Sensu Plans: Difference between revisions

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positive terms and represent them as follows:
positive terms and represent them as follows:


name: Gram positive cell wall
  name: Gram positive cell wall
exact structured synonym: 40nm cell wall
  exact structured synonym: 40nm cell wall
We are proposing this because Gram positive and Gram negative do not
We are proposing this because Gram positive and Gram negative do not
correspond with any taxonomic groupings or combinations of taxonomic
correspond with any taxonomic groupings or combinations of taxonomic
groupings and so cannot be represented as such.
groupings and so cannot be represented as such.
2) Nematoda and Protostomia (the group that used to be called Invertebrata.)
2) Nematoda and Protostomia (the group that used to be called Invertebrata.)

Revision as of 08:24, 12 July 2006

Linguistic sensu

These are current sensu situations in which there are two terms that would have the same name string with completely different meanings. e.g. gametogenesis in plants and animals.

Solution: Use context marker directly in the the name or synonym field. e.g. gametogenesis (plant biologist usage)


Non-Linguistic Sensu

These are current sensu situations in which the sensu designator has been used to distinguish two processes that work towards roughly the same end but happen differently in two different organisms. e.g. eye development in insects and eye development in mammals.

We will try to reduce the need for use of sensu designators in such situations by defining terms properly.

eye development (sensu insecta) might just be called compound eye development, with a definition that clearly distinguishes it from the other kinds of eye development that are currently instantiated in the ontology.

Two designator systems will also be used:

1) In the definition we will put a reference to the canonical species. The taxon id will be provided as a definition dbxref.

2) An in_organism relationship (one per term only) will be added to show the full set of organisms that may include this process. The definition of the in_organism relationship is: "All instances of this process occur in some instance of this taxonomic group at all times." Since the relationship is defined this way we will be able to choose a taxon that is broader than the set of organisms that actually exhibit the process.

  name: compound eye development 
  def: [non-circular definition of compound eye development] as
  described in Drosophila melanogaster.
  in_organism: Insecta (Or whatever grouping includes all compound eyed
  species.)
  

N.B.

1) We are planning to remove sensu status from Gram negative and Gram positive terms and represent them as follows:

  name: Gram positive cell wall
  exact structured synonym: 40nm cell wall

We are proposing this because Gram positive and Gram negative do not correspond with any taxonomic groupings or combinations of taxonomic groupings and so cannot be represented as such.

2) Nematoda and Protostomia (the group that used to be called Invertebrata.)

  We are going to look through all these terms and see if they are
  really needed. Some of the examples that we have looked at so far
  have just been grouping terms for collections of sensu designated
  terms that all cite invertebrate taxa. These could easily be removed.