Sensu Plans

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This is a proposal for future use of sensu. I (Jennifer) am examining some test cases to assess the viability of our plans.)

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. An alternative scenario is to distinguish two components that are structurally different (in terms of their part_of links) in two different organisms. e.g. photosystem I in Cyanobacteria and Viridiplantae - one is part of the plastid the other part of thylakoid.

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.

---For a discusiion of the eye terms, see sourceforge item#1573845. One idea is to call the vertebrate (and mollusc) eyes camera-type eyes. I will add synonyms for the eye terms to reflect this usage.[dph;10/10/2006]

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
  synonym: "40nm cell wall" EXACT STRUCTURED []

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.

Summary: By Jennifer Clark from conference call of 12 July 2006 between Jennifer Clark, Chris Mungall, Amelia Ireland and Jane Lomax.

Note: If we have sufficient structural differentiae then it isn't necessary to have in_organism relations. This would be nice to have, but could actually be considered a separate project -- Chris

This is to be implemented as soon as possible. We should try to arrange a webex meeting to do this.