Trillium

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