Question about cork cells in grasses (fwd) (PR#58)

[Katica Ilic]

Dear Ron,

Thank you for the request for a new term in Plant Ontology. Cork cells in the
epidermis of grasses and bamboos are certainly different from the 'bark' cork
cells (phellem, derived from the cork cambium), common in dicots and many
monocots. 

Following your request, we are going to introduce a new term to PO, 'cork cell
(sensu Poaceae)', which will be placed under tissue node, under term 'epidermis'
(and also in the cell type node, as an instance of epidermal cell).

The proposed structure will appear as following:

PO:0009002 : cell
 (i) PO:0004013 : epidermal cell
    (i) PO:0004009 : silica cell
    (i) cork cell (sensu Poaceae)
and

  PO:0009007 : tissue
      (i) PO:0009014 : dermal tissue
         (i) PO:0005679 : epidermis
             (p) PO:0004013 : epidermal cell
                 (i) cork cell (sensu Poaceae)
                 (i) PO:0004009 : silica cell

In both nodes, silica cell and cork cell are at the same level (instances of
epidermal cell). Although silica cell and cork cell usually appear in pairs in
the epidermis of grasses, and both are types of short cells, I did not include
term 'short cell' in this proposal, to avoid proliferation of sensu terms. 

Now, I need to explain why the new term 'cork cell (sensu Poaceae)' has 'sensu'
designation and silica cell doesn't (nor the other cork cell term), and why
'sensu' is used in the term name.

The reason to create terms with 'sensu' designation in PO is to distinguish
different concepts that are named with the same word or phrase. There are cases
where a term has different meaning depending on to which taxa the term is
applied. Such terms are distinguished from one another by their definitions and
by the sensu designation (sensu means 'in the sense of') in the term name.
Therefore, cork cell (sensu Poaceae) means 'cork cell as in grasses'; not to be
confused with the existing PO term 'cork cell' (PO:0004003), since there is no
relationship in the ontology between these two terms. Silica cell doesn't have
sensu designation since this cell is common for many dicots too, it is not
specific for Poaceae. Similarly, 'cork cell' (phellem) is common throughout
angiosperms and gymnosperms, and this term doesn't have specific sensu
designation either.

I hope this would meet your requirement. Please let us know if you need
additional terms in Plant Ontology. The updated version of the PO can be viewed
at the end of the month (after next scheduled update) using ontology browser.
However, you can download the new ontology OBO file with the new term (and
assigned PO ID) early next week from our cvs on the POC web site.

Pankaj has already addressed your question about a failed query when using term
names in plural.

Best regards,

Katica Ilic, POC Project Coordinator
 
> Ron Skadsen wrote:
> 
>> Dear Ontologists,
>>
>> I tried your site to find some information on cork cells.  These are
>> small cells commonly paired with silica cells in grasses.  We have a
>> gene promoter that causes expression of a reporter gene in cork cells.
>> Your listing has only the common cork cell, as derived from the
>> cambium.  Is there a way to tease out an entry for the different cork
>> cells?  Also, a search of "cork cells" on your site yield zero matches.
>>
>> Cheers,
>>
>> Ron Skadsen
>>
>> USDA/ARS
>> Cereal Crops Research Unit
>> 506 Walnut St.
>> Madison, WI  53726
>> ph    (608)262-3672
>> FAX (608)264-5528