November 2003 - tdwg-content

Combining DELTA items; character dependencies
by Mike Dallwitz 25 Nov '03

25 Nov '03

- From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> - To: "Mike Dallwitz" <mike.dallwitz(a)netspeed.com.au> > I am just back from the TDWG meeting in Lisbon and working on the > minutes for SDD. In Lisbon we had two questions concerning DELTA. > DELTA, as far as I know, can generate something like genus > descriptions from multiple species descriptions. I have worked myself > relatively little with the Confor program itself and I now cannot > find any information about this in the DELTA Users manual. This is carried out by the Intkey command 'Output Summary'. Any subset of the taxa can be combined in this way. The output is a text file in DELTA format. It can be done interactively, or by means of a script, which can be run whenever the data are changed. For details, see the DELTA-L posting Subject: Combining DELTA items Date: Fri, 27 Oct 2000 which is available in the list archive at http://listserv.surfnet.nl/archives/delta-l.html We intended to put in the DELTA Editor a more general mechanism for passing information between items. This would have allowed, for example, species items to use information coded in genus items, and vice versa. It would also have replaced the 'variant items' mechanism. See Dallwitz, M. J., Paine, T. A. and Zurcher, E. J. (1993 onwards). Proposed new features for the DELTA system. http://delta-intkey.com > Character dependencies: > We had a long discussion about how dependencies should be handled. We > believe it makes sense to support both Applicable and Inapplicable > versions concurrently and tried to analyse what that means. > In that context we started to wonder, how the DELTA definitions are > to be interpreted. > In the DELTA users guide under "*DEPENDENT CHARACTERS" I find for > "4,2:16 10,1/3:12-13:20:30-35" > "Attribute 4,2 implies that character 16 is inapplicable. Attributes > 10,1 and 10,3 imply that characters 12, 13, 20, and 30-35 are > inapplicable." > We have two options to interpret this: > 1. Attributes 10,1 and 10,3 means both 1 and 3 must be scored to make > the dependent characters inapplicable. > 2. Attributes 10,1 and 10,3 means any of 1 and 3 or both must be > scored to make the dependent characters inapplicable. > I as well as all members present in the group assumed that the first > option is what is meant, and DEltaAccess implements it that way. It's not clear from the description, but the second option is the one I intended. I can't think of a plausible case where the first option would be appropriate. The sample data supplied with the DELTA programs contains a relevant example. > However, I found that in the case of more than one dependency in a > single character the two forms Inapplicable and Applicable can NOT be > converted. What confuses me now is that under "APPLICABLE CHARACTERS" > it is stated that "This is equivalent to the DEPENDENT CHARACTERS > directive in Section 3.5.1." This seems to imply a convertibility to > me. The directives _are_ convertible. The example in Section 3.5.1 of the DELTA User's Guide is taken from the sample data. To confirm that the two forms are equivalent, take the 'APPLICABLE CHARACTERS' version given in the User's Guide, and substitute it for the 'DEPENDENT CHARACTERS' version in the specifications file of the sample data. Then run 'Confor check', and you will find that no errors are reported. > We are really homing in on a version that should be at least a good > basis for trying it out. I did try originally to have it open, > including options for pure ontological schemata and pure state- > matrices (like in LucID, in contrast to the character matrices DELTA > uses). I can only say that by and large we are homing in on a DELTA > like model (including LucID). Actually, DELTA and Lucid are not qualitatively different in this regard - they both have the states organized into characters. The only differences are in the kinds and amount of information associated with each state in the data matrix. Associated with each state, the current version of DELTA has an unrestricted amount of free-text information, Intkey has 1 bit of information (present/absent), and Lucid has 8 bits of coded information. The proposed new version of DELTA (Dallwitz et al., loc. cit.) had both free text and coded information associated with each state and character in the matrix. The coded information included all the types used by the current Lucid. At least one program, MEKA, does use a state matrix, i.e. the states are not grouped into characters. -- Mike Dallwitz 13 Warrambool Close, Giralang ACT 2617, Australia Phone: +61 2 6241 2884 Email: mike.dallwitz(a)netspeed.com.au Internet: delta-intkey.com

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Re: InternalNotes/ReportedNotes [Request for voting]
by Kevin Thiele 18 Nov '03

18 Nov '03

I have transferred the content of this email to the wiki - see http://efgblade.cs.umb.edu/twiki/bin/view/SDD/ChangeName It would be *much* better if any comments are made through the wiki, and voting (though this may be a trivial example) is conducted there. If any luddites insist on carrying on a conversation on the list, I will laboriously transfer it all to the wiki. Cheers - k ----- Original Message ----- From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> Sent: Wednesday, November 19, 2003 3:03 AM Subject: InternalNotes/ReportedNotes [Request for voting] > In the current version of the SDD schema we have: > > InternalNotes: A single element for all languages, intended for > internal documentation, annotations, memos during the development > process of either the terminology or descriptions. This is sort of > like a scrap page for authors or editors. > > ReportedNotes: Free form notes/comments/annotations that address the > consumer of descriptive data. Multiple representations for each > audience/language addressed are available. > > The pair InternalNotes/ReportedNotes is intended to express the fact > that Internal Notes are not usually published, whereas reported notes > are an essential part of the descriptive data. > > ---- > > I am currently thinking about whether different element names may be > more acceptable or intuitive. > > * Using Annotation instead of InternalNotes > * Using FreeFormText instead of ReportedNotes. > > We could use Notes instead of ReportedNotes, but I find the pair > Annotation/Notes easily confusible. > > Please do "vote" on this issue on the email list! > > Gregor > ---------------------------------------------------------- > 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: Agents, Contributors, etc.
by Kevin Thiele 18 Nov '03

