December 2001 - tdwg-content

Workshops in Spring
by Gregor Hagedorn 21 Dec '01

21 Dec '01

Dear collegues as has been announced at the TDWG meeting in Sydney we are planning 2 workshops in March 2002 to discuss the topic that remain open during the email discussions. Karen Wilson and Nicolas Bailly have informed me that the dates of the other meetings are fixed. For the Workshop in Sydney the best dates seem to be the 13-14 March 2002. Please inform me if you think that we should try to find another date that fits into the BioForum 2 schedule (see http://plantnet.rbgsyd.gov.au/bioforum/index.html) For Paris, we may have a choice between the 6. and 10. of March. Please send me a direct mail (g.hagedorn(a)bba.de) if you are considering attending this extra 1 day workshop in Paris, and write which day you would prefer. I wish all of you a very nice Christmas celebration and holiday, Best wishes Gregor Hagedorn ---------------------------------------------------------- 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: HTML in XML
by Jim Croft 21 Dec '01

21 Dec '01

Leigh wrote: > Except for this kind of usage. Mixed content is perfect for marking up > free-form text. Bad for mapping data into data structures (in most > cases a database). > If I had XML data containing this structure, I'd simply store the contents > as the raw XML. This is how I would like to do business as well, but unfortunately once you do this in common databases, they lose access to all the useful structural stuff in there... One day 'xml' might be a common database content type, up there with text, integers, real numbers, dates and the like, with real database facilities to manage and use this content... maybe it is already there... somewhere... jim

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Re: HTML in XML
by Jim Croft 20 Dec '01

20 Dec '01

Tim wrote: ><species_comments>The nature of Carcinus maenas is blah blah >blah.</species_comments> This is horrible mixed content stuff, and I am told that this is ipso facto, evil, and we will burn in hell for eternity for considering such a construct... >What I would like to do is have this attribute parsed using XSL and retain >the formatting over species names. Wouldn't we all... >When the text is processed normally the >HTML tags are dropped. If it is kept as CDATA the tags are not dropped but >also not processed. Any clues how to handle this? In one test application where plant names embedded in text were surrounded by <taxon></taxon> (more meaningful than ), I fudged it using fragments like the following xsl: <xsl:for-each select="note"> <xsl:apply-templates/> </xsl:for-each> .... <xsl:template match="taxon"> <xsl:apply-templates/> </xsl:template> which spewed the output to browser compatible html. The result was a series of note paragraphs with italicised species names... Not very elegant, pretty trivial, and I am not particularly proud of it. But hey, it worked and current IE and NS browsers knew what to do with it... jim ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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HTML in XML
by Tim Jones 20 Dec '01

20 Dec '01

Hi all you XML gurus, Has anyone had any experience storing HTML markup within an XML document. I would like to have a document that describes a species and one of the attributes is a descriptive piece of text eg. <species_comments>The nature of Carcinus maenas is blah blah blah.</species_comments> What I would like to do is have this attribute parsed using XSL and retain the formatting over species names. When the text is processed normally the HTML tags are dropped. If it is kept as CDATA the tags are not dropped but also not processed. Any clues how to handle this? Cheers Tim --------------------------------------------------------- Database Manager Centre for Research on Introduced Marine Pests GPO Box 1538, Hobart Tas 7000, Australia. Phone : (03) 62325222 (switch), (03) 62325213 (direct) Mobile: 0411 560057 Fax : (03) 62325485 E-mail: tim.jones(a)marine.csiro.au ---------------------------------------------------------

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Re: HTML in XML
by Leigh Dodds 20 Dec '01

20 Dec '01

> Tim wrote: > ><species_comments>The nature of Carcinus maenas is blah blah > >blah.</species_comments> > > This is horrible mixed content stuff, and I am told that this is ipso > facto, evil, and we will burn in hell for eternity for considering such a > construct... Except for this kind of usage. Mixed content is perfect for marking up free-form text. Bad for mapping data into data structures (in most cases a database). If I had XML data containing this structure, I'd simply store the contents as the raw XML. L.

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Re: HTML in XML
by Leigh Dodds 20 Dec '01

20 Dec '01

> <species_comments>The nature of Carcinus maenas is blah blah > blah.</species_comments> > > What I would like to do is have this attribute parsed using XSL and retain > the formatting over species names. When the text is processed normally the > HTML tags are dropped. That's because you're hitting the default template rules, which strips elements but retains their content. > If it is kept as CDATA the tags are not dropped but > also not processed. If you mean you've got Carcinus maenas or something similar, then the XSLT processor won't treat them as tags, but text. >Any clues how to handle this? You need a template rule that copies over the contents of this element into the result tree unchanged. something like: <xsl:template match="species_comments"> <xsl:copy> <xsl:copy-of select="@*"/> <xsl:apply-templates/> </xsl:copy> </xsl:template> This should copy the contents unchanged (including attributes) into the output. HtH, Cheers, L.

