POC Conf. Call 8-16-11

POC meeting, Webex Conference Call; Date: Tuesday Aug 16th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_8-2-11?

Syncing PO and CL

CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.

CL will provide bridge files as part of the CL release process.

Problematic xrefs to CL terms from PO

PO has xrefs to 46 CL terms. Most are fine. 9 are not under CL's category for plant cells, and a few are potentially problematic.

plant cell

PO:0009002 (plant cell) xref to CL:0000610 (plant cell).

CL defines plant cell as "A cell found in seeded plants."

Suggest that CL adopt PO's definition of plant cell.

epidermal cells

• PO:0004013 (epidermal cell) xref to CL:0000362 (epidermal cell)

CL:0000362 is_a squamose epithelial cell, is_a general ecto-epithelial cell

• PO:0000332 (epidermal pavement cell) xref to CL:0000400 (pavement cell)

CL:0000400 is_a epidermal cell

• PO:0000115 (socket cell) xref to CL:0000297 (socket cell)

CL:0000297 is_a epidermal cell, is_a supportive cell

• PO:0000282 (trichome) xref to CL:0000282 (trichome)

CL:0000282 is_a epidermal cell.

The xref from PO:0000282 to CL:0000282 should be on removed, and instead, there should be an xref from PO:0008030 (trichome cell) to CL:0000282. CL may want to obsolete CL:0000282 along with the other plant cell types, unless it is meant to refer to hairs on any type of organism.

others

• PO:0000423 (zygote) xref to CL:0000365 (zygote).

CL:0000365 is_a cell by lineage, is_a early embryonic cell. This is probably fine.

• PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).

CL:0000618 has no definition, but is_a columnar/cuboidal epithelial cell. Suggest we remove this xref and the CL obsolete the term.

• PO:0000263 (atrichoblast) xref to CL:0000332 (atrichoblast).

CL:0000332 is_a epidermal initial, is_a non-terminally differentiated cell (second is_a relation is redundant).

PO definition of atrichblast is: A root epidermal cell that is formed after asymmetric division of an epidermal initial and does not give rise to a root hair.

Suggest that CL obsolete CL:0000332, because it is a plant cell, and their definition is not up to date.

• PO:0004011 (initial cell) CL:0000034 stem cell CL:0000266 meristemoid PO:0000070 is_a cell, is_a cell by function

PO cell types that should reference cell types in CL

A few types of cells may fall are equivalent to remaining CL terms. If so, then they should have a general xref, then assert the general xrefs as relations using the header "treat-xrefs-as-equivalent: CL" (see obo format guidelines).

PO:0009002 plant cell > CL:0000610 plant cell

PO:0000423 zygote > CL:0000365 zygote

New terms for CL

There are four terms in CL for which PO does not have equivalent terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.

See conducting cells for non-vascular plants.