18 Nov '03

I think it's a good idea that there's some traffic on the email list - we just weren't getting people onto the wiki. What we need are some succinct and brilliant wiki discussions, and by email point people to the wiki to get them going. -k ----- Original Message ----- From: "Robert A. Morris" <ram(a)CS.UMB.EDU> To: <TDWG-SDD(a)LISTSERV.NHM.KU.EDU> Sent: Wednesday, November 19, 2003 2:28 AM Subject: Re: Agents, Contributors, etc. > For technical reasons, it would be FAR better if people start at > http://efgblade.cs.umb.edu/twiki/bin/view/SDD/ > than the address that Gregor gave. > > The first time you try to make a contribution to the wiki you will be > invited to register. > > I really hope most discussion takes place in the wiki, not in email. > It's a better discussion medium as most people agree after the 15 minute > learning curve. > > > Bob Morris > > > Gregor Hagedorn wrote: > > > Hello everybody, > > > > The silence after Lisbon this time unexpectedly does not mean we are > > back to sleep. Together with Bob and Kevin I use all available time > > in hammering out a new version of the SDD schema incorporating the > > discussions from Lisbon and increasing the logic and consistency of > > the schema. > > > > Before we publish the entire schema, I would like to raise some > > isolated and specific points in the coming days on the email list. I > > would also like to point to Bobs WIKI > > (http://efgblade.cs.umb.edu/twiki/bin/edit/SDD/) where some > > discussions among us are going on. > > > > -- > Robert A. Morris, Professor of Computer Science > University of Massachusetts at Boston > 100 Morrissey Blvd; Boston, MA 02125 > http://www.cs.umb.edu/~ram http://www.cs.umb.edu/efg > phone: (+1)617-287-6466 fax: (+1)617-287-6433

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InternalNotes/ReportedNotes [Request for voting]
by Gregor Hagedorn 18 Nov '03

18 Nov '03

In the current version of the SDD schema we have: InternalNotes: A single element for all languages, intended for internal documentation, annotations, memos during the development process of either the terminology or descriptions. This is sort of like a scrap page for authors or editors. ReportedNotes: Free form notes/comments/annotations that address the consumer of descriptive data. Multiple representations for each audience/language addressed are available. The pair InternalNotes/ReportedNotes is intended to express the fact that Internal Notes are not usually published, whereas reported notes are an essential part of the descriptive data. ---- I am currently thinking about whether different element names may be more acceptable or intuitive. * Using Annotation instead of InternalNotes * Using FreeFormText instead of ReportedNotes. We could use Notes instead of ReportedNotes, but I find the pair Annotation/Notes easily confusible. Please do "vote" on this issue on the email list! Gregor ---------------------------------------------------------- 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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Agents, Contributors, etc.
by Gregor Hagedorn 18 Nov '03

18 Nov '03

Hello everybody, The silence after Lisbon this time unexpectedly does not mean we are back to sleep. Together with Bob and Kevin I use all available time in hammering out a new version of the SDD schema incorporating the discussions from Lisbon and increasing the logic and consistency of the schema. Before we publish the entire schema, I would like to raise some isolated and specific points in the coming days on the email list. I would also like to point to Bobs WIKI (http://efgblade.cs.umb.edu/twiki/bin/edit/SDD/) where some discussions among us are going on. Topic: Agents ============= After Lisbon I changed the ContributorsDocumentation/Contributor structure within Resources to "Agents/Agent". Kevin writes: > don't like "agents" much - what about "Contributors" instead of > "Agents" and change the current "Contributors" to "OtherContributors". > After all, authors and editors are subsets of contributors, surely. > Agents is an awkward term. I basically agree with Kevin, Agents is not very nice. I used it simply because ABCD is doing so. However I don't like Contributors either. 1. I find it confusing being used twice with different meaning. OtherContributors (i.e. other than Authors or Editors) is not very nice either. 2. More fundamentally, all resources in SDD are objects and should have object names. "Contributors" is a _role_ name and therefore not very appropriate. The list of persons or organizations may be used in other circumstances, albeit we currently have none in SDD. Any good other term to denote "Person or Organization" in general, without naming their role? Gregor ---------------------------------------------------------- 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: Agents, Contributors, etc.
by Robert A. Morris 18 Nov '03

18 Nov '03

For technical reasons, it would be FAR better if people start at http://efgblade.cs.umb.edu/twiki/bin/view/SDD/ than the address that Gregor gave. The first time you try to make a contribution to the wiki you will be invited to register. I really hope most discussion takes place in the wiki, not in email. It's a better discussion medium as most people agree after the 15 minute learning curve. Bob Morris Gregor Hagedorn wrote: > Hello everybody, > > The silence after Lisbon this time unexpectedly does not mean we are > back to sleep. Together with Bob and Kevin I use all available time > in hammering out a new version of the SDD schema incorporating the > discussions from Lisbon and increasing the logic and consistency of > the schema. > > Before we publish the entire schema, I would like to raise some > isolated and specific points in the coming days on the email list. I > would also like to point to Bobs WIKI > (http://efgblade.cs.umb.edu/twiki/bin/edit/SDD/) where some > discussions among us are going on. > -- Robert A. Morris, Professor of Computer Science University of Massachusetts at Boston 100 Morrissey Blvd; Boston, MA 02125 http://www.cs.umb.edu/~ram http://www.cs.umb.edu/efg phone: (+1)617-287-6466 fax: (+1)617-287-6433

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