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Re: (XML)Pedagogy
by Leigh Dodds 30 Nov '99

30 Nov '99

>Just say for the moment that we'll have several vocabularies by large domains: >biological descriptions (generalities) >botany >zoology >Virology >Microbiology >geography >ecology Just to comment here, one approach being taken by the XHTML working group is to take modular approach with future version of the specification (XHTML 1.1. onwards). This allows defined portions of the spec to be replaced with vendor specific extensions, e.g. replace all the form elements with some extended/amended syntax, or the same with tables, etc. Such an approach might benefit this effort, in that a core set of descriptive markup for characters can be defined, and then allow additional modular extensions for the differing disciplines. This has the advantage of providing a small initial spec and data model which can then be extended. (an approach thats worth considering even without modularity included in the final design). L.

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Re: Item description data in XML (XML)
by Robert A. (Bob) Morris 30 Nov '99

30 Nov '99

[Forgive me if this duplicates. My mailer claims I sent it, but I never got it and I don't see it in the archives] Gregor Hagedorn writes: > > It is difficult to add information about obovate or length. Noel > already noted that we may be running into this "properties of > properties" problem. > > General question: Is there any reason why attributes exist at all? > What is the advantage of > > <leaf shape="obovate" length_mm="31"/> > > over > > <leaf> > <shape>obovate</shape> > <length>31</length> > <MeasurementUnit>mm</MeasurementUnit>=" > </leaf> > Popular wisdom often asserts there is no difference, but there are important differences for database work which are less so (except 1 below) for documents (hence the popular wisdom). These things are true of attributes in XML but not necessarily of elements (the tags + stuff between them) depending on the grammar defining the vocabulary: 1. Attributes are order independent 2. There can only be one attribute,value pair for each attribute. 3. With DTD's (which are the wrong thing to consider here but that is another story), you can enumerate the permitted values of attributes. You can work around this for elements but it may be pointless, verbose, and fragile, especially because of the order dependence of elements. 4. (Subtle and technical)References to XML objects essentially must appear as attributes. This is the only way you can get non-tree graph structure in XML documents, and also is the way you would make a data value conveniently be another object. So if "obvate" were actually some complex object that held more information, you would probably find it named as the value of an "idref", not as text data. While specimen and species documents may prove to representable by trees, keys probably will not be.

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Re: Item description data in XML (XML)
by Noel Cross 30 Nov '99

30 Nov '99

On Tue, 30 Nov 1999, Gregor Hagedorn wrote: > > General question: Is there any reason why attributes exist at all? > What is the advantage of > > <leaf shape="obovate" length_mm="31"/> > > over > > <leaf> > <shape>obovate</shape> > <length>31</length> > <MeasurementUnit>mm</MeasurementUnit>=" > </leaf> > In general a tag can provide the same function as an attribute, as in the case you mention, but there are some situations where attributes are useful. For example, in cases where text is being marked up and the text itself cannot be altered, new data can be stored in attributes. In this case country IDs can added without altering the text: "They can be found in <country id="EN">England</country> and in <country id="IT">Italy</country>." Also in cases where you don't want your tagged items to be rendered by a browser. For example, if you add some RDF metadata: <rdf:RDF> <rdf:Description about="http://www.veggies.org/carrot.jpg"> <s:Family>Apiaceae</s:Family> </rdf:Description> </rdf:RDF> The this case the word "Apiaceae" would be rendered in the page, while in this case: <rdf:RDF> <rdf:Description about="http://www.veggies.org/carrot.jpg" s:Family="Apiaceae" </rdf:RDF> the word "Apiaceae" would not appear in the page. There are probably more fundamental differences that Liegh, Bob, and others could come up with -- these are just two that come to mind. Best, -Noel

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Re: Markup of text descriptions Vs. structured data (GEN)
by Jim Croft 30 Nov '99

30 Nov '99

>These issues should be seen quite separately, and that we need both > >1. A markup language for text documents. This includes: > - existing descriptions, captured by OCR or other means, where the > markup would be manually (or automated/data mining?) > - computer generated natural language descriptions that are > published as electronic documents. A new CSIRO package could have > a ToNat command that automatically adds the necessary, hidden > markup code. >2. A data language for new observations, including repeated > measurements or repeated observations of categorical data, e.g. > shape of multiple leaves in a single specimen. Further, many > structures for knowledge managements (data revision, annotation, > quality control and assessment) need to be implemented here. > >The issues overlap, and it would be beneficial to use as much common >syntax as possible, but fundamentally I believe them to be quite >different. Gregor Can you explain in more detail why they should be fundamentally different? Aren't the differences just a matter a matter of degree, different points on a continuum of data as it were? And aren't the basic principles applicable across the whole? Is not the issue we are dealing with here one of how to deal with biological descriptive information whether at the level of individual components of the specimen (e.g. each of the leaves), the specimen as a whole (e.g. the variation of leaves on a specimen) or the taxon (e.g. the variation of leaves across all specimens of the species, or the higher level taxon)? Or at any other level, or mixture of levels, we might chose? Is it not possible, and indeed preferrable, to have a single scheme that covers all of these situations? I am finding it a bit difficult to get a grip of this discussion and where it is going (or where it is coming from, for that matter). I thought I understood (and agree with) your previous post about the need for a definition component as distinct from the the description and data in the same manner as the DTDs of SGML, but I am now not so sure if that is what, or all of what, is being suggested. jim __________________________________________________________________________ Jim Croft ~ jrc(a)anbg.gov.au ~ http://www.anbg.gov.au/people/croft.jim.html ph 02-6246-5500 ~ fx 02-6246-5248 ~ GPO Box 1600 Canberra ACT 2601

