Open Hypermedia Systems Working Group

Taxonomic 1 - Scenario

Preliminaries

Authors
Peter J. Nürnberg
U Aarhus, Denmark
@%AUTHOR2
@%AFFIL2

Updates
Most recent: 15 June 1997 (initial version)


References


• Nürnberg, P, Leggett, J., and Schneider, E. 1997. As we should have thought. Proceedings of HT 97.
  
• Nürnberg, P, Leggett, J., Schneider, E., and Schnase, J. 1996. HOSS: A new paradigm for computing. Proceedings of HT 96.
  
• Parunak, H. 1991. Don't link me in: set based hypermedia for taxonomic reasoning. Proceedings of HT 91.
  

Other Links


• Analysis
  
• OHS mailing list discussion (when available)

Scenario Description

Background

Botanical taxonomists build taxonomies over samples of plants. Taxonomies consist of taxa and specimens. In this case, a specimen is a plant sample and some data about the sample, such as collection date, collection location, accession number, etc. A taxon is an abstraction that groups together like specimens and/or like taxa. It has a name, a set of characteristics, and a group of children specimens and/or taxa. Taxa are singly parented.

There are many difficulties and managing these botanical taxonomies. Firstly, not all taxonomists agree on the same set of taxa over a given set of specimens. Secondly, even if two taxonomists agree on what taxa should be constructed, they may disagree on the grouping criteria for some subset of the taxon. Thirdly, even if they agree on these two issues, they may disagree on the attributes of some subset of the taxa, such as name. Fourthly, even if two taxonomists agree on all of these issues at some point in time, the taxonomies they create may change over time, as new data is added, new interpretations are made, etc.

In addition to the creation and manipulation of taxonomic structure, the characters also want to be able to add and manipulate navigational hypertext structures over their specimens, taxa, and taxonomies.

Scenario

JB, Terry, Ronnie, and Howie are botanical taxonomists. They are working on a part of a taxonomy covering a family of plants known as foo plants. They are all well-respected researchers in the field of foo plants, and have made their taxonomies available on-line to other researchers in their field. Pat and John are also taxonomists working with foo plants. They want to use the taxonomies published by JB, Terry, Ronnie, and Howie. All of these researchers use a computer system to create and manipulate taxonomies over the foo family and the relevant specimen records (with digital images of the plants, etc.).

JB, Terry, Ronnie, and Howie share plant specimens. Currently, they have 3 specimens. They all agree that the specimens represent three different species of foo plant, and that the names of these three types should be widget, gadget, and doodad.

JB believes that the the family foo has two genera: bar and baz. The bar genus contains the widget and gadget species, while the baz genus contains the doodad species. This is shown below.

foo	bar	widget
		gadget
	baz	doodad

Terry essentially agrees with JB on the groupings used, but he believes that the baz genus should in fact be named the zab family. His taxonomy is shown below.

foo	bar	widget
		gadget
	zab	doodad

Ronnie essentially agrees with JB and Terry, but feels that the gadget species should instead be grouped under the baz genus. His taxonomy is shown below.

foo	bar	widget
	baz	gadget
		doodad

Finally, Howie essentially agrees with Ronnie, but believes that there should be a third genus introduced, named weeble. He thinks the doodad species belongs in the weeble genus. His taxonomy is shown below.

foo	bar	widget
	baz	gadget
	weeble	doodad

Pat and John would like to publish their latest work on foo plants. They have conducted their work using Terry's taxonomy. However, the journal in which they would like to publish their work uses JB's taxonomy. They would like their system to compare Terry's and JB's taxonomies and list which taxonomies have identical children but different names. This will allow them to find the taxon names that can be changed by text substitution to accommodate the journal. They find that where they use the genus name zab, the journal uses the name baz. They change their article text appropriately.

Later, the journal decides to switch the taxonomy it uses to Ronnie's. This poses a problem for the editors. If they do not change the previous article by Pat and John, the results will be out-of-date with respect to newer articles published under Ronnie's taxonomy. However, if they do change the article to reflect the change in the journal's standard taxonomy, they risk changing the meaning of Pat and John's work in unintended ways. The journal editors solve this problem by providing on-line readers with "active" documents. Readers can choose to see either the original text, or the text as modified to fit the new journal standard. To guard against future changes, the modified version is not stored statically, but calculated dynamically when requested by the reader.

Finally, Pat and John find more foo plant specimens. They believe that these specimens are members of Howie's "weeble" genus, and have decided to adopt Howie's position. They make these specimens available on-line, and create annotations on Howie's taxonomy that present their arguments and pointers to the new specimens. JB, reads these arguments and decides that there is still not sufficient evidence for a separate weeble genus. He posts his replies to Pat and John as further annotations to Howie's taxonomy. Terry, who has always believed that the species doodad is in its own genus, posts further replies, arguing in support of the notion of a weeble genus, but that this genus should be named zab. These arguments become part of Howie's taxonomy, allowing readers and fellow researchers to see the rationale behind his decisions.

Oddly enough, Howie decides that the new specimens actually support the creation of a fourth genus of the foo family: wobble. However, he cannot simply replace his old taxonomy with a new one. This would complicate the matter of where to put the argumentation concerning his current taxonomy. He decides to create a new version his current taxonomy. The old taxonomy is still accessible, but by default, visitors to Howie's taxonomy see his new thinking.