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Re: Character hierarchies
by Robert A. (Bob) Morris 12 Dec '01

12 Dec '01

Jim Croft writes: > Date: Sat, 1 Dec 2001 07:28:21 +1100 > From: Jim Croft <jrc(a)anbg.gov.au> > To: TDWG-SDD(a)usobi.org > Subject: Re: Character hierarchies > > >The other qualifiers (misinterps etc) aren't in there yet, but will come. > >We'll have to be much more sophisticated that in my example, of course. > > > >Now how about "definately known to be unknown" > > Very droll... However, Greg and I have discussed this in depth over a ^^^^^^^ > bottle of red and have come to the firm conclusion that without the ^^^^^^^^^^^^^ over "a" bottle of wine, or over "a quantity of bottles of red wine wine more than zero and of indeterminate number" ? > attribute of "often misinterpreted as definitely known to be unknown", and > the corresponding "rarely misinterpreted as definitely known to be > unknown", accurate representation of author intent in biological > descriptions will never be possible... > > So get to it - we expect to see this in the next software release, real > soon now... > > jim > > ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~ >

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Working Document
by Georgina MacKenzie 11 Dec '01

11 Dec '01

Kevin Thiele's working document for the SDD group is now available from the TDWG web site at: http://www.tdwg.org/tdwg2001/SDD_TDWG_2001.htm Georgina MacKenzie, Secretary, Newsletter Editor and Webmaster, International Working Group on Taxonomic Databases (TDWG) gmackenzie(a)york.biosis.org Telephone: +44 1904 642816 Fax: +44 1904 612793 54 Micklegate, York, YO1 6WF, UK ********************************************************************* This email is intended for the addressee(s) only. If you are not an intended recipient please inform the sender. BIOSIS UK does not accept responsibility for the contents of this message. *********************************************************************

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Re: Questions on Dependencies and identifiers
by Kevin Thiele 06 Dec '01

06 Dec '01

Jim wrote | Thinking further about Kevin's two types of dependency, context and | content (or whatever the terminology was), isn't the former an artifact | of the character set we have decided to use and the latter an artifact | of the taxa we are covering? The former is just not possible, the latter | might be possible but is just not there. If this really is the case and | one sort of dependency arises from the character state and another | arises from the taxa being considered, then it is very likely that they | should be modelled in slightly or completely different ways. This resulted from c.10 minutes thinbking in response to Steve's point. It does seem to be true that there are these 2 types of dependencies, but we need to think much more about (a) whether they need to be treated differently and (b) whether there aren't even more types. Again, shall we keep this thread going or set it aside to pick up later. I'm inclined to the latter. Cheers - k

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Re: Questions on Dependencies and identifiers
by Kevin Thiele 06 Dec '01

06 Dec '01

Barry - these are just the sort of problems that Challenge 1 was designed to throw up. In retrospect, though, it's perhaps too complex already. Maybe as we consider it we can break it up into sub-challenges? Dependencies are indeed a large issue that need to be dealt with carefully. Should we set them aside for the time being or do you want to deal with them now? When I put in that bit about mucronate within a notch my thought was that there would be two states "obtuse" and "mucronate within an apical notch" and obviously Jim's right that it's dependent on the context - the other taxa in the treatment - whether to treat it like this or otherwise. Your interpretation: | Apex shape | obtuse | notched | | Apex projection | immucronate | mucronate within notch (dependent on 'Apex shape - notched') seems to have a dependency between a state of one character and a state of another character (I'll use the character/state terminology for the time being here for simplicity). This is not the way it's usually done - dependencies usually set up a relationship between an entire character and a state of another character. e.g. the character Leaf shape ovate/elliptic will be dependent on the state "present" of the character "Leaves present/absent". In an interactive key the behaviour will be that if someone chooses Leaves absent then the character Leaf Shape will disappear. Likewise when building natural language descriptions, if a taxon has no leaves then the leaf descriptive characters will all be skipped. You seem to be doing something else here, and I'm not sure what's the behaviour you were trying to get. Can you give us a fragment of your model for the simplest case extractable from Challenge 1, without the complications of numeric characters, dependencies etc. Yes, there's a real need for character lists and identifiers. Do we go with e.g. <Feature Name = "Leaves"> <Value>ovate</Value> </Feature> or <Feature FeatureID="23" valueID = "6"> The former certainly makes for better human-readability, but is this important? I would have thought that a computer can make sense of either, and we can support both. The parser would simply need to know that if the attribute FeatureID is specified then use that and look up the idref to get the name, else if the attribute Name is specified then use that. Presumably our document structure will be the same whether we use Names or Idrefs? Cheers - k

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