February 2000 - tdwg-content

Re: SDD Specifications Document
by Bob Morris 22 Feb '00

22 Feb '00

Kevin Thiele wrote: > Dear list_eners > <XML data modeling spec proposal>... I'm not competent to address the proposal, but I would like to try to influence the directions that may emerge from it in several ways: (a).On theoretical and practical grounds, DTD's are now understood to be a weak way to describe the schemata (small 'S') of XML documents. The specialists should argue about whether RDF or XML-Schema's (uppercase 'S') work better (or try each on for size) and if there is a compelling reason to have a DTD then derive one from the Schema. Aside from (or perhaps actually because of) the lack of typing, inheritance, and ordering mechanisms, DTDs add restrictions on the kinds of schema inference that can be made from particular XML documents that might be a query result, and because of that make it less straightforward to mediate between the answers to queries on two different databases. These issues are explored in the book "Data on the Web" by Abitoul et al., and in the literature behind it. (b). Mixed content (a mixture of text and elements) is a really bad idea, as is well known in the SGML community. Our own limited experience has been that dealing with it in display code necessitates to code obscurely. I can't tell whether anything in the proposal would lead this way. Maybe some pseudo-code XML-like examples would enlighten. (c). One should keep in mind that queries can be constructed by software, not just by people. The latter are far better than the former at resolving ambiguity and supplying reasonable defaults. So for example, we should always ask at the end if we have given enough to formulate queries and interpret their answers in a non-interactive fashion. Put another way, data exchange is a minor reason to adopt XML compared to its utility for the construction of queries and the interpretation of their answers. (Here's a trivial example, soon to be easily fixed: the data returned by the experimental XML facility at ITIS*ca conforms to a DTD in all but one case: that where there is no data matching the query. In that case, it returns the same HTML "sorry no answer" page that the html interface does, thereby requiring an XML application to have special knowledge of this case---which would not bother a human at all but sure startled our little application.) Bob Morris

1 0

XHTML
by Susan B. Farmer 12 Feb '00

12 Feb '00

>>>From the HTML Writers Guild Newsletter ---------- Begin INcluded Taxt 1. XHTML: Bridging the Gap between HTML and XML (Kynn Bartlett, HWG President, kynn(a)hwg.org) On 26 January 2000, the World Wide Web Consortium released the newest flavor of HTML -- XHTML. The HTML Writers Guild is proud to have played a role in the development of this specification, and we would like to thank Ann Navarro and Frank Boumphrey for their dedication and hard work in the W3C's HTML Working Group. But what _is_ XHTML, and what does it mean to members of the Guild? WHAT IS XHTML? To understand that, first we need to review what HTML is. Hypertext Markup Language was created as an "application" of SGML (Standard Generalized Markup Language), which is a "meta-language" for describing other markup languages. Extensible Hypertext Markup Language (XHTML) is simply a version of HTML but defined as an application of XML (Extensible Markup Language). XML was developed as another "meta-language", not as complex as SGML but powerful enough for use in web environments. WHY XHTML? Why an XML-based HTML, if we already have "normal" HTML? By using XHTML, we have access to the strengths of XML -- extensibility and interoperability. Developers can extend XHTML through modules, DTDs, schemas, and incorporation of other XML-based languages. XSLT (Extensible Stylesheet Language Transformations), which allow XML documents to be easily changed from one representation to another, will make it easy to adapt XHTML pages for a wide variety of browsers and user agents. WHAT IS XHTML LIKE? If you're already familiar with HTML 4.01, you'll find that XHTML 1.0 offers the same features and abilities you've always had. (Future versions of XHTML will expand beyond simply "translating" the HTML specification into XML.) There are some differences in syntax, however; the most notable ones include: * Documents must be "well formed" -- an XML term meaning that tags must match and be nested properly * Element and attribute names must be in lower case * For non-empty elements, end tags are required -- no more optional </P> or </LI> tags * Attribute values must always be enclosed in quotes * Empty elements must either have an end tag, or the start tag must end with /> If you're like at least half of the web designers out there, the second bullet point above might stand out and you may be asking: WHY LOWER CASE? In HTML, tags and attributes are not case sensitive. This means that <BODY>, <body>, <Body>, and even <bOdY> refer to the same thing; you can have your opening tag be <body> and your closing tag </BODY>, and it all works fine. XML, the language used to build XHTML, is case sensitive. <Body> is considered a different tag from <BODY>, <body>, or <bOdY>, in XML. Because of this, a standard for XHTML tags had to be set -- and the most likely choices were "all uppercase" (such as <BODY>), or "all lowercase" (such as <body>). In the end, lowercase won out, although it really could have gone either way; a semi-arbitrary choice had to be made. DO CURRENT BROWSERS SUPPORT XHTML? No and yes. Current browser releases do not speak XHTML, they speak HTML. However, it is possible to write XHTML in a way that is compatible with HTML, and will not break on existing HTML-based browsers. These are described in Appendix C of the XHTML specification. As an example, the "hr" (horizontal rule) tag must be closed, and would normally be written in XHTML as either <hr/> or <hr></hr>. However, this will confuse many existing HTML-based browsers; instead, you can write the tag as <hr /> -- note the space. This is legitimate XHTML and is compatible with HTML browsers. HOW CAN I LEARN MORE ABOUT XHTML? The complete spec for XHTML 1.0 is available via the web from the W3C's web site: http://www.w3.org/TR/xhtml1/ For a chance to experience XHTML and XML first-hand -- or perhaps just view the source of some web pages written in XHTML -- read on to the next article! --------- End Included Text Susan Susan Farmer sfarmer(a)goldsword.com Botany Department, University of Tennessee http://www.goldsword.com/sfarmer/Trillium

