POC Conf. Call 1-3-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 3rd, 2012 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11?

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Mistake in the CL/PO coordination

CM raised the issue below: spot the inconsistency:

/ PO:0025131 ! plant anatomical entity 
 is_a PO:0009011 ! plant structure 
  is_a PO:0000004 ! in vitro plant structure 
   is_a PO:0000005 ! cultured plant cell ***  
  is_a PO:0009002 ! plant cell [xref: GO:0005623] 
   is_a PO:0000005 ! cultured plant cell ***  

/ CL:0000000 ! cell [xref: FMA:68646] [xref: GO:0005623 "cell"] [xref: KUPO:0000002] [xref: WBbt:0004017] [xref: XAO:0003012]

 is_a CL:0000003 ! cell in vivo
  is_a CL:0000004 ! cell by organism
   is_a CL:0000255 ! eukaryotic cell
    is_a CL:0000610 ! plant cell ***  [xref: PO:0009002]

if the xrefs are equivalent and in vivo is (presumably) disjoint from in vitro, then plant cell is unsatisfiable.

Link to CL:0000610 plant cell on CL.

They should be using our definition of plant cell as well: "A cell which is a plant structure. [source: GO:0005623, POC:Curators]"

• SOLUTION 1:

With it's current placement, CL:0000610 must really be equivalent to a PO:0009002 that is in-vivo - this doesn't correspond to a named class in PO. We could rename CL:0000610 to "in vivo plant cell" and have a bridging axioms that says this is a subclass of PO:0009002

• SOLUTION 2:

obsolete CL:0000610, with a consider link (not replaced by) to PO:0009002

add an xref to PO:0009002 to CL:0000000 (just as we have for the other taxon-centric AOs).

Remove: 'treat-xrefs-as-equivalent: PO'

Add: 'treat-xref-as-genus-differentia: PO part_of NCBITaxon:nnnnn ! viridiplantae'

• SOLUTION 3:

move CL:0000610 ! plant cell to be a direct child of CL:0000000 ! cell

we would probably want to move CL:0000255 ! eukaryotic cell at the same time

From CM:

"I don't like solution 1. Neutral w.r.t. 2 and 3."

"Note that whatever the solution, we need a consistent cross-ontology naming strategy. I don't think it's necessary to prefix every in-vivo class with "in-vivo". But we need to be consistent. At the moment "eukaryotic cell" means "eukaryotic in vivo cell", whereas "plant cell" (in PO) means "plant cell, in vivo or in-vitro".

"How about this: if we have a taxonomic qualification, it doesn't imply in-vivo. If we have a named cell type (e.g. "neuron") or some other qualification, it implies in-vivo?"

CL should us the PO definition of plant cell. We should put it on the CL plant tracker.

The problem is if someone tries to import PO into CL, because of the conflict with in vivo cell. This should be address in the document from MH proposing changes to CL.

PJ raised an issue with experimentally modified cell -- you can experimentally modify a cell then stick it back in an organism, so it is in vivo.

Not everyone received Melissa's document. RW will circulate to PO internal, and we will review it before we discuss this more.