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Re: (XML)Pedagogy
by Jean-Marc Vanel 29 Nov '99

29 Nov '99

Hello Gregor Hagedorn a écrit : > o Are Vocabulary and Namespace synonymous terms? Here is quotation from http://www.w3.org/TR/PR-rdf-schema (W3C's RDF schema spec.) 4.1.1. Terminology The phrase 'RDF vocabulary' is used here to refer to those resources which evolve over time; 'RDF schema' is used to denote those resources which constitute the particular (unchanging) versions of an RDF vocabulary at any point in time. Thus we might talk about the evolution of the Dublin Core vocabulary. Each version of the Dublin Core vocabulary would be a different RDF schema, and would have a corresponding RDF model and concrete syntactic representation. > o What is XML-DATA? It's a W3C Note of 1998 by Microsoft and others, that is to a large extent implemented in IE5 (but under the name of XML Schema). W3C's "true" XML Schema, still a Working draft, is not very different from 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. Here is a quotation from http://www.w3.org/TR/REC-rdf-syntax (W3C's RDF spec.) Resources All things being described by RDF expressions are called resources. A resource may be an entire Web page; such as the HTML document "http://www.w3.org/Overview.html" for example. A resource may be a part of a Web page; e.g. a specific HTML or XML element within the document source. A resource may also be a whole collection of pages; e.g. an entire Web site. A resource may also be an object that is not directly accessible via the Web; e.g. a printed book. Resources are always named by URIs plus optional anchor ids (see [URI]). Anything can have a URI; the extensibility of URIs allows the introduction of identifiers for any entity imaginable. So we can have an URI for a plant species. The Dublin Core is a particular vocabulary in that it has only properties; other vocabularies, like RDF schema mentioned above have properties and types. See also my recent post about asserting in RDF a butterfly being a plant's pollinizator. One last remark: Dublin Core is a much publicized vocabulary, but it's simple with only 15 properties. A botanical vocabulary will count hundreds of properties (from both organs and features). > 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?) Yes and yes. An article can have an author, and have quotations from others authors in it. > - Is there a limit to a hierarchy of RDF objects in an XML file? No. > > 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 Sad but true; I think that someday Mozilla and Netscape will merge (in functionality because the code and design is completely different). > > * how and why mix several vocabularies, > I would be very interested in this one. OK, warten Sie mal... Ich muss das überlegen. Just say for the moment that we'll have several vocabularies by large domains: * biological descriptions (generalities) * botany * zoology * Virology * Microbiology * geography * ecology May the forgoten disciplins forgive me... They'll have their XML vocabularies too. Jean-Marc

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Re: Character types (RQT)
by Gregor Hagedorn 29 Nov '99

29 Nov '99

> This means that anyone using the format 'offline' doesn't need to > access some resource storage (i.e. the net) to make a successful > identification. My use of "external resource" was rather unclear. I am thinking in terms of a database information system, so external resource means any URL or file based document. Thus external in my use could just as well be a local resource as a internet resource. If an information system is distributed on CD, all images, formatted text, and audio etc. would be on that CD. Any better terms than "external resource"? I don't like media resource/hypermedia etc., because I feel this is not very adequate for resources like a query/identification interface. > Yes, rendering a graphical representation of (say) a leaf onto the screen > would be a good application for vector graphics. However again some > additional > text describing the image/shape would be useful - for those applications > that don't support vector graphics, or indeed visually impaired users. A resource in my model has specific attributes (which are different from characters), esp. indication of scope (to which items/character/state it belongs + flags whether it is to be used as default resource for this scope), a caption, which contains the description, media types, etc. 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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Markup of text descriptions Vs. structured data (GEN)
by Gregor Hagedorn 29 Nov '99

29 Nov '99

Jean-Marc Varel, Don Kirkup and others have repeatedly touched the problem of existing textual descriptions in their discussions contributed to this list. On the other hand, I myself belong to the group of DELTA/NEXUS minded people, who are concerned mostly with knowledge management of descriptive data that are created new. These issues should be seen quite separately, and that we need both 1. A markup language for text documents. This includes: - existing descriptions, captured by OCR or other means, where the markup would be manually (or automated/data mining?) - computer generated natural language descriptions that are published as electronic documents. A new CSIRO package could have a ToNat command that automatically adds the necessary, hidden markup code. 2. A data language for new observations, including repeated measurements or repeated observations of categorical data, e.g. shape of multiple leaves in a single specimen. Further, many structures for knowledge managements (data revision, annotation, quality control and assessment) need to be implemented here. The issues overlap, and it would be beneficial to use as much common syntax as possible, but fundamentally I believe them to be quite different. See also the separate post "Item description data in XML (XML)" for discussion of how to achieve this in XML and with XML examples. 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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(GEN) Schema independence
by Gregor Hagedorn 29 Nov '99