1 0

(GEN) Maize ontology & interoperable ontologies
by Vincent, Leszek 11 Feb '00

11 Feb '00

Dear subscribers to TDWG-SDD On Jan. 31, 2000 I sent an email to you (copy below) about developing a containment hierarchy for Maize & expanding this to include the rest of the Poaceae and hopefully subsequently the rest of the monocots & dicots (via interoperable ontologies). I'm presenting some of this work at the next Maize Genetics Conference (March) [http://www.agron.missouri.edu/Coop/Conf/2000.html] & include a copy of the abstract below F.Y.I. -------------- Conference abstract: Developing systematic descriptors and containment hierarchies for maize The Systematic Descriptors component of the Missouri Maize Project is aiming to provide descriptors in appropriate 'containment hierarchies' (biological terms, their relationships and associations) for maize. We wish to design a structure that has wide contribution from scientists studying maize and many other plant species. Databases comprising all sorts of information on monocots and dicots will need to be increasingly interoperable to facilitate future concurrent searches of these databases and so be helpful to a wide range of end-users. Developing systematic descriptors in containment hierarchies which accommodate maize data is a challenge on its own. But developing a structure that can accommodate present and future data from other monocot and dicot taxa, is another very relevant and stimulating challenge. An overview has been developed and the framework is forming. We are seeking feedback on the framework and content. NSF award 9872655. ----------------------- For further info. on this project please access: http://www.agron.missouri.edu/mnl/74/89vincent.html - a publication in the Maize News Letter. Should you have any comments, suggestions... about the development of containment hierarchies for maize (in a formal ontology) and the subsequent development of interoperable ontologies, I'd love to hear from you. Thanks for your time. Sincerely, - Leszek Vincent ======================== Text of email of Jan. 31: Dear subscribers to TDWG I've been 'listening' to the contributions on Lexicons, XML etc. for a while now and thought I should seek your comments because your contributions have sparked several developments in my thinking. I'm wrestling with the development of a hierarchy (containment hierarchies) of systematic descriptors for corn/maize/ Zea mays for the Missouri Maize Project (see URLs below). While this is challenging for maize/corn on its own, an added challenge is my desire to develop containment hierarchies which are compatible with databases for other grass crops e.g. rice (Oryza). To add to the challenge I have the ideal of trying to accommodate the 'interests' of similar databases for various DICOT crops e.g. soybean, cotton. While I do appreciate that such an all encompassing approach is maybe impossible to achieve I thought that it would still be good to get some other folks opinions on this. Having some kind of 'generic' structure which accommodates monocots & dicots should greatly facilitate the interoperability of these databases. It's the interoperability scenario which really got me on to thinking about this issue. Conducting simultaneous searches of dicot & monocot databases for morphological data down to molecular (e.g. sequence) data is not too far fetched. But I'm battling to find info. which addresses/refers to such 'generic' standards. I'd be grateful to have your thoughts on the above. ======================== xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox P. Leszek D. Vincent Ph.D., FLS Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall, University of Missouri-Columbia, MO 65211-7020, USA. Ph: (573) 884-3716 (Agronomy), (573) Fax:(573) 884-7850; Ph/Fax (Home): (573) 441-1228; Email: Leszek(a)missouri.edu Plant Systematist on the Missouri Maize Project - NSF award 9872655 - (http://www.cafnr.missouri.edu/mmp/ and http://www.agron.missouri.edu/) xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox

1 0

Re: (LEX) Containment Hierarchies
by P. F. Stevens 01 Feb '00

01 Feb '00

When one starts to "spread" morphological databases in botany one runs into innumerable problems, as I think I mentioned some time ago. In this case, thinking of monocots and "dicots", will we allow monocots to have stipules? What do we do with the intravaginal squamules of many Alismatales which, as far as I can see, are colleters under another name? But why should they not have a different name, since they are likely of independent origin from colleters in dicots? But, if one takes that tack, can we use the terms haplostemony and diplostemony in monocots, as Ronse Decraene questioned in a monocot symposium volume about four years ago? Indeed, do monocots ever have sepals or petals? Why should "hypogeal" and "epigeal" mean different things for monocot and dicot seedlings? These are not insoluble problems, but I have seen no recent discussions on how to clarify botanical terminology, although I think that this is definitely needed - and it needs to be an international effort, not least because we can have the same botanical term meaning different things in different languages (I think "crassinucellate" is an example). Peter S.

1 0