29 Nov '99

> > * 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. Exactly (says a mycologist). Also, what about at least 20 different name spaces for protists, 50 or so for bacteria. Viruses, mycoplasms, viroids, ... Biological diversity is well beyond our current grasp. We should admit that we do NOT understand it in any way sufficiently. Even what we understand is obscured by terminoly inadequacies or concurrent, but not entirely synonymous terminology. From my own experience, I think that unifying character definition even among fairly closely related groups of a small group of the fungi can be a challenging task. Richard Pankhurst could probably step in here and explain why it is so difficult to even draw up a core consensus character set for all higher plants (an effort he is concerned with for several years now). The tendency in this discussion to assume that things like leaf, petiole, veins etc. should be directly coded into the standard worries me. The examples are fine for the purpose of discussion, but I hope that most people agree that the schema independence of DELTA (and principally also NEXUS, although NEXUS leaves most of the definition to free text in a published article) is a big achievement, and I would not like to sacrifice it. This does not mean that we should not try to unify character schemas, but it definitely should be a separate task. We need a general standard, and an applied standard that acutally uses a defined namespace. So, I believe we need: o Character schema definition language, expressed in XML-DTD or better XML-Schema - Researchers working on weird stuff like Tardigrada should not be required to wait until somebody creates a schema for them, but must go ahead and develop their own schema. - DELTA is, in part, such a language. o Character schema (an applied character definition, that acutally defines names, type, constraints, etc. for a set of characters), expressed in the new Character schema definition language. - The character definition of a DELTA data set is such a schema. - The thing to achieve would be, to express this in such a way that it becomes a usable XML Namespace definition, while still linking into the Character schema definition language! I could then be directly used by XML tools, but it would be developed with added value by the more relevant additional definition in the Character schema definition language! o An application to express item descriptions using these tools. - Example: DELTA ITEM DESCRIPTION. Thus I envision something like: + Character definition language, adding special metainformation to: + Standard XML Namespace definition, which, however, can be used independently Both together form a character schema of a new standard, which would be used in item descriptions. The item descriptions themselves have two components: + A markup language to mark existing (or computer generated) free textual descriptions + A data language, to exactly define the data used, including knowledge management support See also the separate post "Markup of text descriptions Vs. structured data (GEN)" 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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Item description data in XML (XML)
by Gregor Hagedorn 29 Nov '99

29 Nov '99

In the separate post "Markup of text descriptions Vs. structured data (GEN)" I suggested that we need to distinguish between markup and data. Markup would be: <leaf>leaves usually obovate, 3 cm long</leaf> or <leaf>leaves usually <shape>obovate</shape>, <length>3 cm<length> long</leaf> Don suggested to encode the data element like: <leaf shape="obovate" length_mm="31"/> (NB: Please read the hardcoded namespace as an example only, see my separate "(GEN) Schema independence" post) As far as I understand XML, these attributes would be automatically hidden from view, which is fine for the markup purpose. However, I would prefer a coding method, which would allow comprehensive use of XML for the data definition part as well. 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? 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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Character types (RQT)
by Gregor Hagedorn 29 Nov '99

29 Nov '99

Stuart Poss wrote: > Are existing methods and this discussion > restricted to "morphological characters"? Personally I think that morpho-anatomical characters are not sufficiently different from other character like those mentioned in Stuarts post. I would want to discuss them here as well. Interesting things may, however, happen regarding character types. Besides an expanded list of character types (including date/time, ordered categorical: linear, cyclic, tree, or complex/reticulate) new types may appear. A new type that I am specially interested in, is the "alignment" type. A while ago on DELTA-L somebody commented that alignments can principally be treated as a group of categorical characters, just as they are in NEXUS. However, I believe this treatment is not adequate for the following reasons: o the homology of these characters is dependend on the alignment, especially: o adding new items (sequences) may change the homology assumptions within the remaining sequences o the naming/identification of characters would be extremely difficult to handle, because a base position depends on the alignment I believe that these special considerations require a special character type for aligned sequence data --- What other character types do you think are necessary? --- Whether images/audio/video material etc. should be considered character, I am doubtful. I currently prefer to summarize them together with formatted text documents and database access (information systems/Identification or query interfaces) or any other URLs as "external resources". I am not as clear about this as I would wish. One criterium could be that analytically accessible, well structured information should be considered a character (thus including restricted vocabulary text information, e.g. "lists") whereas only human usable resources should be treated different. Vector graphics lie somewhere in between... I appreciated the recent contributions about the parameterizations of shapes, I think this will be helpful! 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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